Re: [gmx-users] Intel compiling failed
On 04/05/2013 04:59 PM, Carsten Kutzner wrote: Hm, this is another issue now. What version of the Intel compiler are you using? With icc 13.0 it works for me, but I remember having problems with older versions as well. Carsten I am using 2011 sp2 version. probably I should try the new one thank you very much best Albert -- 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] Intel compiling failed
On Apr 5, 2013, at 4:21 PM, Albert wrote: > On 04/05/2013 12:38 PM, Carsten Kutzner wrote: >> Hi Albert, >> >> one reason for the error you see could be that you are using a non-Intel >> MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well. >> >> Carsten > > > thanks a lot both Carsten and Justin. > > I've compiled both fftw and openmpi with intel icc and ifort well. However, > when I try to compile gromacs, it failed?: Hm, this is another issue now. What version of the Intel compiler are you using? With icc 13.0 it works for me, but I remember having problems with older versions as well. Carsten > > > cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda > -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs-4.6.1 > -DCMAKE_PREFIX_PATH=/home/albert/install/fftw-3.3.3 > -DCMAKE_CXX_COMPILER=/home/albert/install/openmpi-1.6.4/bin/mpiCC > -DCMAKE_C_COMPILER=/home/albert/install/openmpi-1.6.4/bin/mpicc > > > > [ 0%] [ 0%] [ 0%] [ 0%] Building NVCC (Device) object > src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o > Building NVCC (Device) object > src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o > Building NVCC (Device) object > src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o > Building NVCC (Device) object > src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o > cc1plus: error: unrecognized command line option '-ip' > cc1plus: error: unrecognized command line option '-ip' > CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message): > Error generating > /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o > > > cc1plus: error: unrecognized command line option '-ip'make[2]: *** > [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] > Error 1 > cc1plus: error: unrecognized command line option '-ip' > make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 > make[1]: *** Waiting for unfinished jobs > > CMake Error at cuda_tools_generated_copyrite_gpu.cu.o.cmake:198 (message): > Error generating > /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o > > > make[2]: *** > [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_copyrite_gpu.cu.o] > Error 1 > make[2]: *** Waiting for unfinished jobs > CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message): > Error generating > /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o > > > CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:198 (message): > Error generating > /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o > > > make[2]: *** > [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] > Error 1 > make[2]: *** > [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o] > Error 1 > make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 > make: *** [all] Error 2 > > > best > Albert > -- > 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Intel compiling failed
On 04/05/2013 12:38 PM, Carsten Kutzner wrote: Hi Albert, one reason for the error you see could be that you are using a non-Intel MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well. Carsten thanks a lot both Carsten and Justin. I've compiled both fftw and openmpi with intel icc and ifort well. However, when I try to compile gromacs, it failed?: cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs-4.6.1 -DCMAKE_PREFIX_PATH=/home/albert/install/fftw-3.3.3 -DCMAKE_CXX_COMPILER=/home/albert/install/openmpi-1.6.4/bin/mpiCC -DCMAKE_C_COMPILER=/home/albert/install/openmpi-1.6.4/bin/mpicc [ 0%] [ 0%] [ 0%] [ 0%] Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o cc1plus: error: unrecognized command line option '-ip' cc1plus: error: unrecognized command line option '-ip' CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message): Error generating /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o cc1plus: error: unrecognized command line option '-ip'make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] Error 1 cc1plus: error: unrecognized command line option '-ip' make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs CMake Error at cuda_tools_generated_copyrite_gpu.cu.o.cmake:198 (message): Error generating /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_copyrite_gpu.cu.o] Error 1 make[2]: *** Waiting for unfinished jobs CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message): Error generating /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:198 (message): Error generating /home/albert/install/00-source/gromacs-4.6.1/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 best Albert -- 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] Intel compiling failed
On Apr 5, 2013, at 12:52 PM, Justin Lemkul wrote: > > > On 4/5/13 6:38 AM, Carsten Kutzner wrote: >> Hi Albert, >> >> one reason for the error you see could be that you are using a non-Intel >> MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well. >> > > Is there any point in compiling FFTW in parallel? I have never once done it > nor found it necessary. Hi, you are absolutely right, sorry I did not express that clearly. The thing is, if you compile the FFTW using the Intel compiler and then compile Gromacs using Intels mpicc or mpigcc compiler wrapper, you will get these undefined references to _intel* at link time. To make it work, you need to use the mpiicc (two i's here) compiler wrapper for Gromacs. Carsten > > -Justin > >> On Apr 5, 2013, at 12:25 PM, Albert wrote: >> >>> Hello: >>> >>> I am trying to compile gromacs with intel compiler. However, it failed when >>> I compile FFTW3 with command: >>> >>> >>> ./configure --enable-sse --enable-float --with-pic --enable-single >>> --enable-static --enable-mpi --prefix=/home/albert/install/fftw-3.3.3 >>> CC=icc CXX=icc F77=ifort >>> >>> here is the log file: >>> >>> mp.c:(.text+0x3148): undefined reference to `_intel_fast_memset' >>> ../libbench2/libbench2.a(mp.o):mp.c:(.text+0x3488): more undefined >>> references to `_intel_fast_memset' follow >>> collect2: ld returned 1 exit status >>> make[3]: *** [mpi-bench] Error 1 >>> make[3]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi' >>> make[2]: *** [all] Error 2 >>> make[2]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi' >>> make[1]: *** [all-recursive] Error 1 >>> make[1]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3' >>> >>> >>> make: *** [all] Error 2 >>> >>> thank you very much >>> best >>> Albert >>> -- >>> 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 >> >> >> -- >> Dr. Carsten Kutzner >> Max Planck Institute for Biophysical Chemistry >> Theoretical and Computational Biophysics >> Am Fassberg 11, 37077 Goettingen, Germany >> Tel. +49-551-2012313, Fax: +49-551-2012302 >> http://www.mpibpc.mpg.de/grubmueller/kutzner >> http://www.mpibpc.mpg.de/grubmueller/sppexa >> > > -- > > > 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Intel compiling failed
On 4/5/13 6:38 AM, Carsten Kutzner wrote: Hi Albert, one reason for the error you see could be that you are using a non-Intel MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well. Is there any point in compiling FFTW in parallel? I have never once done it nor found it necessary. -Justin On Apr 5, 2013, at 12:25 PM, Albert wrote: Hello: I am trying to compile gromacs with intel compiler. However, it failed when I compile FFTW3 with command: ./configure --enable-sse --enable-float --with-pic --enable-single --enable-static --enable-mpi --prefix=/home/albert/install/fftw-3.3.3 CC=icc CXX=icc F77=ifort here is the log file: mp.c:(.text+0x3148): undefined reference to `_intel_fast_memset' ../libbench2/libbench2.a(mp.o):mp.c:(.text+0x3488): more undefined references to `_intel_fast_memset' follow collect2: ld returned 1 exit status make[3]: *** [mpi-bench] Error 1 make[3]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi' make[2]: *** [all] Error 2 make[2]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3' make: *** [all] Error 2 thank you very much best Albert -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Intel compiling failed
Hi Albert, one reason for the error you see could be that you are using a non-Intel MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well. Carsten On Apr 5, 2013, at 12:25 PM, Albert wrote: > Hello: > > I am trying to compile gromacs with intel compiler. However, it failed when I > compile FFTW3 with command: > > > ./configure --enable-sse --enable-float --with-pic --enable-single > --enable-static --enable-mpi --prefix=/home/albert/install/fftw-3.3.3 CC=icc > CXX=icc F77=ifort > > here is the log file: > > mp.c:(.text+0x3148): undefined reference to `_intel_fast_memset' > ../libbench2/libbench2.a(mp.o):mp.c:(.text+0x3488): more undefined references > to `_intel_fast_memset' follow > collect2: ld returned 1 exit status > make[3]: *** [mpi-bench] Error 1 > make[3]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi' > make[2]: *** [all] Error 2 > make[2]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3' > > > make: *** [all] Error 2 > > thank you very much > best > Albert > -- > 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Intel compiling failed
Hello: I am trying to compile gromacs with intel compiler. However, it failed when I compile FFTW3 with command: ./configure --enable-sse --enable-float --with-pic --enable-single --enable-static --enable-mpi --prefix=/home/albert/install/fftw-3.3.3 CC=icc CXX=icc F77=ifort here is the log file: mp.c:(.text+0x3148): undefined reference to `_intel_fast_memset' ../libbench2/libbench2.a(mp.o):mp.c:(.text+0x3488): more undefined references to `_intel_fast_memset' follow collect2: ld returned 1 exit status make[3]: *** [mpi-bench] Error 1 make[3]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi' make[2]: *** [all] Error 2 make[2]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3' make: *** [all] Error 2 thank you very much best Albert -- 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
