[gmx-users] installation error under openSuse 12.2
Date: Mon, 11 Nov 2013 08:27:05 -0800 (PST) From: kolnkempff kolnkem...@gmail.com Subject: [gmx-users] installation error under openSuse 12.2 To: gmx-users@gromacs.org Message-ID: 1384187225465-5012430.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii Dear gmx-users, I am trying to install gromacs-4.6.3 on an older Dell that is running openSuse 12.2 Using DGMX_BUILD_OWN_FFTW=ON failed for me so to get through cmake I had to compile fftw from scratch and I followed the recommendation of going directly to their website. Now I am at the make stage and get the following message: [ 67%] Built target gmxfftw make[2]: *** No rule to make target `//home/koln/bin/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3f.a', needed by `src/gmxlib/libgmx.so.8'. Stop. make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 When I check for libfftw, I get: koln@linux-5bim:~/bin/gromacs-4.6.3/build2 rpm -qf /usr/lib/libfftw3f.* libfftw3-3-32bit-3.3.2-1.1.2.x86_64 Any suggestions for how to get past this obstacle would be greatly appreciated! This is an known issue in OpenSuse! We added a workaround a while ago: https://gerrit.gromacs.org/#/c/2540/ Until Gromacs release 4.6.4. you will have to change line 41 of src/contrib/fftw/CMakeLists.txt yourself or just install fftw through OpenSuse or by hand. Christoph Koln -- View this message in context: http://gromacs.5086.x6.nabble.com/installation-error-under-openSuse-12-2-tp5012430.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] installation error under openSuse 12.2
Dear gmx-users, I am trying to install gromacs-4.6.3 on an older Dell that is running openSuse 12.2 Using DGMX_BUILD_OWN_FFTW=ON failed for me so to get through cmake I had to compile fftw from scratch and I followed the recommendation of going directly to their website. Now I am at the make stage and get the following message: [ 67%] Built target gmxfftw make[2]: *** No rule to make target `//home/koln/bin/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3f.a', needed by `src/gmxlib/libgmx.so.8'. Stop. make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 When I check for libfftw, I get: koln@linux-5bim:~/bin/gromacs-4.6.3/build2 rpm -qf /usr/lib/libfftw3f.* libfftw3-3-32bit-3.3.2-1.1.2.x86_64 Any suggestions for how to get past this obstacle would be greatly appreciated! Koln -- View this message in context: http://gromacs.5086.x6.nabble.com/installation-error-under-openSuse-12-2-tp5012430.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation error under openSuse 12.2
On 11/11/13 11:27 AM, kolnkempff wrote: Dear gmx-users, I am trying to install gromacs-4.6.3 on an older Dell that is running openSuse 12.2 Using DGMX_BUILD_OWN_FFTW=ON failed for me so to get through cmake I had to compile fftw from scratch and I followed the recommendation of going directly to their website. Now I am at the make stage and get the following message: [ 67%] Built target gmxfftw make[2]: *** No rule to make target `//home/koln/bin/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3f.a', needed by `src/gmxlib/libgmx.so.8'. Stop. make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 When I check for libfftw, I get: koln@linux-5bim:~/bin/gromacs-4.6.3/build2 rpm -qf /usr/lib/libfftw3f.* libfftw3-3-32bit-3.3.2-1.1.2.x86_64 Any suggestions for how to get past this obstacle would be greatly appreciated! Are you building in a clean installation directory? It looks to me that cmake is still trying to build the internal FFTW code, rather than looking for your manually installed FFTW. Providing your full cmake command would also be very useful (hint: always provide it). -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Installation of gromacs 4.5.4 on windows using cygwin
hello, I am trying to install gromacs in cygwin but after issuing make, installation stops with the following error Makefile:1315: recipe for target `gmx_tune_pme.lo' failed make[3]: *** [gmx_tune_pme.lo] Error 1 make[3]: Leaving directory `/usr/local/gromacs-4.5.1/src/tools' Makefile:301: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/usr/local/gromacs-4.5.1/src' Makefile:237: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/usr/local/gromacs-4.5.1/src' Makefile:344: recipe for target `all-recursive' failed make: *** [all-recursive] Error 1 I have configured gromacs 4.5.4 using ./configure --disable-shared--enable-all-static--disable-threads FFTW version : FFTW 3.3 but still I encounter error during make step. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation of gromacs 4.5.4 on windows using cygwin
Looks like you are compiling 4.5.1. You should try compiling the latest version in the 4.5 series, 4.5.7. -- Szilárd On Sun, Sep 15, 2013 at 6:39 PM, Muthukumaran R kuma...@bicpu.edu.in wrote: hello, I am trying to install gromacs in cygwin but after issuing make, installation stops with the following error Makefile:1315: recipe for target `gmx_tune_pme.lo' failed make[3]: *** [gmx_tune_pme.lo] Error 1 make[3]: Leaving directory `/usr/local/gromacs-4.5.1/src/tools' Makefile:301: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/usr/local/gromacs-4.5.1/src' Makefile:237: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/usr/local/gromacs-4.5.1/src' Makefile:344: recipe for target `all-recursive' failed make: *** [all-recursive] Error 1 I have configured gromacs 4.5.4 using ./configure --disable-shared--enable-all-static--disable-threads FFTW version : FFTW 3.3 but still I encounter error during make step. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation on Ubuntu 12.04LTS
As some may end up following these steps let me make a few comments. On Sun, Jun 30, 2013 at 1:06 AM, Mare Libero marelibe...@yahoo.com wrote: Thanks guys! I think it's working now. Just in case others may run into the same difficulties, I am summarizing below what worked for me. I installed both gcc-4.4 and gcc-4.7 from synaptic. Then updated CUDA to 5.0, with the package cuda_5.0.35_linux_64_ubuntu11.10-1.run available from the nvidia site. Compiling cuda toolkit will require gcc-4.4, so I had Actually, AFAIK it's the compilation of the nvidia kernel module that asks for the same compiler to be used as the one the kernel was compiled with. However, if you really have Ubuntu 12.04 it could not be 4.4 that the driver installation asked for (as 12.04 comes with gcc 4.6). to temporarily change some links: sudo ln -s /usr/bin/gcc-4.4 /usr/bin/gcc sudo ln -s /usr/bin/g++-4.4 /usr/bin/g++ That's rather dirty, you could use alternatives instead (see man update-alternatives). Then I installed the toolkit and the samples: sudo ./cuda_5.0.35_linux_64_ubuntu11.10-1.run -toolkit Installing the CUDA samples required some extra packages on my system: sudo apt-get install freeglut3 sudo ln -s /usr/lib/x86_64-linux-gnu/libglut.so.3 /usr/lib/libglut.so I don't remember ever having to employ such hacks. In general, I would strongly advise against such practices as messing with your standard lib locations could cause update/installation issues down the road. sudo ./cuda_5.0.35_linux_64_ubuntu11.10-1.run -samples Then update my .bashrc: export LD_LIBRARY_PATH=/usr/local/cuda-5.0/lib64/:/usr/local/cuda-5.0/lib:$LD_LIBRARY_PATH export PATH=/usr/local/cuda-5.0/bin/:$PATH Finally confirm that CUDA 5.0 is the defoult compiler: nvcc -version Now I changed back the gcc links to install gromacs: sudo ln -s /usr/bin/gcc-4.7 /usr/bin/gcc sudo ln -s /usr/bin/g++-4.7 /usr/bin/g++ Like above, using alternatives is a better practice. CUDA apparently check which gcc version is used, and will complain for gcc version above 4.6. Gromacs on the other end will require gcc-4.7. I found a GROMACS does not *require* 4.6, but it is strongly recommended. solution on a blog, and comment out the compiler-check in the CUDA header file /usr/local/cuda-5.0/include/host_config.h Comment out: //#if __GNUC__ 4 || (__GNUC__ == 4 __GNUC_MINOR__ 6) //#error -- unsupported GNU version! gcc 4.7 and up are not supported! //#endif /* __GNUC__ 4 || (__GNUC__ == 4 __GNUC_MINOR__ 6) */ As it has been discussed on the list before, it's typically safe to do this, but be warned that sometimes (although rarely) using non-officially supported combination of gcc nvcc can lead to compilation issues (workarounds available online). Now I could cmake/make/install gromacs: cmake .. -DGMX_GPU=ON -DGMX_BUILD_OWN_FFTW=ON make sudo make install And add the /usr/local/gromacs/bin/ directory to my path. Source /usr/local/gromacs/bin/GMXRC instead - you get the path set up and more (e.g. flag/option autocomplete). I am still trying to fix the issues with the intel compiler. The gcc compiled version benchmark at 52ns/day with the lysozyme in water tutorial. icc 12 and 13 should just work with CUDA 5.0. Cheers, -- Szilárd Thanks again. From: Szilárd Páll szilard.p...@cbr.su.se To: Mare Libero marelibe...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, June 27, 2013 10:47 AM Subject: Re: [gmx-users] Installation on Ubuntu 12.04LTS On Thu, Jun 27, 2013 at 12:57 PM, Mare Libero marelibe...@yahoo.com wrote: Hello everybody, Does anyone have any recommendation regarding the installation of gromacs 4.6 on Ubuntu 12.04? I have the nvidia-cuda-toolkit that comes in synaptic (4.0.17-3ubuntu0.1 installed in /usr/lib/nvidia-cuda-toolkit) and the drivers 304.88. Apparently, this is not compatible with gcc-4.5 and higher. When I issue: $ cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON $ make the compilation ends with: In file included from /usr/lib/nvidia-cuda-toolkit/include/cuda_runtime.h:59:0, from command-line:0: /usr/include/host_config.h:82:2: error: #error -- unsupported GNU version! gcc 4.5 and up are not supported! If I downgrade to gcc-4.4 this error disappears, but gromacs compilation fails with a different error: cc1plus: error: unrecognized command line option -fexcess-precision=fast CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message): Error generating /home/me/Downloads/gromacs-4.6.2/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 I guess what happens
Re: [gmx-users] Installation on Ubuntu 12.04LTS
Thanks guys! I think it's working now. Just in case others may run into the same difficulties, I am summarizing below what worked for me. I installed both gcc-4.4 and gcc-4.7 from synaptic. Then updated CUDA to 5.0, with the package cuda_5.0.35_linux_64_ubuntu11.10-1.run available from the nvidia site. Compiling cuda toolkit will require gcc-4.4, so I had to temporarily change some links: sudo ln -s /usr/bin/gcc-4.4 /usr/bin/gcc sudo ln -s /usr/bin/g++-4.4 /usr/bin/g++ Then I installed the toolkit and the samples: sudo ./cuda_5.0.35_linux_64_ubuntu11.10-1.run -toolkit Installing the CUDA samples required some extra packages on my system: sudo apt-get install freeglut3 sudo ln -s /usr/lib/x86_64-linux-gnu/libglut.so.3 /usr/lib/libglut.so sudo ./cuda_5.0.35_linux_64_ubuntu11.10-1.run -samples Then update my .bashrc: export LD_LIBRARY_PATH=/usr/local/cuda-5.0/lib64/:/usr/local/cuda-5.0/lib:$LD_LIBRARY_PATH export PATH=/usr/local/cuda-5.0/bin/:$PATH Finally confirm that CUDA 5.0 is the defoult compiler: nvcc -version Now I changed back the gcc links to install gromacs: sudo ln -s /usr/bin/gcc-4.7 /usr/bin/gcc sudo ln -s /usr/bin/g++-4.7 /usr/bin/g++ CUDA apparently check which gcc version is used, and will complain for gcc version above 4.6. Gromacs on the other end will require gcc-4.7. I found a solution on a blog, and comment out the compiler-check in the CUDA header file /usr/local/cuda-5.0/include/host_config.h Comment out: //#if __GNUC__ 4 || (__GNUC__ == 4 __GNUC_MINOR__ 6) //#error -- unsupported GNU version! gcc 4.7 and up are not supported! //#endif /* __GNUC__ 4 || (__GNUC__ == 4 __GNUC_MINOR__ 6) */ Now I could cmake/make/install gromacs: cmake .. -DGMX_GPU=ON -DGMX_BUILD_OWN_FFTW=ON make sudo make install And add the /usr/local/gromacs/bin/ directory to my path. I am still trying to fix the issues with the intel compiler. The gcc compiled version benchmark at 52ns/day with the lysozyme in water tutorial. Thanks again. From: Szilárd Páll szilard.p...@cbr.su.se To: Mare Libero marelibe...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, June 27, 2013 10:47 AM Subject: Re: [gmx-users] Installation on Ubuntu 12.04LTS On Thu, Jun 27, 2013 at 12:57 PM, Mare Libero marelibe...@yahoo.com wrote: Hello everybody, Does anyone have any recommendation regarding the installation of gromacs 4.6 on Ubuntu 12.04? I have the nvidia-cuda-toolkit that comes in synaptic (4.0.17-3ubuntu0.1 installed in /usr/lib/nvidia-cuda-toolkit) and the drivers 304.88. Apparently, this is not compatible with gcc-4.5 and higher. When I issue: $ cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON $ make the compilation ends with: In file included from /usr/lib/nvidia-cuda-toolkit/include/cuda_runtime.h:59:0, from command-line:0: /usr/include/host_config.h:82:2: error: #error -- unsupported GNU version! gcc 4.5 and up are not supported! If I downgrade to gcc-4.4 this error disappears, but gromacs compilation fails with a different error: cc1plus: error: unrecognized command line option -fexcess-precision=fast CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message): Error generating /home/me/Downloads/gromacs-4.6.2/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 I guess what happens is that you are using gcc 4.5 for the CPU code and gcc 4.4 as the nvcc host compiler. However, the compiler options used for gcc (CMAKE_CXX_FLAGS) get propagated to nvcc; -fexcess-precision=fast is supported by gcc 4.5, but not by 4.4, hence the error when compiling CUDA code. Also, I tried the Intel compilers that comes with the non-commercial Intel c++ composer XE (which I believe are recommended). The compilation produces a number of warnings, and then dies with the following error: $ CC=/opt/intel/bin/icc cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON [ 63%] Building C object share/template/CMakeFiles/template.dir/template.c.o make[2]: *** No rule to make target `src/gmxlib/libgmx.so.8', needed by `share/template/template'. Stop. make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 This should work, but CUDA 4.0 is ancient surely does not support icc 13. I suggest that you get CUDA 5.0 and use gcc 4.7 (or a new icc). If you really want to stick to CUDA 4.0, try using gcc 4.4 as the general C++ compiler (CMAKE_CXX_COMPILER) which should avoid the above error. Thanks in advance for your help, Al -- gmx-users mailing list gmx-users@gromacs.org
[gmx-users] Installation on Ubuntu 12.04LTS
Hello everybody, Does anyone have any recommendation regarding the installation of gromacs 4.6 on Ubuntu 12.04? I have the nvidia-cuda-toolkit that comes in synaptic (4.0.17-3ubuntu0.1 installed in /usr/lib/nvidia-cuda-toolkit) and the drivers 304.88. Apparently, this is not compatible with gcc-4.5 and higher. When I issue: $ cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON $ make the compilation ends with: In file included from /usr/lib/nvidia-cuda-toolkit/include/cuda_runtime.h:59:0, from command-line:0: /usr/include/host_config.h:82:2: error: #error -- unsupported GNU version! gcc 4.5 and up are not supported! If I downgrade to gcc-4.4 this error disappears, but gromacs compilation fails with a different error: cc1plus: error: unrecognized command line option -fexcess-precision=fast CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message): Error generating /home/me/Downloads/gromacs-4.6.2/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 Also, I tried the Intel compilers that comes with the non-commercial Intel c++ composer XE (which I believe are recommended). The compilation produces a number of warnings, and then dies with the following error: $ CC=/opt/intel/bin/icc cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON [ 63%] Building C object share/template/CMakeFiles/template.dir/template.c.o make[2]: *** No rule to make target `src/gmxlib/libgmx.so.8', needed by `share/template/template'. Stop. make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 Thanks in advance for your help, Al -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation on Ubuntu 12.04LTS
On Thu, Jun 27, 2013 at 12:57 PM, Mare Libero marelibe...@yahoo.com wrote: Hello everybody, Does anyone have any recommendation regarding the installation of gromacs 4.6 on Ubuntu 12.04? I have the nvidia-cuda-toolkit that comes in synaptic (4.0.17-3ubuntu0.1 installed in /usr/lib/nvidia-cuda-toolkit) and the drivers 304.88. Apparently, this is not compatible with gcc-4.5 and higher. When I issue: $ cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON $ make the compilation ends with: In file included from /usr/lib/nvidia-cuda-toolkit/include/cuda_runtime.h:59:0, from command-line:0: /usr/include/host_config.h:82:2: error: #error -- unsupported GNU version! gcc 4.5 and up are not supported! If I downgrade to gcc-4.4 this error disappears, but gromacs compilation fails with a different error: cc1plus: error: unrecognized command line option -fexcess-precision=fast CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message): Error generating /home/me/Downloads/gromacs-4.6.2/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 CUDA 4.0 is two years old, so I would(did) get the latest package from Nvidia rather than rely on synaptic to be up to date with emerging technologies. And use a more recent gcc! Also, I tried the Intel compilers that comes with the non-commercial Intel c++ composer XE (which I believe are recommended). The compilation produces a number of warnings, and then dies with the following error: Yeah CUDA's wrapper compiler does not play perfectly with non-gcc, but the result should be OK. We have filed bug reports with CUDA. $ CC=/opt/intel/bin/icc cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON [ 63%] Building C object share/template/CMakeFiles/template.dir/template.c.o make[2]: *** No rule to make target `src/gmxlib/libgmx.so.8', needed by `share/template/template'. Stop. make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 On the other hand, FFTW development is nearly stopped, so libfftw3-dev from synaptic is fine, and I suspect the origin of this issue is either a race condition in the internal FFTW build (which will go away if you make again), or perhaps icc being evil and conveniently wrapping an FFTW interface over its MKL. We believe we've fixed the latter, but there are too many moving targets... Mark Thanks in advance for your help, Al -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation on Ubuntu 12.04LTS
On Thu, Jun 27, 2013 at 12:57 PM, Mare Libero marelibe...@yahoo.com wrote: Hello everybody, Does anyone have any recommendation regarding the installation of gromacs 4.6 on Ubuntu 12.04? I have the nvidia-cuda-toolkit that comes in synaptic (4.0.17-3ubuntu0.1 installed in /usr/lib/nvidia-cuda-toolkit) and the drivers 304.88. Apparently, this is not compatible with gcc-4.5 and higher. When I issue: $ cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON $ make the compilation ends with: In file included from /usr/lib/nvidia-cuda-toolkit/include/cuda_runtime.h:59:0, from command-line:0: /usr/include/host_config.h:82:2: error: #error -- unsupported GNU version! gcc 4.5 and up are not supported! If I downgrade to gcc-4.4 this error disappears, but gromacs compilation fails with a different error: cc1plus: error: unrecognized command line option -fexcess-precision=fast CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message): Error generating /home/me/Downloads/gromacs-4.6.2/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 I guess what happens is that you are using gcc 4.5 for the CPU code and gcc 4.4 as the nvcc host compiler. However, the compiler options used for gcc (CMAKE_CXX_FLAGS) get propagated to nvcc; -fexcess-precision=fast is supported by gcc 4.5, but not by 4.4, hence the error when compiling CUDA code. Also, I tried the Intel compilers that comes with the non-commercial Intel c++ composer XE (which I believe are recommended). The compilation produces a number of warnings, and then dies with the following error: $ CC=/opt/intel/bin/icc cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON [ 63%] Building C object share/template/CMakeFiles/template.dir/template.c.o make[2]: *** No rule to make target `src/gmxlib/libgmx.so.8', needed by `share/template/template'. Stop. make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 This should work, but CUDA 4.0 is ancient surely does not support icc 13. I suggest that you get CUDA 5.0 and use gcc 4.7 (or a new icc). If you really want to stick to CUDA 4.0, try using gcc 4.4 as the general C++ compiler (CMAKE_CXX_COMPILER) which should avoid the above error. Thanks in advance for your help, Al -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] installation Gromacs-Fedora18
Dear Gromacs users, I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and gromacs4.5.5.tar.gz I have followed these commands to install: $ tar -zxvf fftw-3.3.2/ $ cd fftw-3.3.2/ $ ./configure --prefix /home/safa/programs/fftw-3.3.2 --enable-threads --enable-sse2 --enable-shared $ make $ make install $ cd $ tar zxvf gromacs-4.5.5.tar.gz $ cd gromac-4.5.5/ $../configure --prefix /home/safa/programs/gromacs-4.5.5 LDFLAGS=-L/home/safa/fftw-3.3.2/lib CPPFLAGS=-I/home/safa/programs/fftw-3.3.2/include --disable-float When I wrote the last command I got this error. checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... yes checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking if pthread_setaffinity_np is available... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... no checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library
Re: [gmx-users] installation Gromacs-Fedora18
On 5/3/13 5:39 AM, Souilem Safa wrote: Dear Gromacs users, I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and gromacs4.5.5.tar.gz I have followed these commands to install: $ tar -zxvf fftw-3.3.2/ $ cd fftw-3.3.2/ $ ./configure --prefix /home/safa/programs/fftw-3.3.2 --enable-threads --enable-sse2 --enable-shared $ make $ make install $ cd $ tar zxvf gromacs-4.5.5.tar.gz $ cd gromac-4.5.5/ $../configure --prefix /home/safa/programs/gromacs-4.5.5 LDFLAGS=-L/home/safa/fftw-3.3.2/lib CPPFLAGS=-I/home/safa/programs/fftw-3.3.2/include --disable-float When I wrote the last command I got this error. checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... yes checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking if pthread_setaffinity_np is available... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... no checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux
Re: [gmx-users] installation Gromacs-Fedora18
this is what I do to install gromacs 4.5.5 on fedora 18 fftw libraries cd fftw-3.3.3_folder ./configure --enable-threads --enable-shared --enable-float --prefix=/usr/local/fftw make make install make clean in this way I install single precision (--enable-float) fftw libraries in /usr/local/fftw (you can put it where you want) be sure to enable shared because gromacs seems need it if you want double precision remove --enable-float gromacs 4.5.5 cd to folder ./configure CPPFLAGS=-I/usr/local/fftw/include LDFLAGS=-L/usr/localfftw/lib --with-fft=fftw3 make make install make clean --disable-float for double precision and --enable-mpi if you need mpi remember that fftw and gromacs must have the same precision. hope this helps you cheers Francesco On Fri, 3 May 2013, at 09:39 AM, Souilem Safa wrote: Dear Gromacs users, I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and gromacs4.5.5.tar.gz I have followed these commands to install: $ tar -zxvf fftw-3.3.2/ $ cd fftw-3.3.2/ $ ./configure --prefix /home/safa/programs/fftw-3.3.2 --enable-threads --enable-sse2 --enable-shared $ make $ make install $ cd $ tar zxvf gromacs-4.5.5.tar.gz $ cd gromac-4.5.5/ $../configure --prefix /home/safa/programs/gromacs-4.5.5 LDFLAGS=-L/home/safa/fftw-3.3.2/lib CPPFLAGS=-I/home/safa/programs/fftw-3.3.2/include --disable-float When I wrote the last command I got this error. checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... yes checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking if pthread_setaffinity_np is available... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... g++
Re: [gmx-users] installation Gromacs-Fedora18
many thanks to you all, I did installation as root it works well I like gromacs users discussion. It is very useful :) On 3 May 2013 19:10, Francesco frac...@myopera.com wrote: this is what I do to install gromacs 4.5.5 on fedora 18 fftw libraries cd fftw-3.3.3_folder ./configure --enable-threads --enable-shared --enable-float --prefix=/usr/local/fftw make make install make clean in this way I install single precision (--enable-float) fftw libraries in /usr/local/fftw (you can put it where you want) be sure to enable shared because gromacs seems need it if you want double precision remove --enable-float gromacs 4.5.5 cd to folder ./configure CPPFLAGS=-I/usr/local/fftw/include LDFLAGS=-L/usr/localfftw/lib --with-fft=fftw3 make make install make clean --disable-float for double precision and --enable-mpi if you need mpi remember that fftw and gromacs must have the same precision. hope this helps you cheers Francesco On Fri, 3 May 2013, at 09:39 AM, Souilem Safa wrote: Dear Gromacs users, I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and gromacs4.5.5.tar.gz I have followed these commands to install: $ tar -zxvf fftw-3.3.2/ $ cd fftw-3.3.2/ $ ./configure --prefix /home/safa/programs/fftw-3.3.2 --enable-threads --enable-sse2 --enable-shared $ make $ make install $ cd $ tar zxvf gromacs-4.5.5.tar.gz $ cd gromac-4.5.5/ $../configure --prefix /home/safa/programs/gromacs-4.5.5 LDFLAGS=-L/home/safa/fftw-3.3.2/lib CPPFLAGS=-I/home/safa/programs/fftw-3.3.2/include --disable-float When I wrote the last command I got this error. checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... yes checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking if pthread_setaffinity_np is available... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes
[gmx-users] Installation Problems with Gromacs4.6
Hello Gromacs Users.
I have been trying to install Gromacs4.6 on our HPC facility. I think I
have correctly provided all the necessary mpi and fftw library paths. But
when i try to run configure it gives me the following error:
CMake Error at cmake/FindFFTW.cmake:105 (message):
Could not find fftwf_plan_r2r_1d in
/home/aacharya/softwares/fftw-3.3.3/lib/libfftw3f.so, take a look at the
error message in
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeError.log to
find out what went wrong. If you are using a static lib (.a) make sure
you
have specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
-DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
CMakeLists.txt:894 (find_package)
As suggested here I looked into the CMakeError.log file of which I can't
make any sense.
Source file was:
#include mpi.h
int main(void) {
void* buf;
MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM, MPI_COMM_WORLD);
}
Determining if the function fftwf_plan_r2r_1d exists in the
/home/aacharya/softwares/fftw-3.3.3/lib failed with the following output:
Change Dir: /home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake cmTryCompileExec2668319475/fast
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2668319475.dir/build.make
CMakeFiles/cmTryCompileExec2668319475.dir/build
gmake[1]: Entering directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_progress_report
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp/CMakeFiles
1
Building C object
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d -o
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -c
/home/aacharya/softwares/cmake-2.8.10.2/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2668319475
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_link_script
CMakeFiles/cmTryCompileExec2668319475.dir/link.txt --verbose=1
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d
-L/home/aacharya/softwares/fftw-3.3.3/lib
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -o
cmTryCompileExec2668319475 -rdynamic -lm
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o: In
function `main':
CheckFunctionExists.c:(.text+0x15): undefined reference to
`fftwf_plan_r2r_1d'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTryCompileExec2668319475] Error 1
gmake[1]: Leaving directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec2668319475/fast] Error 2
Kindly help. I tried installing 4.5.6 and it got installed without any
such problems. I need 4.6 because my tpr files are produced in Gromacs4.6
and I am using the Verlet cutoff scheme.
Thanks in advance
With Regards
Abhishek Acharya
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Installation Problems with Gromacs4.6
On Fri, Mar 1, 2013 at 7:29 PM, Abhishek Acharya aacha...@iitk.ac.inwrote:
Hello Gromacs Users.
I have been trying to install Gromacs4.6 on our HPC facility. I think I
have correctly provided all the necessary mpi and fftw library paths.
OK, but you'll make trouble-shooting easier if you tell us what you've done
:-)
CC=mpicc cmake .. -DCMAKE_PREFIX_PATH=$HOME/softwares/fftw-3.3.3 is the
simplest form likely to work.
But
when i try to run configure it gives me the following error:
CMake Error at cmake/FindFFTW.cmake:105 (message):
Could not find fftwf_plan_r2r_1d in
/home/aacharya/softwares/fftw-3.3.3/lib/libfftw3f.so, take a look at the
error message in
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeError.log to
find out what went wrong. If you are using a static lib (.a) make sure
you
have specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
-DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
CMakeLists.txt:894 (find_package)
As suggested here I looked into the CMakeError.log file of which I can't
make any sense.
Source file was:
#include mpi.h
int main(void) {
void* buf;
MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM, MPI_COMM_WORLD);
}
Determining if the function fftwf_plan_r2r_1d exists in the
/home/aacharya/softwares/fftw-3.3.3/lib failed with the following output:
Change Dir: /home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake cmTryCompileExec2668319475/fast
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2668319475.dir/build.make
CMakeFiles/cmTryCompileExec2668319475.dir/build
gmake[1]: Entering directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_progress_report
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp/CMakeFiles
1
Building C object
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d -o
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -c
/home/aacharya/softwares/cmake-2.8.10.2/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2668319475
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_link_script
CMakeFiles/cmTryCompileExec2668319475.dir/link.txt --verbose=1
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d
-L/home/aacharya/softwares/fftw-3.3.3/lib
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -o
cmTryCompileExec2668319475 -rdynamic -lm
That looks weird. CMake is not trying to link to your FFTW library at all,
but all I can guess with current information is that something with your
call to cmake isn't working.
Mark
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o: In
function `main':
CheckFunctionExists.c:(.text+0x15): undefined reference to
`fftwf_plan_r2r_1d'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTryCompileExec2668319475] Error 1
gmake[1]: Leaving directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec2668319475/fast] Error 2
Kindly help. I tried installing 4.5.6 and it got installed without any
such problems. I need 4.6 because my tpr files are produced in Gromacs4.6
and I am using the Verlet cutoff scheme.
Thanks in advance
With Regards
Abhishek Acharya
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
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--
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Re: [gmx-users] installation
Erik, thanks for your answer. I typed which mdrun and I got this output: *~$ which mdrun* */usr/local/gromacs/bin/mdrun* Then, I typed just mdrun and I got this: *~$ mdrun* * * * :-) G R O M A C S (-:* * * * Green Red Orange Magenta Azure Cyan Skyblue* * * * :-) VERSION 4.6 (-:* * * *Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, * * Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, * * Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, * *Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, * * Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, * *Michael Shirts, Alfons Sijbers, Peter Tieleman,* * * * Berk Hess, David van der Spoel, and Erik Lindahl.* * * * Copyright (c) 1991-2000, University of Groningen, The Netherlands.* * Copyright (c) 2001-2012,2013, The GROMACS development team at* *Uppsala University The Royal Institute of Technology, Sweden.* *check out http://www.gromacs.org for more information.* * * * This program is free software; you can redistribute it and/or* * modify it under the terms of the GNU Lesser General Public License* *as published by the Free Software Foundation; either version 2.1* * of the License, or (at your option) any later version.* * * *:-) mdrun (-:* * * *Option Filename Type Description* ** * -s topol.tpr InputRun input file: tpr tpb tpa* * -o traj.trr Output Full precision trajectory: trr trj cpt* * -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)* *-cpi state.cpt Input, Opt. Checkpoint file* *-cpo state.cpt Output, Opt. Checkpoint file* * -cconfout.gro Output Structure file: gro g96 pdb etc.* * -e ener.edr Output Energy file* * -g md.log Output Log file* *-dhdl dhdl.xvg Output, Opt. xvgr/xmgr file* *-fieldfield.xvg Output, Opt. xvgr/xmgr file* *-tabletable.xvg Input, Opt. xvgr/xmgr file* *-tabletftabletf.xvg Input, Opt. xvgr/xmgr file* *-tablep tablep.xvg Input, Opt. xvgr/xmgr file* *-tableb table.xvg Input, Opt. xvgr/xmgr file* *-rerunrerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt* *-tpitpi.xvg Output, Opt. xvgr/xmgr file* *-tpid tpidist.xvg Output, Opt. xvgr/xmgr file* * -eisam.edi Input, Opt. ED sampling input* * -eo edsam.xvg Output, Opt. xvgr/xmgr file* * -j wham.gct Input, Opt. General coupling stuff* * -jobam.gct Output, Opt. General coupling stuff* *-ffout gct.xvg Output, Opt. xvgr/xmgr file* *-devout deviatie.xvg Output, Opt. xvgr/xmgr file* *-runav runaver.xvg Output, Opt. xvgr/xmgr file* * -px pullx.xvg Output, Opt. xvgr/xmgr file* * -pf pullf.xvg Output, Opt. xvgr/xmgr file* * -ro rotation.xvg Output, Opt. xvgr/xmgr file* * -ra rotangles.log Output, Opt. Log file* * -rs rotslabs.log Output, Opt. Log file* * -rt rottorque.log Output, Opt. Log file* *-mtx nm.mtx Output, Opt. Hessian matrix* * -dn dipole.ndx Output, Opt. Index file* *-multidirrundir Input, Opt., Mult. Run directory* *-membed membed.dat Input, Opt. Generic data file* * -mp membed.top Input, Opt. Topology file* * -mn membed.ndx Input, Opt. Index file* * * *Option Type Value Description* *--* *-[no]h bool no Print help info and quit* *-[no]version bool no Print version info and quit* *-niceint0 Set the nicelevel* *-deffnm string Set the default filename for all file options* *-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none* *-[no]pd bool no Use particle decompostion* *-dd vector 0 0 0 Domain decomposition grid, 0 is optimize* *-ddorder enum interleave DD node order: interleave, pp_pme or cartesian* *-npmeint-1 Number of separate nodes to be used for PME, -1 * *is guess* *-nt int0 Total number of threads to start (0 is guess)* *-ntmpi int0 Number of thread-MPI threads to start (0 is guess)* *-ntomp int0 Number of OpenMP threads per MPI process/thread * *to start (0 is guess)* *-ntomp_pme int0 Number of OpenMP threads per MPI process/thread * *to start (0 is -ntomp)* *-pin enum autoFix threads (or processes) to specific cores:* *auto, on or off* *-pinoffset int0 The starting logical core number for pinning to * *cores; used to avoid pinning
Re: [gmx-users] installation
On 2/14/13 9:40 AM, David Sáez wrote: Erik, thanks for your answer. I typed which mdrun and I got this output: *~$ which mdrun* */usr/local/gromacs/bin/mdrun* Then, I typed just mdrun and I got this: *~$ mdrun* * * * :-) G R O M A C S (-:* * * * Green Red Orange Magenta Azure Cyan Skyblue* * * * :-) VERSION 4.6 (-:* * * *Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, * * Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, * * Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, * *Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, * * Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, * *Michael Shirts, Alfons Sijbers, Peter Tieleman,* * * * Berk Hess, David van der Spoel, and Erik Lindahl.* * * * Copyright (c) 1991-2000, University of Groningen, The Netherlands.* * Copyright (c) 2001-2012,2013, The GROMACS development team at* *Uppsala University The Royal Institute of Technology, Sweden.* *check out http://www.gromacs.org for more information.* * * * This program is free software; you can redistribute it and/or* * modify it under the terms of the GNU Lesser General Public License* *as published by the Free Software Foundation; either version 2.1* * of the License, or (at your option) any later version.* * * *:-) mdrun (-:* * * *Option Filename Type Description* ** * -s topol.tpr InputRun input file: tpr tpb tpa* * -o traj.trr Output Full precision trajectory: trr trj cpt* * -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)* *-cpi state.cpt Input, Opt. Checkpoint file* *-cpo state.cpt Output, Opt. Checkpoint file* * -cconfout.gro Output Structure file: gro g96 pdb etc.* * -e ener.edr Output Energy file* * -g md.log Output Log file* *-dhdl dhdl.xvg Output, Opt. xvgr/xmgr file* *-fieldfield.xvg Output, Opt. xvgr/xmgr file* *-tabletable.xvg Input, Opt. xvgr/xmgr file* *-tabletftabletf.xvg Input, Opt. xvgr/xmgr file* *-tablep tablep.xvg Input, Opt. xvgr/xmgr file* *-tableb table.xvg Input, Opt. xvgr/xmgr file* *-rerunrerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt* *-tpitpi.xvg Output, Opt. xvgr/xmgr file* *-tpid tpidist.xvg Output, Opt. xvgr/xmgr file* * -eisam.edi Input, Opt. ED sampling input* * -eo edsam.xvg Output, Opt. xvgr/xmgr file* * -j wham.gct Input, Opt. General coupling stuff* * -jobam.gct Output, Opt. General coupling stuff* *-ffout gct.xvg Output, Opt. xvgr/xmgr file* *-devout deviatie.xvg Output, Opt. xvgr/xmgr file* *-runav runaver.xvg Output, Opt. xvgr/xmgr file* * -px pullx.xvg Output, Opt. xvgr/xmgr file* * -pf pullf.xvg Output, Opt. xvgr/xmgr file* * -ro rotation.xvg Output, Opt. xvgr/xmgr file* * -ra rotangles.log Output, Opt. Log file* * -rs rotslabs.log Output, Opt. Log file* * -rt rottorque.log Output, Opt. Log file* *-mtx nm.mtx Output, Opt. Hessian matrix* * -dn dipole.ndx Output, Opt. Index file* *-multidirrundir Input, Opt., Mult. Run directory* *-membed membed.dat Input, Opt. Generic data file* * -mp membed.top Input, Opt. Topology file* * -mn membed.ndx Input, Opt. Index file* * * *Option Type Value Description* *--* *-[no]h bool no Print help info and quit* *-[no]version bool no Print version info and quit* *-niceint0 Set the nicelevel* *-deffnm string Set the default filename for all file options* *-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none* *-[no]pd bool no Use particle decompostion* *-dd vector 0 0 0 Domain decomposition grid, 0 is optimize* *-ddorder enum interleave DD node order: interleave, pp_pme or cartesian* *-npmeint-1 Number of separate nodes to be used for PME, -1 * *is guess* *-nt int0 Total number of threads to start (0 is guess)* *-ntmpi int0 Number of thread-MPI threads to start (0 is guess)* *-ntomp int0 Number of OpenMP threads per MPI process/thread * *to start (0 is guess)* *-ntomp_pme int0 Number of OpenMP threads per MPI process/thread * *to start (0 is -ntomp)* *-pin enum autoFix threads (or processes) to specific cores:* *auto, on or off* *-pinoffset int0 The starting logical core number for pinning to * *
Re: [gmx-users] installation
Thanks Justin, I'm gonna take your advice. On Thu, Feb 14, 2013 at 11:43 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/14/13 9:40 AM, David Sáez wrote: Erik, thanks for your answer. I typed which mdrun and I got this output: *~$ which mdrun* */usr/local/gromacs/bin/mdrun* Then, I typed just mdrun and I got this: *~$ mdrun* * * * :-) G R O M A C S (-:* * * * Green Red Orange Magenta Azure Cyan Skyblue* * * * :-) VERSION 4.6 (-:* * * *Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, * * Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, * * Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, * *Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, * * Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, * *Michael Shirts, Alfons Sijbers, Peter Tieleman,* * * * Berk Hess, David van der Spoel, and Erik Lindahl.* * * * Copyright (c) 1991-2000, University of Groningen, The Netherlands.* * Copyright (c) 2001-2012,2013, The GROMACS development team at* *Uppsala University The Royal Institute of Technology, Sweden.* *check out http://www.gromacs.org for more information.* * * * This program is free software; you can redistribute it and/or* * modify it under the terms of the GNU Lesser General Public License* *as published by the Free Software Foundation; either version 2.1* * of the License, or (at your option) any later version.* * * *:-) mdrun (-:* * * *Option Filename Type Description* *-**--**-* * -s topol.tpr InputRun input file: tpr tpb tpa* * -o traj.trr Output Full precision trajectory: trr trj cpt* * -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)* *-cpi state.cpt Input, Opt. Checkpoint file* *-cpo state.cpt Output, Opt. Checkpoint file* * -cconfout.gro Output Structure file: gro g96 pdb etc.* * -e ener.edr Output Energy file* * -g md.log Output Log file* *-dhdl dhdl.xvg Output, Opt. xvgr/xmgr file* *-fieldfield.xvg Output, Opt. xvgr/xmgr file* *-tabletable.xvg Input, Opt. xvgr/xmgr file* *-tabletftabletf.xvg Input, Opt. xvgr/xmgr file* *-tablep tablep.xvg Input, Opt. xvgr/xmgr file* *-tableb table.xvg Input, Opt. xvgr/xmgr file* *-rerunrerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt* *-tpitpi.xvg Output, Opt. xvgr/xmgr file* *-tpid tpidist.xvg Output, Opt. xvgr/xmgr file* * -eisam.edi Input, Opt. ED sampling input* * -eo edsam.xvg Output, Opt. xvgr/xmgr file* * -j wham.gct Input, Opt. General coupling stuff* * -jobam.gct Output, Opt. General coupling stuff* *-ffout gct.xvg Output, Opt. xvgr/xmgr file* *-devout deviatie.xvg Output, Opt. xvgr/xmgr file* *-runav runaver.xvg Output, Opt. xvgr/xmgr file* * -px pullx.xvg Output, Opt. xvgr/xmgr file* * -pf pullf.xvg Output, Opt. xvgr/xmgr file* * -ro rotation.xvg Output, Opt. xvgr/xmgr file* * -ra rotangles.log Output, Opt. Log file* * -rs rotslabs.log Output, Opt. Log file* * -rt rottorque.log Output, Opt. Log file* *-mtx nm.mtx Output, Opt. Hessian matrix* * -dn dipole.ndx Output, Opt. Index file* *-multidirrundir Input, Opt., Mult. Run directory* *-membed membed.dat Input, Opt. Generic data file* * -mp membed.top Input, Opt. Topology file* * -mn membed.ndx Input, Opt. Index file* * * *Option Type Value Description* *-**-* *-[no]h bool no Print help info and quit* *-[no]version bool no Print version info and quit* *-niceint0 Set the nicelevel* *-deffnm string Set the default filename for all file options* *-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none* *-[no]pd bool no Use particle decompostion* *-dd vector 0 0 0 Domain decomposition grid, 0 is optimize* *-ddorder enum interleave DD node order: interleave, pp_pme or cartesian* *-npmeint-1 Number of separate nodes to be used for PME, -1 * *is guess* *-nt int0 Total number of threads to start (0 is guess)* *-ntmpi int0 Number of thread-MPI threads to start (0 is guess)* *-ntomp int0 Number of OpenMP threads per MPI process/thread * *to start (0 is guess)* *-ntomp_pme int0 Number of OpenMP threads per MPI process/thread * *to
Re: [gmx-users] installation
It shouldn't generate output. It will make your system find your gromacs installation, however. Try e.g. which mdrun. Erik On Feb 13, 2013, at 5:06 AM, David Sáez wrote: Thanks for your answer Justin. I followed your advice: When I type *$ source /usr/local/gromacs/bin/GMXRC* *$* Nothing happened, the prompt returns normally and no action is executed. Do you have any idea? On Tue, Feb 12, 2013 at 11:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/12/13 9:24 PM, David Sáez wrote: Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04 laptop. As I am not a a skilled user, I tried the Quick and Dirty Installation, After following the instructions I obtained this message when trying to execute GMXRC: david@HAL-9000:~$ /usr/local/gromacs/bin/GMXRC /usr/local/gromacs/bin/GMXRC: line 34: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 43: CSH:: command not found /usr/local/gromacs/bin/GMXRC.**csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.**csh: line 8: `if (! $? LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Could someone give some help? Note the first error - you need to source the file. $ source /usr/local/gromacs/bin/GMXRC -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- David A. Sáez San Martín Químico-Farmacéutico Concepción, Chile -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] installation
Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04 laptop. As I am not a a skilled user, I tried the Quick and Dirty Installation, After following the instructions I obtained this message when trying to execute GMXRC: david@HAL-9000:~$ /usr/local/gromacs/bin/GMXRC /usr/local/gromacs/bin/GMXRC: line 34: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 43: CSH:: command not found /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Could someone give some help? Thanks in advance. -- David A. Sáez San Martín Químico-Farmacéutico Concepción, Chile -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation
On 2/12/13 9:24 PM, David Sáez wrote: Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04 laptop. As I am not a a skilled user, I tried the Quick and Dirty Installation, After following the instructions I obtained this message when trying to execute GMXRC: david@HAL-9000:~$ /usr/local/gromacs/bin/GMXRC /usr/local/gromacs/bin/GMXRC: line 34: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 43: CSH:: command not found /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Could someone give some help? Note the first error - you need to source the file. $ source /usr/local/gromacs/bin/GMXRC -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation
Thanks for your answer Justin. I followed your advice: When I type *$ source /usr/local/gromacs/bin/GMXRC* *$* Nothing happened, the prompt returns normally and no action is executed. Do you have any idea? On Tue, Feb 12, 2013 at 11:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/12/13 9:24 PM, David Sáez wrote: Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04 laptop. As I am not a a skilled user, I tried the Quick and Dirty Installation, After following the instructions I obtained this message when trying to execute GMXRC: david@HAL-9000:~$ /usr/local/gromacs/bin/GMXRC /usr/local/gromacs/bin/GMXRC: line 34: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 43: CSH:: command not found /usr/local/gromacs/bin/GMXRC.**csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.**csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Could someone give some help? Note the first error - you need to source the file. $ source /usr/local/gromacs/bin/GMXRC -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- David A. Sáez San Martín Químico-Farmacéutico Concepción, Chile -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Installation Error
Hi Justin, I am trying to install gromacs-4.5.5 on a Linux work station (x86_64) but I am getting an error. The error message is attached in the mail in a text file Installation_error.txt. I have installed fftw-3.3.3 in my system. I have checked threads on the mailing list which have reported the same error and have also followed whatever solution has been provided but unfortunately its still not successful. Now I am at a fix Could you please suggest me what should I do next for successfully installing gromacs on my machine? could it be some compatibilty issue or m I missing out something crucial? - Bharati Bharati Dutta Research Associate Discovery Informatics Piramal Life Sciences Limited 1, Nirlon Complex, Goregaon Link Road, Goregaon(E) Mumbai, Maharashtra 400 063 India bharati.du...@piramal.com This communication may contain information that is proprietary confidential or exempt from disclosure. If you are not the intended recipient please note that any other dissemination distribution use or copying of this communication is strictly prohibited. Anyone who receives this message in error should notify the sender immediately by telephone or by return e-mail and delete it from his or her computer. /usr/bin/ld: /usr/local/lib/libfftw3f.a(mapflags.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/home/gromacs-4.5.5/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation Error
See http://www.gromacs.org/Documentation/Installation_Instructions_4.5#Details_for_building_the_FFTW_prerequisite On Fri, Dec 7, 2012 at 9:08 AM, BHARATI DUTTA bharati.du...@piramal.comwrote: Hi Justin, I am trying to install gromacs-4.5.5 on a Linux work station (x86_64) but I am getting an error. The error message is attached in the mail in a text file Installation_error.txt. I have installed fftw-3.3.3 in my system. I have checked threads on the mailing list which have reported the same error and have also followed whatever solution has been provided but unfortunately its still not successful. Now I am at a fix Could you please suggest me what should I do next for successfully installing gromacs on my machine? could it be some compatibilty issue or m I missing out something crucial? - Bharati -- *Bharati Dutta* Research Associate Discovery Informatics *Piramal Life Sciences Limited*http://www.piramallifesciences.com 1, Nirlon Complex, Goregaon Link Road, Goregaon(E) Mumbai, Maharashtra 400 063 India *bharati.du...@piramal.com* bharati.du...@piramal.com -- This communication may contain information that is proprietary confidential or exempt from disclosure. If you are not the intended recipient please note that any other dissemination distribution use or copying of this communication is strictly prohibited. Anyone who receives this message in error should notify the sender immediately by telephone or by return e-mail and delete it from his or her computer. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Installation problems with MacOS 10.7.5
Dear Users,
I have problems with the installation of GROMACS 4.5.5 on MacOS 10.7.5.
GCC version 4.2.1
FFTW is: FFTW-3.3.2.
The CMAke command
cmake -DGMX_THREAD_MPI=OFF \
-DFFTW3F_INCLUDE_DIR=$FFTWDIR/include \
-DFFTW3F_LIBRARIES=$FFTWDIR/lib \
-DGMX_X11=OFF \
-DCMAKE_INSTALL_PREFIX=$(pwd) \
-DGMX_MPI=OFF \
-DGMX_THREADS=OFF \
-DBUILD_SHARED_LIBS=OFF \
/Users/jaschone/Downloads/gromacs-4.5.5
Where CCDIR is the location of the GCC binary, FFTWDIR is the location
of the FFTW stuff.
I get the following error mesage:
WARNING: Target md requests linking to directory
/Users/jaschone/progs/lib. Targets may link only to libraries. CMake
is dropping the item.
and for the other binaries I get similar messages.
Using MAKE results in the follwing error:
/Users/jaschone/Downloads/gromacs-4.5.5/src/kernel/gmxdump.c:150:11:
warning: expression result unused [-Wunused-value]
if (state,tpx.bF) {
^
1 warning generated.
Undefined symbols for architecture x86_64:
_fftwf_plan_guru_dft_r2c, referenced from:
_fft5d_plan_3d in libmd.a(fft5d.c.o)
and then similar errors for other routines.
The complete STD.OUT and STD.ERR files for the CMAKE and the MAKE
command were saved.
Does anyone has an idea for an solution?
--
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Re: [gmx-users] Installation problems with MacOS 10.7.5
You need to name libraries with FFTW3F_LIBRARIES, not the library path.
That explains the dropped dependency and subsequent problems.
Mark
On Mon, Nov 26, 2012 at 4:19 PM, Stefan Jasconek
stjas...@students.uni-mainz.de wrote:
Dear Users,
I have problems with the installation of GROMACS 4.5.5 on MacOS 10.7.5.
GCC version 4.2.1
FFTW is: FFTW-3.3.2.
The CMAke command
cmake -DGMX_THREAD_MPI=OFF \
-DFFTW3F_INCLUDE_DIR=$FFTWDIR/**include \
-DFFTW3F_LIBRARIES=$FFTWDIR/**lib \
-DGMX_X11=OFF \
-DCMAKE_INSTALL_PREFIX=$(pwd) \
-DGMX_MPI=OFF \
-DGMX_THREADS=OFF \
-DBUILD_SHARED_LIBS=OFF \
/Users/jaschone/Downloads/**gromacs-4.5.5
Where CCDIR is the location of the GCC binary, FFTWDIR is the location of
the FFTW stuff.
I get the following error mesage:
WARNING: Target md requests linking to directory
/Users/jaschone/progs/lib. Targets may link only to libraries. CMake is
dropping the item.
and for the other binaries I get similar messages.
Using MAKE results in the follwing error:
/Users/jaschone/Downloads/**gromacs-4.5.5/src/kernel/**gmxdump.c:150:11:
warning: expression result unused [-Wunused-value]
if (state,tpx.bF) {
^
1 warning generated.
Undefined symbols for architecture x86_64:
_fftwf_plan_guru_dft_r2c, referenced from:
_fft5d_plan_3d in libmd.a(fft5d.c.o)
and then similar errors for other routines.
The complete STD.OUT and STD.ERR files for the CMAKE and the MAKE command
were saved.
Does anyone has an idea for an solution?
--
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Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
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Re: [gmx-users] Installation in a SGI Cluster
Check to see if the MPICC and MPI_HOME environment variables are set correctly to configure (it can't find mpicc). On 2012-09-25 12:06:14PM -0300, Diego Nolasco wrote: Hello GROMACS users, I am facing some problems to configure the gromacs installation in a x86_64 GNU/Linux SGI Cluster XE with Suse. I am using ./configure --enable-mpi --without-x --disable-float and the error comes as below: checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... no checking for mpcc... no checking for hcc... no checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with cc I would really appreciate if someone assist me in this regard. Thank's in advance, Diego Nolasco. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation of GROMACS on server
Yes, it could be possible. You have to install it on your local folder where you have the right permissions. This is specified with the --prefix option on the configure script (if using automake/automake installation) or the corresponding option with cmake (I don't know wich one is it, check the website or use cmake -i for an interactive installation) Keep in mind the dependencies, such as fftw libraries, which you might also need to install in your local folder if they are not already installed. Javier El 22/05/12 10:47, Shima Arasteh escribió: Dear gmx users, If I am not admin of the server, would it be possible that I install the GROMACS 4.5.5 in my account (user) or upgrade the GROMACS version? Thanks for your suggestions in advance. Sincerely, Shima -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] Installation of GROMACS on server
A good place to start your reading: http://www.gromacs.org/Documentation/Installation_Instructions Javier El 22/05/12 11:48, Shima Arasteh escribió: Would you guide me to a link which may help me? Thanks so much. Sincerely, Shima *From:* Anirban reach.anirban.gh...@gmail.com *To:* Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tuesday, May 22, 2012 1:33 PM *Subject:* Re: [gmx-users] Installation of GROMACS on server On Tue, May 22, 2012 at 2:17 PM, Shima Arasteh shima_arasteh2...@yahoo.com mailto:shima_arasteh2...@yahoo.com wrote: Dear gmx users, If I am not admin of the server, would it be possible that I install the GROMACS 4.5.5 in my account (user) or upgrade the GROMACS version? You can install latest version of GROMACS in your local directory by giving the --prefix=YOUR_PATH option with ./configure, without being the admin. -Anirban Thanks for your suggestions in advance. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] installation issues
Dear All, I have tried installing gromacs (after installing fftw3 library)on a GPU system using the following : ./configure --with-fft=fftw3 --enable-float After I type make I get the following error after sometime. . . . /usr/bin/ld: /home/anupam/fftw-3.3.1/.libs/libfftw3f.a(apiplan.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /home/anupam/fftw-3.3.1/.libs/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/home/anupam/gromacs-4.5.5/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/anupam/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/anupam/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 Please help me out in this regard. Thanks Anupam -- Graduate Student, Laboratory of Computational Biology, Center For DNA Fingerprinting And Diagnostics, 4-1-714 to 725/2, Tuljaguda complex Mozamzahi Road, Nampally, Hyderabad-51 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation issues
On 17/04/2012 11:12 PM, anupam sinha wrote: Dear All, I have tried installing gromacs (after installing fftw3 library)on a GPU system using the following : ./configure --with-fft=fftw3 --enable-float After I type make I get the following error after sometime. . . . /usr/bin/ld: /home/anupam/fftw-3.3.1/.libs/libfftw3f.a(apiplan.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /home/anupam/fftw-3.3.1/.libs/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la http://libmd.la] Error 1 make[3]: Leaving directory `/home/anupam/gromacs-4.5.5/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/anupam/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/anupam/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 See http://www.gromacs.org/Documentation/Installation_Instructions#Details_for_building_the_FFTW_prerequisite Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] installation problem of gromacs 4.0.7 on Rocks cluster
Dear Gmx Users, I am facing problem while installing gromacs 4.0.7 on the rocks cluster 1. command: ./configure --enable-float --enable-threads --enable-sse --enable-mpi we got the following error: checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... no checking for mpcc... no checking for hcc... no checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with cc 2. command ./configure --enable-float --enable-threads --enable-sse --enable-mpi --program-suffix=_mpi MPICC=/usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx we got the following error: checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx checking whether the MPI cc command works... yes checking for catamount... no checking for pthreads... yes checking how to run the C preprocessor... /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx -E checking whether /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx accepts -O3... yes checking whether /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx accepts -funroll-all-loops... yes checking whether /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking for int... yes checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. though the installation completes without the --enable mpi the gcc compiler version used is 4.1.2. i will be grateful if someone can help us out on how to resolve this issue. thanking you, Parul Tewatia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation problem of gromacs 4.0.7 on Rocks cluster
On 13/02/2012 9:56 PM, Parul tew wrote: Dear Gmx Users, I am facing problem while installing gromacs 4.0.7 on the rocks cluster 1. command: ./configure --enable-float --enable-threads --enable-sse --enable-mpi If you were using an up-to-date version of GROMACS (and it is likely that you should do so), then you would not be able to compile with threads and with MPI. However this GROMACS version silently ignores the request for threads, because it wasn't implemented back then. we got the following error: checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... no checking for mpcc... no checking for hcc... no checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with cc 2. command ./configure --enable-float --enable-threads --enable-sse --enable-mpi --program-suffix=_mpi MPICC=/usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx mpicxx is intended to be a C++ compiler. This may or may not work correctly as a C compiler. we got the following error: checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx checking whether the MPI cc command works... yes checking for catamount... no checking for pthreads... yes checking how to run the C preprocessor... /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx -E checking whether /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx accepts -O3... yes checking whether /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx accepts -funroll-all-loops... yes checking whether /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking for int... yes checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. though the installation completes without the --enable mpi the gcc compiler version used is 4.1.2. Something is wrong with the setup of your MPI compiler - perhaps what I suggested above. You should verify that these work before attempting to troubleshoot GROMACS installation further. See http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites where you are advised not to use this version of GCC. I don't know for sure, but this version of MVAPICH could be too old to be useful. Mark i will be grateful if someone can help us out on how to resolve this issue. thanking you, Parul Tewatia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] installation problem
Hi All, I've installed fftw-3.3 on my computer when I try to install GROMACS I run into problems. A little information: Here are the values for LDFLAGS and CPPFLAGS echo $LDFLAGS -L/home/ramone/mygromacs/lib The content of this directory is the following: libfftw3f.a libfftw3f.la* pkgconfig/ echo $CPPFLAGS -I/home/ramone/mygromacs/include The content of this directory is the following: fftw3.f fftw3.f03 fftw3.h here is the command I use inside the gromacs-4.5.5 directory ./configure --prefix=$SOFT --with-gsl --disable-float --with-qmmm-orca --without-qmmm-gaussian --disable-shared I get the following error checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3... no configure: error: Cannot find fftw3 library Any help would be greatly appreciated. Ramon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] installation of FFTW
Hi I am working with RHEL 6 beta, I unable to install the FFTW package while installation I found the following error, make[3]: Leaving directory `/home/Ithayaraja/Desktop/ fftw-3.3.1-beta1/tools' make[2]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/tools' Making all in m4 make[2]: Entering directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4' make[1]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1' can you help me to find out where i did wrong? Thanks in advance -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of FFTW
On 14/09/2011 3:24 PM, ITHAYARAJA wrote: Hi I am working with RHEL 6 beta, I unable to install the FFTW package while installation I found the following error, There is no error reported in what you have shown. make[3]: Leaving directory `/home/Ithayaraja/Desktop/ fftw-3.3.1-beta1/tools' make[2]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/tools' Making all in m4 make[2]: Entering directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4' make[1]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1' can you help me to find out where i did wrong? Not without knowing your configure line, knowing that you have followed the instructions on the GROMACS webpage, seeing what the actual error message was, and knowing why you're trying to use a beta of a version of FFTW that is a few years out of date. :) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation gromacs in Scientific Linux
On 7/09/2011 1:01 PM, Nathalia Garces wrote: Hello, The last 6 months I've been working with gromacs (4.5.3 and 4.5.4) in Ubuntu (10.4) and it has worked fine. The problem started when I changed the linux distribution to Scientific Linux (5.3)... I followed the same steps to download/configure gromacs but something's wrong or missing because the simulations that I had been running on UBUNTU crashed in SL. Maybe you just got lucky. The success of poorly-conditioned numerical integration procedures can vary with what the user ate for lunch. Well, not quite, but you get the idea. :) You can make a better assessment by transferring a fully equilibrated .tpr from your working machine to your non-working machine and seeing whether that runs. The command I use is very simple: / mdrun -v -s topol.tpr/ In Ubuntu the simulation ends fine but in SL the application starts to write on prompt at early steps (around 100) /Step XX, time 0.XX (ps) LINCS WARNING/ /relative constraint deviation after LINCS:/ /rms XX, max XX (between atoms XX and XX)/ /bonds that rotated more than 30 degrees:/ /.../ //Wrote pdb files with previous and current coordinates// / / Until the simulation ends (around 250) with a message of / Segmentation fault / I tried different ways to configure gromacs but none of them seems to resolve the problem 1) ./configure --prefix=my path make make install 2) ./configure --with-fft=fftw3 --prefix=my path --without-x make make install 3)./configure --program-suffix= --disable-float --prefix=my path --exec-prefix=my path --enable-all-static --with-fft=fftw3 --without-x make make install You will need an FFTW install with float/double precision matching that of the GROMACS configure command. Moreover, I downloaded the benchmark posted in the gromacs web page to test the simulations with other .tpr files. I run the first simulation (implicit solvent) in UBUNTU and worked OK but the one on SL crashed (around step 460) with the first two options of configuration. The last configuration enabled the simulation to run OK( I decided to stop it at 4000 steps)... This bewilders me because the last configuration permitted the benchmark to run OK but not my file. I don't think my file has an unstable system because it works all right in UBUNTU (and also Debian!) One possibility is some kind of dynamic linking failure from all your different installations. If you always install to a --prefix that you can delete later, then you can be sure that this kind of problem cannot occur when you are testing different installations. In addition, I upgraded my linux distribution to the latest SL 5.x release but it didn't make any change! I hope you can help me with some guide on how to proceed a GOOD instalation in SL or to let me know what is my problem and what I am missing. Be sure you are following all the advice on the installation page of the GROMACS webpages. Mark Thank you for four answer, Nathalia Garces -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Installation gromacs in Scientific Linux
Hello, The last 6 months I've been working with gromacs (4.5.3 and 4.5.4) in Ubuntu (10.4) and it has worked fine. The problem started when I changed the linux distribution to Scientific Linux (5.3)... I followed the same steps to download/configure gromacs but something's wrong or missing because the simulations that I had been running on UBUNTU crashed in SL. The command I use is very simple: * mdrun -v -s topol.tpr* In Ubuntu the simulation ends fine but in SL the application starts to write on prompt at early steps (around 100) *Step XX, time 0.XX (ps) LINCS WARNING* *relative constraint deviation after LINCS:* *rms XX, max XX (between atoms XX and XX)* *bonds that rotated more than 30 degrees:* *...* *Wrote pdb files with previous and current coordinates* * * Until the simulation ends (around 250) with a message of * Segmentation fault * I tried different ways to configure gromacs but none of them seems to resolve the problem 1) ./configure --prefix=my path make make install 2) ./configure --with-fft=fftw3 --prefix=my path --without-x make make install 3)./configure --program-suffix= --disable-float --prefix=my path --exec-prefix=my path --enable-all-static --with-fft=fftw3 --without-x make make install Moreover, I downloaded the benchmark posted in the gromacs web page to test the simulations with other .tpr files. I run the first simulation (implicit solvent) in UBUNTU and worked OK but the one on SL crashed (around step 460) with the first two options of configuration. The last configuration enabled the simulation to run OK( I decided to stop it at 4000 steps)... This bewilders me because the last configuration permitted the benchmark to run OK but not my file. I don't think my file has an unstable system because it works all right in UBUNTU (and also Debian!) In addition, I upgraded my linux distribution to the latest SL 5.x release but it didn't make any change! I hope you can help me with some guide on how to proceed a GOOD instalation in SL or to let me know what is my problem and what I am missing. Thank you for four answer, Nathalia Garces -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation of gromacs-gpu on windows
Thanks a lot! Now we decided to use gromacs under linux and the installation of gromacs and gromacs-gpu has passed without errors Problem is solved :) 2011/7/8 Szilárd Páll szilard.p...@cbr.su.se: Well, unfortunately I don't know of any step-by-step tutorial, but from what I remember the workflow is pretty straightforward and looks something like this: - Download dependencies, there is precompiled OpenMM and FFTW for Windows. - Run CMake, you'll have to set up the library dependencies manually, at least that's what I did; use the Visual Studio generator which should give you project files/solutions/whatever they're called. - Open the project in VS and compile; after this step you should have a working mdru-gpu. You can go back to cygwin and run it from there (note that you might have to juggle around with libraries and LD_LIBRARY_PATh in cygwin). As I did this 1 year ago the above might not be accurate and slight details might be missing. Let me know if you succeed. Cheers, -- Szilárd On Fri, Jul 1, 2011 at 11:35 AM, Андрей Гончар gontc...@gmail.com wrote: Thank you for your reply! Now can I have your attention for another quetsion? I'm not very experienced in Visual Studio because I do almost all of my work under linux. But now it is necessary to compile gromacs-gpu under windows. Could someone point me to a tutorial or how-to about step-by-step compiling of gpu-accelerated gromacs under windows, because now i'm totally confused... Thanks in advance! 2011/6/30 Szilárd Páll szilard.p...@cbr.su.se: Dear Andrew, Compiling on Windows was tested only using MSVC and I have no idea if it works or not under cygwin. You should just try, both cmake and gcc is available for cygwin so you might be lucky and get mdrun-gpu compiled without any additional effort. All binaries on the Gromacs webpage _are outdated_ which is clearly stated on the respective page. Cheers, -- Szilárd On Fri, Jun 24, 2011 at 9:54 AM, Андрей Гончар gontc...@gmail.com wrote: Hello! I have a misunderstood about the installation of gpu-enabled gromacs under windows. I'll try to explain: in system requirements of gromacs-gpu it is wrote that Nvidia CUDA libraries have to be installed. But is it possible to do under cygwin? This quertion appears because we run gromacs under windows and so under cygwin. Is there a way to compile gromacs-gpu on cygwin? Will the binaries from gromacs-gpu page work and if so which of them to prefer to run under cygwin? Those for windows or for linux? -- Andrew Gontchar -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Андрей Гончар -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Андрей Гончар -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation of gromacs-gpu on windows
I think you made the right decision! :) -- Szilárd On Fri, Jul 8, 2011 at 12:50 PM, Андрей Гончар gontc...@gmail.com wrote: Thanks a lot! Now we decided to use gromacs under linux and the installation of gromacs and gromacs-gpu has passed without errors Problem is solved :) 2011/7/8 Szilárd Páll szilard.p...@cbr.su.se: Well, unfortunately I don't know of any step-by-step tutorial, but from what I remember the workflow is pretty straightforward and looks something like this: - Download dependencies, there is precompiled OpenMM and FFTW for Windows. - Run CMake, you'll have to set up the library dependencies manually, at least that's what I did; use the Visual Studio generator which should give you project files/solutions/whatever they're called. - Open the project in VS and compile; after this step you should have a working mdru-gpu. You can go back to cygwin and run it from there (note that you might have to juggle around with libraries and LD_LIBRARY_PATh in cygwin). As I did this 1 year ago the above might not be accurate and slight details might be missing. Let me know if you succeed. Cheers, -- Szilárd On Fri, Jul 1, 2011 at 11:35 AM, Андрей Гончар gontc...@gmail.com wrote: Thank you for your reply! Now can I have your attention for another quetsion? I'm not very experienced in Visual Studio because I do almost all of my work under linux. But now it is necessary to compile gromacs-gpu under windows. Could someone point me to a tutorial or how-to about step-by-step compiling of gpu-accelerated gromacs under windows, because now i'm totally confused... Thanks in advance! 2011/6/30 Szilárd Páll szilard.p...@cbr.su.se: Dear Andrew, Compiling on Windows was tested only using MSVC and I have no idea if it works or not under cygwin. You should just try, both cmake and gcc is available for cygwin so you might be lucky and get mdrun-gpu compiled without any additional effort. All binaries on the Gromacs webpage _are outdated_ which is clearly stated on the respective page. Cheers, -- Szilárd On Fri, Jun 24, 2011 at 9:54 AM, Андрей Гончар gontc...@gmail.com wrote: Hello! I have a misunderstood about the installation of gpu-enabled gromacs under windows. I'll try to explain: in system requirements of gromacs-gpu it is wrote that Nvidia CUDA libraries have to be installed. But is it possible to do under cygwin? This quertion appears because we run gromacs under windows and so under cygwin. Is there a way to compile gromacs-gpu on cygwin? Will the binaries from gromacs-gpu page work and if so which of them to prefer to run under cygwin? Those for windows or for linux? -- Andrew Gontchar -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Андрей Гончар -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Андрей Гончар -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] Installation of gromacs-gpu on windows
I think so! 2011/7/8 Szilárd Páll szilard.p...@cbr.su.se: I think you made the right decision! :) -- Szilárd On Fri, Jul 8, 2011 at 12:50 PM, Андрей Гончар gontc...@gmail.com wrote: Thanks a lot! Now we decided to use gromacs under linux and the installation of gromacs and gromacs-gpu has passed without errors Problem is solved :) 2011/7/8 Szilárd Páll szilard.p...@cbr.su.se: Well, unfortunately I don't know of any step-by-step tutorial, but from what I remember the workflow is pretty straightforward and looks something like this: - Download dependencies, there is precompiled OpenMM and FFTW for Windows. - Run CMake, you'll have to set up the library dependencies manually, at least that's what I did; use the Visual Studio generator which should give you project files/solutions/whatever they're called. - Open the project in VS and compile; after this step you should have a working mdru-gpu. You can go back to cygwin and run it from there (note that you might have to juggle around with libraries and LD_LIBRARY_PATh in cygwin). As I did this 1 year ago the above might not be accurate and slight details might be missing. Let me know if you succeed. Cheers, -- Szilárd On Fri, Jul 1, 2011 at 11:35 AM, Андрей Гончар gontc...@gmail.com wrote: Thank you for your reply! Now can I have your attention for another quetsion? I'm not very experienced in Visual Studio because I do almost all of my work under linux. But now it is necessary to compile gromacs-gpu under windows. Could someone point me to a tutorial or how-to about step-by-step compiling of gpu-accelerated gromacs under windows, because now i'm totally confused... Thanks in advance! 2011/6/30 Szilárd Páll szilard.p...@cbr.su.se: Dear Andrew, Compiling on Windows was tested only using MSVC and I have no idea if it works or not under cygwin. You should just try, both cmake and gcc is available for cygwin so you might be lucky and get mdrun-gpu compiled without any additional effort. All binaries on the Gromacs webpage _are outdated_ which is clearly stated on the respective page. Cheers, -- Szilárd On Fri, Jun 24, 2011 at 9:54 AM, Андрей Гончар gontc...@gmail.com wrote: Hello! I have a misunderstood about the installation of gpu-enabled gromacs under windows. I'll try to explain: in system requirements of gromacs-gpu it is wrote that Nvidia CUDA libraries have to be installed. But is it possible to do under cygwin? This quertion appears because we run gromacs under windows and so under cygwin. Is there a way to compile gromacs-gpu on cygwin? Will the binaries from gromacs-gpu page work and if so which of them to prefer to run under cygwin? Those for windows or for linux? -- Andrew Gontchar -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Андрей Гончар -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Андрей Гончар -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post
Re: [gmx-users] Installation of gromacs-gpu on windows
Well, unfortunately I don't know of any step-by-step tutorial, but from what I remember the workflow is pretty straightforward and looks something like this: - Download dependencies, there is precompiled OpenMM and FFTW for Windows. - Run CMake, you'll have to set up the library dependencies manually, at least that's what I did; use the Visual Studio generator which should give you project files/solutions/whatever they're called. - Open the project in VS and compile; after this step you should have a working mdru-gpu. You can go back to cygwin and run it from there (note that you might have to juggle around with libraries and LD_LIBRARY_PATh in cygwin). As I did this 1 year ago the above might not be accurate and slight details might be missing. Let me know if you succeed. Cheers, -- Szilárd On Fri, Jul 1, 2011 at 11:35 AM, Андрей Гончар gontc...@gmail.com wrote: Thank you for your reply! Now can I have your attention for another quetsion? I'm not very experienced in Visual Studio because I do almost all of my work under linux. But now it is necessary to compile gromacs-gpu under windows. Could someone point me to a tutorial or how-to about step-by-step compiling of gpu-accelerated gromacs under windows, because now i'm totally confused... Thanks in advance! 2011/6/30 Szilárd Páll szilard.p...@cbr.su.se: Dear Andrew, Compiling on Windows was tested only using MSVC and I have no idea if it works or not under cygwin. You should just try, both cmake and gcc is available for cygwin so you might be lucky and get mdrun-gpu compiled without any additional effort. All binaries on the Gromacs webpage _are outdated_ which is clearly stated on the respective page. Cheers, -- Szilárd On Fri, Jun 24, 2011 at 9:54 AM, Андрей Гончар gontc...@gmail.com wrote: Hello! I have a misunderstood about the installation of gpu-enabled gromacs under windows. I'll try to explain: in system requirements of gromacs-gpu it is wrote that Nvidia CUDA libraries have to be installed. But is it possible to do under cygwin? This quertion appears because we run gromacs under windows and so under cygwin. Is there a way to compile gromacs-gpu on cygwin? Will the binaries from gromacs-gpu page work and if so which of them to prefer to run under cygwin? Those for windows or for linux? -- Andrew Gontchar -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Андрей Гончар -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation of gromacs-gpu on windows
Thank you for your reply! Now can I have your attention for another quetsion? I'm not very experienced in Visual Studio because I do almost all of my work under linux. But now it is necessary to compile gromacs-gpu under windows. Could someone point me to a tutorial or how-to about step-by-step compiling of gpu-accelerated gromacs under windows, because now i'm totally confused... Thanks in advance! 2011/6/30 Szilárd Páll szilard.p...@cbr.su.se: Dear Andrew, Compiling on Windows was tested only using MSVC and I have no idea if it works or not under cygwin. You should just try, both cmake and gcc is available for cygwin so you might be lucky and get mdrun-gpu compiled without any additional effort. All binaries on the Gromacs webpage _are outdated_ which is clearly stated on the respective page. Cheers, -- Szilárd On Fri, Jun 24, 2011 at 9:54 AM, Андрей Гончар gontc...@gmail.com wrote: Hello! I have a misunderstood about the installation of gpu-enabled gromacs under windows. I'll try to explain: in system requirements of gromacs-gpu it is wrote that Nvidia CUDA libraries have to be installed. But is it possible to do under cygwin? This quertion appears because we run gromacs under windows and so under cygwin. Is there a way to compile gromacs-gpu on cygwin? Will the binaries from gromacs-gpu page work and if so which of them to prefer to run under cygwin? Those for windows or for linux? -- Andrew Gontchar -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Андрей Гончар -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation of gromacs-gpu on windows
Dear Andrew, Compiling on Windows was tested only using MSVC and I have no idea if it works or not under cygwin. You should just try, both cmake and gcc is available for cygwin so you might be lucky and get mdrun-gpu compiled without any additional effort. All binaries on the Gromacs webpage _are outdated_ which is clearly stated on the respective page. Cheers, -- Szilárd On Fri, Jun 24, 2011 at 9:54 AM, Андрей Гончар gontc...@gmail.com wrote: Hello! I have a misunderstood about the installation of gpu-enabled gromacs under windows. I'll try to explain: in system requirements of gromacs-gpu it is wrote that Nvidia CUDA libraries have to be installed. But is it possible to do under cygwin? This quertion appears because we run gromacs under windows and so under cygwin. Is there a way to compile gromacs-gpu on cygwin? Will the binaries from gromacs-gpu page work and if so which of them to prefer to run under cygwin? Those for windows or for linux? -- Andrew Gontchar -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Installation of gromacs-gpu on windows
Hello! I have a misunderstood about the installation of gpu-enabled gromacs under windows. I'll try to explain: in system requirements of gromacs-gpu it is wrote that Nvidia CUDA libraries have to be installed. But is it possible to do under cygwin? This quertion appears because we run gromacs under windows and so under cygwin. Is there a way to compile gromacs-gpu on cygwin? Will the binaries from gromacs-gpu page work and if so which of them to prefer to run under cygwin? Those for windows or for linux? -- Andrew Gontchar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Installation error
I have already posted this error report on 6 Dec 2010 but still have not getting any solution. So I am thankful if any one can rectify the solution of installation problem i.e. While installing gromacs-4.5.3 I got an error on executing make command. I am installing this gromacs version on cygwin. The error written below, please tell me solution of this error. Creating library file: .libs/libgmx.dll.a .libs/checkpoint.o:checkpoint.c:(.text+0xcd): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x13c): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x236): undefined reference to `_xdr_double' .libs/checkpoint.o:checkpoint.c:(.text+0x256): undefined reference to `_xdr_vector' .libs/checkpoint.o:checkpoint.c:(.text+0x3f0): undefined reference to `_xdr_float' .libs/checkpoint.o:checkpoint.c:(.text+0x408): undefined reference to `_xdr_vector' .libs/checkpoint.o:checkpoint.c:(.text+0x64e): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0xfad): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0xff0): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x10a3): undefined reference to `_xdr_double' .libs/checkpoint.o:checkpoint.c:(.text+0x10bb): undefined reference to `_xdr_vector' .libs/checkpoint.o:checkpoint.c:(.text+0x127d): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x12c0): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x1372): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x138a): undefined reference to `_xdr_vector' .libs/checkpoint.o:checkpoint.c:(.text+0x1fb9): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x24cf): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x256a): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x2606): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x2642): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x26d4): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x2755): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x2791): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x27de): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x283a): undefined reference to `_xdr_u_char' .libs/checkpoint.o:checkpoint.c:(.text+0x287a): undefined reference to `_xdr_u_char' .libs/checkpoint.o:checkpoint.c:(.text+0x28ba): undefined reference to `_xdr_u_char' .libs/checkpoint.o:checkpoint.c:(.text+0x28fa): undefined reference to `_xdr_u_char' .libs/checkpoint.o:checkpoint.c:(.text+0x293a): undefined reference to `_xdr_u_char' .libs/checkpoint.o:checkpoint.c:(.text+0x297a): more undefined references to `_xdr_u_char' follow .libs/checkpoint.o:checkpoint.c:(.text+0x2f00): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x2f8e): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x2ffc): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x3070): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x30e4): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x3158): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x31cc): more undefined references to `_xdr_string' follow .libs/checkpoint.o:checkpoint.c:(.text+0x3236): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x328f): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x32d3): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x334a): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x3412): undefined reference to `_xdr_double' .libs/checkpoint.o:checkpoint.c:(.text+0x3457): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x34b1): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x3501): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x3551): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x358e): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x35d2): more undefined references to `_xdr_int' follow .libs/checkpoint.o:checkpoint.c:(.text+0x392f): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x3a31): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x3a75): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x4cb4): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x5216): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x6c90): undefined reference to `_xdr_int'
Re: [gmx-users] Installation error
On 15/04/2011 12:29 AM, pawan raghav wrote: I have already posted this error report on 6 Dec 2010 but still have not getting any solution. So I am thankful if any one can rectify the solution of installation problem i.e. While installing gromacs-4.5.3 I got an error on executing make command. I am installing this gromacs version on cygwin. The error written below, please tell me solution of this error. Apparently you have some kind of XDR library linking issue. Perhaps that is caused by some other library floating around. GROMACS has its own version if the system one is broken, but perhaps some Windows DLL is confusing things. My Cygwin install builds with cmake perfectly. I haven't tried configure in a long while. Mark Creating library file: .libs/libgmx.dll.a .libs/checkpoint.o:checkpoint.c:(.text+0xcd): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x13c): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x236): undefined reference to `_xdr_double' .libs/checkpoint.o:checkpoint.c:(.text+0x256): undefined reference to `_xdr_vector' .libs/checkpoint.o:checkpoint.c:(.text+0x3f0): undefined reference to `_xdr_float' .libs/checkpoint.o:checkpoint.c:(.text+0x408): undefined reference to `_xdr_vector' .libs/checkpoint.o:checkpoint.c:(.text+0x64e): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0xfad): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0xff0): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x10a3): undefined reference to `_xdr_double' .libs/checkpoint.o:checkpoint.c:(.text+0x10bb): undefined reference to `_xdr_vector' .libs/checkpoint.o:checkpoint.c:(.text+0x127d): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x12c0): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x1372): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x138a): undefined reference to `_xdr_vector' .libs/checkpoint.o:checkpoint.c:(.text+0x1fb9): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x24cf): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x256a): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x2606): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x2642): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x26d4): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x2755): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x2791): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x27de): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x283a): undefined reference to `_xdr_u_char' .libs/checkpoint.o:checkpoint.c:(.text+0x287a): undefined reference to `_xdr_u_char' .libs/checkpoint.o:checkpoint.c:(.text+0x28ba): undefined reference to `_xdr_u_char' .libs/checkpoint.o:checkpoint.c:(.text+0x28fa): undefined reference to `_xdr_u_char' .libs/checkpoint.o:checkpoint.c:(.text+0x293a): undefined reference to `_xdr_u_char' .libs/checkpoint.o:checkpoint.c:(.text+0x297a): more undefined references to `_xdr_u_char' follow .libs/checkpoint.o:checkpoint.c:(.text+0x2f00): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x2f8e): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x2ffc): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x3070): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x30e4): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x3158): undefined reference to `_xdr_string' .libs/checkpoint.o:checkpoint.c:(.text+0x31cc): more undefined references to `_xdr_string' follow .libs/checkpoint.o:checkpoint.c:(.text+0x3236): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x328f): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x32d3): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x334a): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x3412): undefined reference to `_xdr_double' .libs/checkpoint.o:checkpoint.c:(.text+0x3457): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x34b1): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x3501): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x3551): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x358e): undefined reference to `_xdr_int' .libs/checkpoint.o:checkpoint.c:(.text+0x35d2): more undefined references to `_xdr_int' follow
Re: [gmx-users] Installation error
You are really PATIENT waiting for FOUR months for the answers. Ask the person around you they might be able to provide useful suggestions. There might be some libs linking problem. I have never tried the Cygwin, you may really try searching first before waiting. lina P.S if I were you, I would try on linux. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] installation of gromacs
Hi Nuno, I have still problems with the insatllation of the 4.0.7 version. After unpacking of fftw and gromacs, I did: In the fftw folder: ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float make -j make install export CPPFLAGS=-I$HOME/local/fftw3/include export LDFLAGS=-L$HOME/local/fftw3/lib In the gromacs-4.0.7 folder: ./configure --prefix=$HOME/local/gromacs --enable-shared At the end I get: checking for void*... yes checking size of void*... configure: error: cannot compute sizeof (void*) What does that mean? Why is this not working? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs
Hi Thomas, please send the complete config.log. After you try what I suggest bellow. I guess the environment variables for compilers and libs are not set correctly, not your fault, we'll check on the config file. #make sure your're usnig bash bash #export the regular variables export CPPFLAGS=-I$HOME/local/fftw3/include export LDFLAGS=-L$HOME/local/fftw3/lib #also try this one export LD_LIBRARY_PATH=$HOME/local/fftw3/lib #and by now, remove the --enable-shared ./configure --prefix=$HOME/local/gromacs On Thu, Mar 17, 2011 at 10:44 AM, Thomas Koller koller-tho...@gmx.de wrote: Hi Nuno, I have still problems with the insatllation of the 4.0.7 version. After unpacking of fftw and gromacs, I did: In the fftw folder: ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float make -j make install export CPPFLAGS=-I$HOME/local/fftw3/include export LDFLAGS=-L$HOME/local/fftw3/lib In the gromacs-4.0.7 folder: ./configure --prefix=$HOME/local/gromacs --enable-shared At the end I get: checking for void*... yes checking size of void*... configure: error: cannot compute sizeof (void*) What does that mean? Why is this not working? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs
On Thu, 2011-03-17 at 10:44 +0100, Thomas Koller wrote: Hi Nuno, I have still problems with the insatllation of the 4.0.7 version. After unpacking of fftw and gromacs, I did: In the fftw folder: ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float make -j make install export CPPFLAGS=-I$HOME/local/fftw3/include export LDFLAGS=-L$HOME/local/fftw3/lib In the gromacs-4.0.7 folder: ./configure --prefix=$HOME/local/gromacs --enable-shared At the end I get: checking for void*... yes checking size of void*... configure: error: cannot compute sizeof (void*) What does that mean? Why is this not working? This means that the compiler does not work properly. I also encountered this error some time ago, but I can not remember, what the reason exactly was. However I would always go for the latest release and preferably fetch the release branch (check the website for a How To) Cheers, Flo Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs
Hi Thomas, the error you see indeed suggests that something is messed up with your compiler. In your case however I think that is due to the CPPFLAGS and LDFLAGS you set. Those sometimes mess with the configure makros. Try export CPPFLAGS= export LDFLAGS= export LD_LIBRARY_PATH= to erase what you set previously (or open a fresh shell actually) And then try using the -with-fftw configure parameter instead. Best Tim On 3/17/11 10:44 AM, Thomas Koller wrote: Hi Nuno, I have still problems with the insatllation of the 4.0.7 version. After unpacking of fftw and gromacs, I did: In the fftw folder: ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float make -j make install export CPPFLAGS=-I$HOME/local/fftw3/include export LDFLAGS=-L$HOME/local/fftw3/lib In the gromacs-4.0.7 folder: ./configure --prefix=$HOME/local/gromacs --enable-shared At the end I get: checking for void*... yes checking size of void*... configure: error: cannot compute sizeof (void*) What does that mean? Why is this not working? Regards, Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] installation of gromacs
Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float - make -j - make install - export CPPFLAGS=-I/home/local/fftw/include - export LDFLAGS=-L/home/local/fftw/lib iii) Then I go (cd) to the folder gromacs-4.0.7 - ./configure --prefix=$HOME/local/gromacs - Now I get the error writen above. Is my way wrong, do I have to insert the fftw folder into the gromacs folder, is the sequence wrong? I wish I can have access soon. :( Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs
On 17/03/11, Thomas Koller koller-tho...@gmx.de wrote: Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float You've installed in /home/local/fftw3... - make -j - make install - export CPPFLAGS=-I/home/local/fftw/include - export LDFLAGS=-L/home/local/fftw/lib ... but told configure later to look in /home/local/fftw That doesn't work. Even when it does, it's likely that you'll still need to look at the last few hundred lines of config.log to actually diagnose the problem... Mark iii) Then I go (cd) to the folder gromacs-4.0.7 - ./configure --prefix=$HOME/local/gromacs - Now I get the error writen above. Is my way wrong, do I have to insert the fftw folder into the gromacs folder, is the sequence wrong? I wish I can have access soon. :( Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs
You got this wrong export CPPFLAGS=-I/home/local/fftw/include export LDFLAGS=-L/home/local/fftw/lib replace by this export CPPFLAGS=-I$HOME/local/fftw/include export LDFLAGS=-L$HOME/local/fftw/lib On Thu, Mar 17, 2011 at 12:24 PM, Thomas Koller koller-tho...@gmx.de wrote: Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float - make -j - make install - export CPPFLAGS=-I/home/local/fftw/include - export LDFLAGS=-L/home/local/fftw/lib iii) Then I go (cd) to the folder gromacs-4.0.7 - ./configure --prefix=$HOME/local/gromacs - Now I get the error writen above. Is my way wrong, do I have to insert the fftw folder into the gromacs folder, is the sequence wrong? I wish I can have access soon. :( Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs
Thomas Koller wrote: Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float - make -j - make install - export CPPFLAGS=-I/home/local/fftw/include - export LDFLAGS=-L/home/local/fftw/lib iii) Then I go (cd) to the folder gromacs-4.0.7 - ./configure --prefix=$HOME/local/gromacs - Now I get the error writen above. Is my way wrong, do I have to insert the fftw folder into the gromacs folder, is the sequence wrong? Your CPPFLAGS and LDFLAGS are wrong. If you installed FFTW in $HOME/local/fftw3, then the appropriate settings are CPPFLAGS=-I$HOME/local/fftw3/include LDFLAGS=-L$HOME/local/fftw3/lib Note that your original error is related to the C compiler, not FFTW. You've been prompted several times to post relevant lines in config.log, but you haven't, so please do, otherwise you (and everyone on the list) will keep hacking away with no result. What C compiler is installed on your system? Where is it installed? Is it in your PATH? -Justin I wish I can have access soon. :( Thomas -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs
On 17/03/11, Diego Enry diego.e...@gmail.com wrote: You got this wrong export CPPFLAGS=-I/home/local/fftw/include export LDFLAGS=-L/home/local/fftw/lib replace by this export CPPFLAGS=-I$HOME/local/fftw/include export LDFLAGS=-L$HOME/local/fftw/lib This is immaterial if Thomas installed to $HOME/local/fftw3 Mark On Thu, Mar 17, 2011 at 12:24 PM, Thomas Koller koller-tho...@gmx.de wrote: Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float - make -j - make install - export CPPFLAGS=-I/home/local/fftw/include - export LDFLAGS=-L/home/local/fftw/lib iii) Then I go (cd) to the folder gromacs-4.0.7 - ./configure --prefix=$HOME/local/gromacs - Now I get the error writen above. Is my way wrong, do I have to insert the fftw folder into the gromacs folder, is the sequence wrong? I wish I can have access soon. :( Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] installation of gromacs
Hello, I did the procedure as described, but at the end of the configuration of gromacs, I obtain this message: checking size of void*... configure: error: cannot compute sizeof (void*) See `config.log' for more details. What is the problem? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs
On 16/03/11, Thomas Koller koller-tho...@gmx.de wrote: Hello, I did the procedure as described, but at the end of the configuration of gromacs, I obtain this message: checking size of void*... configure: error: cannot compute sizeof (void*) See `config.log' for more details. What is the problem? Many possibilities exist. Unfortunately, we don't know anything about your intentions, configure command, system environment or the contents of config.log a few hundred lines from the end where it noticed the error. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] installation of gromacs
Hello, I want to install Gromacs 4.5.3 in my computer. Therefore I downloaded fftw 3.2.2 and did as in the instructions: ./configure --enable-float make make install After that I ran: ./configure with Gromacs, but I always get: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Other alternatives are 'fftw2', or 'mkl' for Intel MKL. You are STRONGLY recommended to use one of these - fftw is free. make is not working after this: make: *** No targets specified and no makefile found. Stop. What is going wrong? Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs
The most basic question is: did you install FFTW as root or superuser ? sudo make install If so, try to provide fftw /lib and /include locations (using CPPFLAGS and LDFLAGS) while configuring GMX. (from the Installation Instructions) setenv CPPFLAGS -I/home/joe/fftw/include setenv LDFLAGS -L/home/joe/fftw/lib If your shell is bash: export CPPFLAGS=-I/home/joe/fftw/include export LDFLAGS=-L/home/joe/fftw/lib *If that does not work. Follow cmake instructions. http://www.gromacs.org/Developer_Zone/Cmake ** I have this problem with ubuntu 10.04, even though FFTW is ok I can only Cmake finds fftw. (even providing CPPFLAGS and LDFLAGS) On Mon, Mar 14, 2011 at 1:05 PM, Thomas Koller koller-tho...@gmx.de wrote: Hello, I want to install Gromacs 4.5.3 in my computer. Therefore I downloaded fftw 3.2.2 and did as in the instructions: ./configure --enable-float make make install After that I ran: ./configure with Gromacs, but I always get: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Other alternatives are 'fftw2', or 'mkl' for Intel MKL. You are STRONGLY recommended to use one of these - fftw is free. make is not working after this: make: *** No targets specified and no makefile found. Stop. What is going wrong? Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs
Hello, it seems FFTW3 is not installed in the LD_LIBRARY_PATH and/or the fftw3 headers can not be found. On Ubuntu, most likely the headers are not installed (available in the package libfftw3-dev). However it is really easy to compile FFTW3 yourself and install it inside your $HOME. Then you do not get in conflict with your system libraries and no administrator privileges are necessary. Furthermore you can compile FFTW3 with the desired flags for example: ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float make -j make install which will install shared fftw3 libs and headers in $HOME/local/fftw3. The flag -sse enables assembler optimization and --enable-float finally gives a single precision library libfftw3f.so . It is strongly suggested to enable assembler to optimize the performance of the FFTW3. Now for the configuration and installation of GROMACS in single precision you can use CMake and or the autotools. For the usage of autotools, the same scheme as describe above applies, however as FFTW3 is not in a standard location, the configure script must be told where to find the required files: CPPFLAGS=-I$HOME/local/fftw3/include LDFLAGS=-L $HOME/local/fftw3/lib ./configure --prefix=$HOME/local/gromacs --enable-shared make -j make install This should install a single-precision version of gromacs with shared libraries in $HOME/local/gromacs. For further specifications ./configure --helps gives many options to choose for example --enable-mpi For CMake the input scheme varies a little bit, but the procedure is the same mkdir build cd build cmake -DFFTW3F_INCLUDE_DIR=$HOME/local/fftw3/include -DFFTW3F_LIBRARIES= $HOME/local/fftw3/lib -DCMAKE_INSTALL_PREFIX=$HOME/local/gromacs make -j make install For CMake a shared build is enabled by default. /Flo On Mon, 2011-03-14 at 13:15 +0100, Diego Enry wrote: The most basic question is: did you install FFTW as root or superuser ? sudo make install If so, try to provide fftw /lib and /include locations (using CPPFLAGS and LDFLAGS) while configuring GMX. (from the Installation Instructions) setenv CPPFLAGS -I/home/joe/fftw/include setenv LDFLAGS -L/home/joe/fftw/lib If your shell is bash: export CPPFLAGS=-I/home/joe/fftw/include export LDFLAGS=-L/home/joe/fftw/lib *If that does not work. Follow cmake instructions. http://www.gromacs.org/Developer_Zone/Cmake ** I have this problem with ubuntu 10.04, even though FFTW is ok I can only Cmake finds fftw. (even providing CPPFLAGS and LDFLAGS) On Mon, Mar 14, 2011 at 1:05 PM, Thomas Koller koller-tho...@gmx.de wrote: Hello, I want to install Gromacs 4.5.3 in my computer. Therefore I downloaded fftw 3.2.2 and did as in the instructions: ./configure --enable-float make make install After that I ran: ./configure with Gromacs, but I always get: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Other alternatives are 'fftw2', or 'mkl' for Intel MKL. You are STRONGLY recommended to use one of these - fftw is free. make is not working after this: make: *** No targets specified and no makefile found. Stop. What is going wrong? Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
On 24/12/2010 6:45 PM, Sergio Manzetti wrote: Hi thanks, but if I use make it says make no Makefile found... Right, so configure didn't work, unlike your statement that it did work... Troubleshoot the step that failed, not things that came after it... Mark On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 23/12/2010 9:12 PM, Sergio Manzetti wrote: Dear Users, I am unable to get pass the first step of ./configure . This step works, but when typing make it says: no targets specified and no makefile found. That suggests configure did not work. Should it be like this, or is it compulsory to use cmake? cmake is not compulsory. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
Not really, there were no errors with ./configure so I downloaded the version through ubunto sudo -apt get install gromacs but it was old version On Fri, Dec 24, 2010 at 10:53 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 24/12/2010 6:45 PM, Sergio Manzetti wrote: Hi thanks, but if I use make it says make no Makefile found... Right, so configure didn't work, unlike your statement that it did work... Troubleshoot the step that failed, not things that came after it... Mark On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 23/12/2010 9:12 PM, Sergio Manzetti wrote: Dear Users, I am unable to get pass the first step of ./configure . This step works, but when typing make it says: no targets specified and no makefile found. That suggests configure did not work. Should it be like this, or is it compulsory to use cmake? cmake is not compulsory. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Not really, there were no errors with ./configure That's simply not possible. The purpose of configuration is to determine specifications of your system, which are then used to write the Makefile. If you have no Makefile, then something failed. If you want to try to figure it out, then please post your complete ./configure command and the resulting screen output. Otherwise, your stuck with all of us telling you that something went wrong, but we don't know what. -Justin so I downloaded the version through ubunto sudo -apt get install gromacs but it was old version On Fri, Dec 24, 2010 at 10:53 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 24/12/2010 6:45 PM, Sergio Manzetti wrote: Hi thanks, but if I use make it says make no Makefile found... Right, so configure didn't work, unlike your statement that it did work... Troubleshoot the step that failed, not things that came after it... Mark On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 23/12/2010 9:12 PM, Sergio Manzetti wrote: Dear Users, I am unable to get pass the first step of ./configure . This step works, but when typing make it says: no targets specified and no makefile found. That suggests configure did not work. Should it be like this, or is it compulsory to use cmake? cmake is not compulsory. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
Thanks Justin, here is it the copy-out: ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... no checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... no checking for c++... no checking for gpp... no checking for aCC... no checking for CC... no checking for cxx... no checking for cc++... no checking for cl.exe... no checking for FCC... no checking for KCC... no checking for RCC... no checking for xlC_r... no checking for xlC... no checking whether we are using the GNU C++ compiler... no checking whether g++ accepts -g... no checking dependency style of g++... none checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... failed checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes configure: creating
Re: [gmx-users] Installation GROMACS UBUNTU
Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks Justin, here is it the copy-out: ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... no checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... no checking for c++... no checking for gpp... no checking for aCC... no checking for CC... no checking for cxx... no checking for cc++... no checking for cl.exe... no checking for FCC... no checking for KCC... no checking for RCC... no checking for xlC_r... no checking for xlC... no checking whether we are using the GNU C++ compiler... no checking whether g++ accepts -g... no checking dependency style of g++... none checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... failed checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no
Re: [gmx-users] Installation GROMACS UBUNTU
Thanks J, I think I will install Ubuntu entirely first, because I just tried to install FFTW now, and managed only to get to make install, then I got permission denied messages, so even though I thought I was the admin, I am seemingly not. On Fri, Dec 24, 2010 at 2:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks Justin, here is it the copy-out: ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... no checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... no checking for c++... no checking for gpp... no checking for aCC... no checking for CC... no checking for cxx... no checking for cc++... no checking for cl.exe... no checking for FCC... no checking for KCC... no checking for RCC... no checking for xlC_r... no checking for xlC... no checking whether we are using the GNU C++ compiler... no checking whether g++ accepts -g... no checking dependency style of g++... none checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... failed checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking
Re: [gmx-users] Installation GROMACS UBUNTU
Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks J, I think I will install Ubuntu entirely first, because I just tried to install FFTW now, and managed only to get to make install, then I got permission denied messages, so even though I thought I was the admin, I am seemingly not. Before blowing away your system, use sudo make install, which will prompt you for your password and should work if you actually are an admin. -Justin On Fri, Dec 24, 2010 at 2:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks Justin, here is it the copy-out: ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... no checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... no checking for c++... no checking for gpp... no checking for aCC... no checking for CC... no checking for cxx... no checking for cc++... no checking for cl.exe... no checking for FCC... no checking for KCC... no checking for RCC... no checking for xlC_r... no checking for xlC... no checking whether we are using the GNU C++ compiler... no checking whether g++ accepts -g... no checking dependency style of g++... none checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... failed checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports
Re: [gmx-users] Installation GROMACS UBUNTU
Thanks again J, is that compulsory each time one installs something new? On Fri, Dec 24, 2010 at 2:50 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks J, I think I will install Ubuntu entirely first, because I just tried to install FFTW now, and managed only to get to make install, then I got permission denied messages, so even though I thought I was the admin, I am seemingly not. Before blowing away your system, use sudo make install, which will prompt you for your password and should work if you actually are an admin. -Justin On Fri, Dec 24, 2010 at 2:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Thanks Justin, here is it the copy-out: ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... no checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... no checking for c++... no checking for gpp... no checking for aCC... no checking for CC... no checking for cxx... no checking for cc++... no checking for cl.exe... no checking for FCC... no checking for KCC... no checking for RCC... no checking for xlC_r... no checking for xlC... no checking whether we are using the GNU C++ compiler... no checking whether g++ accepts -g... no checking dependency style of g++... none checking the maximum length of
Re: [gmx-users] Installation GROMACS UBUNTU
Well here is the FFTW message at make install: /usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h' /usr/bin/install: cannot remove `/usr/local/include/fftw3.h': Permission denied /usr/bin/install -c -m 644 'fftw3.f' '/usr/local/include/fftw3.f' /usr/bin/install: cannot remove `/usr/local/include/fftw3.f': Permission denied make[3]: *** [install-includeHEADERS] Error 1 make[3]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[1]: *** [install] Error 2 make[1]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
Justin, THe FFTW messagte was AFTER sudo make install. On Fri, Dec 24, 2010 at 2:53 PM, Sergio Manzetti sergio.manze...@vestforsk.no wrote: Well here is the FFTW message at make install: /usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h' /usr/bin/install: cannot remove `/usr/local/include/fftw3.h': Permission denied /usr/bin/install -c -m 644 'fftw3.f' '/usr/local/include/fftw3.f' /usr/bin/install: cannot remove `/usr/local/include/fftw3.f': Permission denied make[3]: *** [install-includeHEADERS] Error 1 make[3]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[1]: *** [install] Error 2 make[1]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Justin, THe FFTW messagte was AFTER sudo make install. Then you're not an admin. You can always do the installations in your home directory (for both FFTW and Gromacs) by specifying an appropriate --prefix during configuration. -Justin On Fri, Dec 24, 2010 at 2:53 PM, Sergio Manzetti sergio.manze...@vestforsk.no wrote: Well here is the FFTW message at make install: /usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h' /usr/bin/install: cannot remove `/usr/local/include/fftw3.h': Permission denied /usr/bin/install -c -m 644 'fftw3.f' '/usr/local/include/fftw3.f' /usr/bin/install: cannot remove `/usr/local/include/fftw3.f': Permission denied make[3]: *** [install-includeHEADERS] Error 1 make[3]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[1]: *** [install] Error 2 make[1]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
Thanks, but I will start from scratch. On Fri, Dec 24, 2010 at 3:13 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Sergio Manzetti sergio.manze...@vestforsk.no: Justin, THe FFTW messagte was AFTER sudo make install. Then you're not an admin. You can always do the installations in your home directory (for both FFTW and Gromacs) by specifying an appropriate --prefix during configuration. -Justin On Fri, Dec 24, 2010 at 2:53 PM, Sergio Manzetti sergio.manze...@vestforsk.no wrote: Well here is the FFTW message at make install: /usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h' /usr/bin/install: cannot remove `/usr/local/include/fftw3.h': Permission denied /usr/bin/install -c -m 644 'fftw3.f' '/usr/local/include/fftw3.f' /usr/bin/install: cannot remove `/usr/local/include/fftw3.f': Permission denied make[3]: *** [install-includeHEADERS] Error 1 make[3]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' make[1]: *** [install] Error 2 make[1]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api' Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Installation GROMACS UBUNTU
Dear Users, I am unable to get pass the first step of ./configure . This step works, but when typing make it says: no targets specified and no makefile found. Should it be like this, or is it compulsory to use cmake? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
I would like to suggest to you read [1] Furthermore, you can read INSTALL.cmake file which explains some steps to compile Gromacs through cmake command. [1] http://www.gromacs.org/Developer_Zone/Cmake -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 On Thu, Dec 23, 2010 at 8:12 AM, Sergio Manzetti sergio.manze...@vestforsk.no wrote: Dear Users, I am unable to get pass the first step of ./configure . This step works, but when typing make it says: no targets specified and no makefile found. Should it be like this, or is it compulsory to use cmake? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
On 23/12/2010 9:12 PM, Sergio Manzetti wrote: Dear Users, I am unable to get pass the first step of ./configure . This step works, but when typing make it says: no targets specified and no makefile found. That suggests configure did not work. Should it be like this, or is it compulsory to use cmake? cmake is not compulsory. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
Hi thanks, but if I use make it says make no Makefile found... On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 23/12/2010 9:12 PM, Sergio Manzetti wrote: Dear Users, I am unable to get pass the first step of ./configure . This step works, but when typing make it says: no targets specified and no makefile found. That suggests configure did not work. Should it be like this, or is it compulsory to use cmake? cmake is not compulsory. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation GROMACS UBUNTU
On Fri, Dec 24, 2010 at 3:45 PM, Sergio Manzetti sergio.manze...@vestforsk.no wrote: Hi thanks, but if I use make it says make no Makefile found... Yes, Makefile should be generated by configure. You should check the last few lines that configure output to your screen and the configure log file to see what's wrong. I suggest you go to a experienced Linux user for help if you don't want to figure out how configure and make work. Terry On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 23/12/2010 9:12 PM, Sergio Manzetti wrote: Dear Users, I am unable to get pass the first step of ./configure . This step works, but when typing make it says: no targets specified and no makefile found. That suggests configure did not work. Should it be like this, or is it compulsory to use cmake? cmake is not compulsory. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] installation
Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Since I understood I could set my environment later, I directly complete my make links. Then I added in my .bashrc the line: source /usr/local/gromacs/bin/GMXRC.bash and it was added to mi $PATH and also my $MANPATH seems to be right (/usr/local/gromacs/share/man:) When I type GMXRC in the shell it comes: [rosse...@topolone ~]$ GMXRC /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Is there anyone that could help me? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation
Quoting Rossella Noschese noschese.rosse...@gmail.com: Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Since I understood I could set my environment later, I directly complete my make links. Then I added in my .bashrc the line: source /usr/local/gromacs/bin/GMXRC.bash and it was added to mi $PATH and also my $MANPATH seems to be right (/usr/local/gromacs/share/man:) When I type GMXRC in the shell it comes: [rosse...@topolone ~]$ GMXRC /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Is there anyone that could help me? You don't run GMXRC directly, you have to source GMXRC, but since you've already done that in your .bashrc, there's no need to do it again. -Justin Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation
ok, but when I type luck it says command not found, where's my mistake? 2010/11/24 Justin A. Lemkul jalem...@vt.edu Quoting Rossella Noschese noschese.rosse...@gmail.com: Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Since I understood I could set my environment later, I directly complete my make links. Then I added in my .bashrc the line: source /usr/local/gromacs/bin/GMXRC.bash and it was added to mi $PATH and also my $MANPATH seems to be right (/usr/local/gromacs/share/man:) When I type GMXRC in the shell it comes: [rosse...@topolone ~]$ GMXRC /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Is there anyone that could help me? You don't run GMXRC directly, you have to source GMXRC, but since you've already done that in your .bashrc, there's no need to do it again. -Justin Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation
it was g_luck!!!it changed...ok, now it seems it wors! Thanks 2010/11/24 Rossella Noschese noschese.rosse...@gmail.com ok, but when I type luck it says command not found, where's my mistake? 2010/11/24 Justin A. Lemkul jalem...@vt.edu Quoting Rossella Noschese noschese.rosse...@gmail.com: Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Since I understood I could set my environment later, I directly complete my make links. Then I added in my .bashrc the line: source /usr/local/gromacs/bin/GMXRC.bash and it was added to mi $PATH and also my $MANPATH seems to be right (/usr/local/gromacs/share/man:) When I type GMXRC in the shell it comes: [rosse...@topolone ~]$ GMXRC /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Is there anyone that could help me? You don't run GMXRC directly, you have to source GMXRC, but since you've already done that in your .bashrc, there's no need to do it again. -Justin Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation
On Nov 24, 2010, at 4:04 PM, Rossella Noschese wrote: Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Since I understood I could set my environment later, I directly complete my make links. Then I added in my .bashrc the line: source /usr/local/gromacs/bin/GMXRC.bash and it was added to mi $PATH and also my $MANPATH seems to be right (/usr/local/gromacs/share/man:) When I type GMXRC in the shell it comes: GMXRC is for setting the paths to your Gromacs executables. You can do that by typing source GMXRC, but this you have already done in your bashrc, so everything is already set up and fine! You will find all the Gromacs programs at your fingertips, e.g. mdrun -h prints out help for the main MD program. Carsten [rosse...@topolone ~]$ GMXRC /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Is there anyone that could help me? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs on windows using cygwin
On 5/11/2010 10:48 PM, bharat gupta wrote: I followed the same instructions given in the gromacs manual , step by step ... I first tried installing gromacs with the first command given in the manual and then again I installed with the options for FLAGS but finally ended up with the following error in both the above mentioned conditions :- checking dynamic linker characteristics... Win32 ld.exe I think here's a problem. Your cygwin installation doesn't have a proper linker installed. win32 ld.exe is not up to the job, IIRC. You need (at least) the gcc and binutils packages. When asking for free help, you should copy and paste into these emails the command that is failing. If you'd really followed the instructions, we expect they'd have worked. So in the absence of evidence that you've done it right, we'll have to assume you've made a typo. We don't want to guess what you've done wrong :-) Mark checking how to hardcode library paths into programs... immediate appending configuration tag F77 to libtool checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking for sqrt in -lm... yes checking for fftw3.h... configure: error: Cannot find the default external FFT l ibrary (fftw3). Other alternatives are 'fftw2', or 'mkl' for Intel MKL. You are STRONGLY recommended to use one of these - fftw is free. Use CPPFLAGS and LDFLAGS if the library is installed in a non-standard location. (see FAQ at http://www.gromacs.org) If you dont care about performance you can also specify 'fftpack' to use a slower set of FFTs built into Gromacs. (Just install FFTW3 unless you really know what you are doing). I have installed fftw2.1.5 ... Pls help me rectify the error -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] installation of gromacs on windows using cygwin
Hi there .. I have been trying to install gromacs on windows using cygwin .. and after the installation of the fftw3 package , the moment i install the gromacs using the first command ./configure .. It gives an error that fftw3 package cannot be located .. can anybody pls help find out where am I going wrong ... -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs on windows using cygwin
Hi, If you have installed fftw3 in the standard location it whould work out of the box. Otherwise, you have to set the LDFLAGS and CPPFLAGS to the library and include location respectively. However, there's one more thing I can think of: did you make sure that you compiled fftw3 in single precision mode - case in which the libs are named libfftw3f? Cheers, -- Szilárd On Fri, Nov 5, 2010 at 8:30 AM, bharat gupta bharat.85.m...@gmail.com wrote: Hi there .. I have been trying to install gromacs on windows using cygwin .. and after the installation of the fftw3 package , the moment i install the gromacs using the first command ./configure .. It gives an error that fftw3 package cannot be located .. can anybody pls help find out where am I going wrong ... -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs on windows using cygwin
On 5/11/2010 6:30 PM, bharat gupta wrote: Hi there .. I have been trying to install gromacs on windows using cygwin .. and after the installation of the fftw3 package , the moment i install the gromacs using the first command ./configure .. It gives an error that fftw3 package cannot be located .. can anybody pls help find out where am I going wrong ... Sounds like you might not have followed the installation instructions properly, but unless you tell us exactly what you did, we'd just be wasting time guessing. :-) Meanwhile, check out http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO Mark -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs on windows using cygwin
I followed the same instructions given in the gromacs manual , step by step ... I first tried installing gromacs with the first command given in the manual and then again I installed with the options for FLAGS but finally ended up with the following error in both the above mentioned conditions :- checking dynamic linker characteristics... Win32 ld.exe checking how to hardcode library paths into programs... immediate appending configuration tag F77 to libtool checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking for sqrt in -lm... yes checking for fftw3.h... configure: error: Cannot find the default external FFT l ibrary (fftw3). Other alternatives are 'fftw2', or 'mkl' for Intel MKL. You are STRONGLY recommended to use one of these - fftw is free. Use CPPFLAGS and LDFLAGS if the library is installed in a non-standard location. (see FAQ at http://www.gromacs.org) If you dont care about performance you can also specify 'fftpack' to use a slower set of FFTs built into Gromacs. (Just install FFTW3 unless you really know what you are doing). I have installed fftw2.1.5 ... Pls help me rectify the error -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs on windows using cygwin
I think I was installing the linux version of fftw3 on windows .. I downloaded this file - fftw-3.2.2.pl1-dll32.zipftp://ftp.fftw.org/pub/fftw/fftw-3.2.2.pl1-dll32.zip for installation .. but ./configure command is not working for this file ... as I am getting the following error $ ./configure --enable-sse --enable-float bash: ./configure: No such file or directory -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs on windows using cygwin
bharat gupta wrote: I think I was installing the linux version of fftw3 on windows .. I downloaded this file - fftw-3.2.2.pl1-dll32.zip ftp://ftp.fftw.org/pub/fftw/fftw-3.2.2.pl1-dll32.zip for installation .. but ./configure command is not working for this file ... as I am getting the following error $ ./configure --enable-sse --enable-float bash: ./configure: No such file or directory Looks like you're in the wrong directory. -Justin -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Installation failed
Hi.. every body I am trying to install Gromacs 4.5.1 using updated version of fftw-3.3.1 in single precision in Fedora 9... Giving an error fftw3f library not found... I am mentioning the path before installing but still giving that error Will it be successful in Red Hat enterprize edition Thank You.. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation failed
Kamalesh Roy wrote: Hi.. every body I am trying to install Gromacs 4.5.1 using updated version of fftw-3.3.1 in single precision in Fedora 9... Giving an error fftw3f library not found... I am mentioning the path before installing but still giving that error Please copy and paste your actual command line. No one can tell what you've done wrong. Had you specified everything correctly, it would have worked :) -Justin Will it be successful in Red Hat enterprize edition Thank You.. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Installation of gromacs on a cluster with gcc version 4.1.2
Hi, We had issues with 4.1 series compilers, but we are not longer sure if there really are issues in 4.1.2 and 4.1.3. I would surely avoid 4.1.0 and 4.1.1. But we found that one or two issues in Gromacs only showed up with 4.1.2 and 4.1.3, but there were problems in Gromacs, not gcc. So we are not 100% sure, but version 4.5.1 probably works fine with gcc 4.1.2. Berk Date: Tue, 5 Oct 2010 20:03:41 +0530 From: ras...@chem.iitb.ac.in To: gmx-users@gromacs.org Subject: [gmx-users] Installation of gromacs on a cluster with gcc version 4.1.2 Hi All, I want to install Gromacs 4.5.1 version on a cluster system (high performance computing facility) in our institute. I don't have access to root and thus, I have to install gromacs in my home directory. The problem is that, the cluster has CentOS 5.4 as the operating system and the gcc version is 4.1.2. Gromacs site says that gcc 4.1.x and above are broken compilers and gromacs should not be compiled using them. So I plan to install a compatible version of gcc, for eg. gcc-4.0.4, in my home directory and then install gromacs 4.5.1 using this compiler. Will this be ok? I am asking this question because the new gcc i will install will be compiled with the so called broken compiler version gcc 4.1.2 (which i cannot change). Is this the correct way to ensure that i do not compile gromcas with a broken compiler. Please do reply. Thanxs in advance. Rashmi IIT Bombay -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation of gromacs on a cluster with gcc version 4.1.2
On Tue, 5 Oct 2010 20:03:41 +0530 (IST) ras...@chem.iitb.ac.in wrote: Hi All, I want to install Gromacs 4.5.1 version on a cluster system (high performance computing facility) in our institute. I don't have access to root and thus, I have to install gromacs in my home directory. The problem is that, the cluster has CentOS 5.4 as the operating system and the gcc version is 4.1.2. Gromacs site says that gcc 4.1.x and above are broken compilers and gromacs should not be compiled using them. I haven't had any problems with Gromacs in CentOS 5 compiled with the system compiler. The people at Red Hat have probably fixed all the bugs that caused the problems a long time ago. Another possibility is to ask the admin to install the 4.4 version of GCC, which is readily available in the distribution. -- -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation problem of gromacs binary
- Original Message - From: priyabrata panigrahi priyabra...@gmail.com Date: Friday, August 20, 2010 16:56 Subject: [gmx-users] installation problem of gromacs binary To: gmx-users@gromacs.org I was trying to install gromacs-3.3.3-1.x86_64.rpm. I got the following error error: Failed dependencies: fftw3 = 3.0.1 is needed by gromacs-3.3.3-1.x86_64 libfftw3f.so.3()(64bit) is needed by gromacs-3.3.3-1.x86_64 I installed fftw-3.2.2.tar.gz. Mixing RPM and source distributions doesn't really work, because the RPM database is unaware of anything you've done outside RPM. Either install a *single-precision* FFTW3 RPM, or GROMACS also from source. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] installation problem of gromacs binary
On 2010-08-20 09.14, Mark Abraham wrote: - Original Message - From: priyabrata panigrahi priyabra...@gmail.com Date: Friday, August 20, 2010 16:56 Subject: [gmx-users] installation problem of gromacs binary To: gmx-users@gromacs.org I was trying to install gromacs-3.3.3-1.x86_64.rpm. I got the following error error: Failed dependencies: fftw3 = 3.0.1 is needed by gromacs-3.3.3-1.x86_64 libfftw3f.so.3()(64bit) is needed by gromacs-3.3.3-1.x86_64 I installed fftw-3.2.2.tar.gz. Mixing RPM and source distributions doesn't really work, because the RPM database is unaware of anything you've done outside RPM. Either install a *single-precision* FFTW3 RPM, or GROMACS also from source. Mark And, obviously, you might want to consider a newer gromacs version. For quite a few distributions you can use yum or apt-get gromacs. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] installation problem fftw3 gromacs 4.5.b2
Hi all I am trying to install the latest version. I have installed fftw3 with -enable float and enable thread options, but I am still getting a fftw3 error. the fftw/lib location has all these files: libfftw3f.a libfftw3f_threads.la* libfftw3_threads.la* ../ libfftw3f.la*libfftw3.la* pkgconfig/ libfftw3.a libfftw3f_threads.a libfftw3_threads.a my config command is below: [temi...@abcc1 gromacs-4.5-beta2]$ ./configure --prefix=/users/n2000546794/temizna/gromacs.4.5.b2 --program-prefix=452 --enable-double --enable-mpi --with-x checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for MPI_IN_PLACE in collective operations... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether mpicc accepts -O3... yes checking whether mpicc accepts -msse2... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -std=gnu99... yes checking whether mpicc accepts -fexcess-precision=fast... no checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by mpicc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking whether we are using the GNU C++ compiler... yes checking whether mpicc accepts -g... yes checking dependency style of mpicc... gcc3 checking how to run the C++ preprocessor... mpicc -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from mpicc object... failed checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if mpicc supports -fno-rtti -fno-exceptions... no checking for mpicc option to produce PIC... -fPIC checking if mpicc PIC flag -fPIC works... yes checking if mpicc static flag -static works... yes checking if mpicc supports -c -o file.o... yes checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes configure: creating libtool appending configuration tag CXX to libtool checking for ld used by mpicc... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for mpicc option to produce PIC... -fPIC checking if mpicc PIC flag -fPIC works... yes checking if mpicc static flag -static works... no checking if mpicc supports -c -o file.o... yes checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate appending configuration tag F77 to libtool checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for
Re: [gmx-users] installation problem fftw3 gromacs 4.5.b2
Alpay Temiz wrote: snip checking for fftw3.h... yes checking for main in -lfftw3... no configure: error: Cannot find fftw3 library [temi...@abcc1 gromacs-4.5-beta2]$ echo $LDFFLAGS The proper environment variable is LDFLAGS, not LDFFLAGS. -Justin -L/users/n2000546794/temizna/software/fftw/lib [temi...@abcc1 gromacs-4.5-beta2]$ echo $CPPFLAGS -I/users/n2000546794/temizna/software/fftw/include -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
