[gmx-users] GPU compatibility
Hi, We've got a GPU cluster in our group and have really been looking forward to running gromacs on it with full functionality. Unfortunately, it looks like our NVIDIA Tesla C1060 cards aren't supported by the 4.6 beta. I was just wondering if there was any chance that they would be supported in the full version? These cards are only a couple of years old now and were bought specifically for running MD. Thanks, Cara -- 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] Error during compilation of Gromacs-4.5.5
Hi, The following error pops up during compilation of Gromacs-4.5.5 : /home/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined reference to `pthread_setaffinity_np'. Could you please help me fix it? I am installing it on uname -m = x86_64 uname -r = 2.6.9-5.ELsmp uname -s = Linux uname -v = #1 SMP Wed Jan 5 19:29:47 EST 2005 cc (GCC) 3.4.3 20041212 (Red Hat 3.4.3-9.EL4) glibc : glibc -2.3.4 Thanks & Regards - 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. -- 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] Topolbuild configuration
Hello! I'm trying to download topolbuild1_2_1 in my Mac computer. I understand that the executable file is in the same directory as the Makefile. I also understand the thing about the PATH. For different files I have downloaded, I was able to ./configure it and use make, but for topolbuild, I wasn't able to ./configure it as it prints out an error message. >From the previous thread, I read that "Common practice is to then put it in some central directory for executables (like /usr/local/bin, or some subdirectory of your /home directory, depending on your permissions on the system)." I think that would help me fix my problem, but I'm not so sure how to do this. Could anyone give me an advice regarding this issue? Thank you. Seokyun -- View this message in context: http://gromacs.5086.n6.nabble.com/Topolbuild-configuration-tp5003607.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] failed with intel compiler
On Sun, Dec 9, 2012 at 11:30 AM, Albert wrote: > Hello: > >I am compiling Gromacs4.6beta2 with intel cimpiler by command: > > cmake .. -DGMX_MPI=ON > -DCMAKE_CXX_COMPILER=/soft/intel64/icc/bin/intel64/mpiCC > -DCMAKE_C_COMPILER=/soft/intel64/icc/bin/intel64/icc > You shouldn't use mpiCC as C++ and icc for C. Either both should be mpi or none. Also you say what ICC version you have. > > > /home/albert/Downloads/gromacs/gromacs-4.6-beta2/build/CMakeFiles/CMakeTmp/testCXXCompiler.cxx >catastrophic error: Compiler configuration problem encountered. The >expected target architecture compiler is missing (11.1-intel64 != >12.1-intel64) >(0): internal error: backend signals >compilation aborted for Make sure your compiler environment is setup correctly (you want to load the iccvars.sh and then don't use absolute paths for the icc binary). The error message indicates something is wrong with that. Make sure you can compile a simple test program independent of Gromacs. Roland > -- > 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 > > > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] amber to gromacs error
On Sun, Dec 9, 2012 at 9:46 AM, Albert wrote: > hello: > > I am using the command: > > acpype.py -p prmtop -x S13.rst > > to convert Amber system into Gromacs system, but it failed when I try to > generate .tpr file: > > > WARNING 1 [file prmtop_GMX.top, line 19]: > Too few parameters on line (source file toppush.c, line 300) > WARNING 2 [file prmtop_GMX.top, line 22]: > Too few parameters on line (source file toppush.c, line 300) > Generated 820 of the 820 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 820 of the 820 1-4 parameter combinations > --- > Program grompp, VERSION 4.5.5 > Source code file: toppush.c, line: 1166 > Fatal error: > Atomtype 3C not found > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra) > > Not sure about "too few ...". But it seems you have some atoms with type "3C" that is not included (defined) in top files. > My ligand contains both glycam FF and GAFF parameters from Amber. It is > quite strange when I open the generated .top file because there is even no > "include "amber99SB.ff/forcefiled.itp" line Here is the .top file I got: > My resulting .top and .gro files worked well without these "include ..." stuff, and I believe all the atom types and vdw parameters, bond, angle, and dihedral parameters, as well as atomic charges have already been included in the resulting .top file. > ; prmtop_GMX.top created by acpype (Rev: 7234) on Sun Dec 9 18:35:28 2012 > > [ defaults ] > ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 yes 0.5 0.8333 > > [ atomtypes ] > ;name bond_type mass charge ptype sigma epsilon Amb > N3 N3 0.0 0.0 A 3.25000e-01 7.11280e-01 ; > 1.82 0.1700 > HH 0.0 0.0 A 1.06908e-01 6.56888e-02 ; > 0.60 0.0157 > CX CX 0.0 0.0 A 3.39967e-01 4.57730e-01 ; > 1.91 0.1094 > HP HP 0.0 0.0 A 1.95998e-01 6.56888e-02 ; > 1.10 0.0157 > CT CT 0.0 0.0 A 3.39967e-01 4.57730e-01 ; > 1.91 0.1094 > HC HC 0.0 0.0 A 2.64953e-01 6.56888e-02 ; > 1.49 0.0157 > CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; > 1.91 0.0860 > OO 0.0 0.0 A 2.95992e-01 8.78640e-01 ; > 1.66 0.2100 > NN 0.0 0.0 A 3.25000e-01 7.11280e-01 ; > 1.82 0.1700 > H1 H1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; > 1.39 0.0157 > 3C 3C 0.0 0.0 A 3.39967e-01 4.57730e-01 ; > 1.91 0.1094 > OH OH 0.0 0.0 A 3.06647e-01 8.80314e-01 ; > 1.72 0.2104 > HO HO 0.0 0.0 A 0.0e+00 0.0e+00 ; > 0.00 0. > 2C 2C 0.0 0.0 A 3.39967e-01 4.57730e-01 ; > 1.91 0.1094 > SS 0.0 0.0 A 3.56359e-01 1.04600e+00 ; > 2.00 0.2500 > CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; > 1.91 0.0860 > HA HA 0.0 0.0 A 2.59964e-01 6.27600e-02 ; > 1.46 0.0150 > CO CO 0.0 0.0 A 3.39967e-01 3.59824e-01 ; > 1.91 0.0860 > O2 O2 0.0 0.0 A 2.95992e-01 8.78640e-01 ; > 1.66 0.2100 > C* C* 0.0 0.0 A 3.39967e-01 3.59824e-01 ; > 1.91 0.0860 > CW CW 0.0 0.0 A 3.39967e-01 3.59824e-01 ; > 1.91 0.0860 > H4 H4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; > 1.41 0.0150 > NA NA 0.0 0.0 A 3.25000e-01 7.11280e-01 ; > 1.82 0.1700 > CN CN 0.0 0.0 A 3.39967e-01 3.59824e-01 ; > 1.91 0.0860 > CB CB 0.0 0.0 A 3.39967e-01 3.59824e-01 ; > 1.91 0.0860 > C8 C8 0.0 0.0 A 3.39967e-01 4.57730e-01 ; > 1.91 0.1094 > CC CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; > 1.91 0.0860 > NB NB 0.0 0.0 A 3.25000e-01 7.11280e-01 ; > 1.82 0.1700 > CR CR 0.0 0.0 A 3.39967e-01 3.59824e-01 ; > 1.91 0.0860 > H5 H5 0.0 0.0 A 2.42146e-01 6.27600e-02 ; > 1.36 0.0150 > N2 N2 0.0 0.0 A 3.25000e-01 7.11280e-01 ; > 1.82 0.1700 > CV CV 0.0 0.0 A 3.39967e-01 3.59824e-01 ; > 1.91 0.0860 > SH SH 0.0 0.0 A 3.56359e-01 1.04600e+00 ; > 2.00 0.2500 > HS HS 0.0 0.0 A 1.06908e-01 6.56888e-02
[gmx-users] amber to gromacs error
hello: I am using the command: acpype.py -p prmtop -x S13.rst to convert Amber system into Gromacs system, but it failed when I try to generate .tpr file: WARNING 1 [file prmtop_GMX.top, line 19]: Too few parameters on line (source file toppush.c, line 300) WARNING 2 [file prmtop_GMX.top, line 22]: Too few parameters on line (source file toppush.c, line 300) Generated 820 of the 820 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 820 of the 820 1-4 parameter combinations --- Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1166 Fatal error: Atomtype 3C not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra) My ligand contains both glycam FF and GAFF parameters from Amber. It is quite strange when I open the generated .top file because there is even no "include "amber99SB.ff/forcefiled.itp" line Here is the .top file I got: ; prmtop_GMX.top created by acpype (Rev: 7234) on Sun Dec 9 18:35:28 2012 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb N3 N3 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 HH 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 CX CX 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 HP HP 0.0 0.0 A 1.95998e-01 6.56888e-02 ; 1.10 0.0157 CT CT 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 HC HC 0.0 0.0 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 OO 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 NN 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 H1 H1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 3C 3C 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 OH OH 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 HO HO 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. 2C 2C 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 SS 0.0 0.0 A 3.56359e-01 1.04600e+00 ; 2.00 0.2500 CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 HA HA 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 CO CO 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 O2 O2 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 C* C* 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 CW CW 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H4 H4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 NA NA 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CN CN 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 CB CB 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 C8 C8 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 CC CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 NB NB 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CR CR 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H5 H5 0.0 0.0 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150 N2 N2 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CV CV 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 SH SH 0.0 0.0 A 3.56359e-01 1.04600e+00 ; 2.00 0.2500 HS HS 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 Ho Ho 0.0 0.0 A 3.56359e-02 1.25520e-01 ; 0.20 0.0300 Oh Oh 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 Cg Cg 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 H2 H2 0.0 0.0 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157 Os Os 0.0 0.0 A 3.1e-01 7.11280e-01 ; 1.68 0.1700 Na+ Na+ 0.0 0.0 A 2.43928e-01 3.65846e-01 ; 1.37 0.0874 OW OW 0.0 0.0 A 3.1507
[gmx-users] structure building and manipulating software
Hi, I know that here for discussion about Gromacs,but I want to ask which program is the best for structure building and manipulating. I work on graphene and graphene oxide. best, Amir -- 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] failed with intel compiler
Hello: I am compiling Gromacs4.6beta2 with intel cimpiler by command: cmake .. -DGMX_MPI=ON -DCMAKE_CXX_COMPILER=/soft/intel64/icc/bin/intel64/mpiCC -DCMAKE_C_COMPILER=/soft/intel64/icc/bin/intel64/icc But It fails with the following output: Change Dir: /home/albert/Downloads/gromacs/gromacs-4.6-beta2/build/CMakeFiles/CMakeTmp Run Build Command:/usr/bin/gmake "cmTryCompileExec/fast" /usr/bin/gmake -f CMakeFiles/cmTryCompileExec.dir/build.make CMakeFiles/cmTryCompileExec.dir/build gmake[1]: Entering directory `/home/albert/Downloads/gromacs/gromacs-4.6-beta2/build/CMakeFiles/CMakeTmp' /usr/bin/cmake -E cmake_progress_report /home/albert/Downloads/gromacs/gromacs-4.6-beta2/build/CMakeFiles/CMakeTmp/CMakeFiles 1 Building CXX object CMakeFiles/cmTryCompileExec.dir/testCXXCompiler.cxx.o /soft/intel64/icc/bin/intel64/mpiCC -o CMakeFiles/cmTryCompileExec.dir/testCXXCompiler.cxx.o -c /home/albert/Downloads/gromacs/gromacs-4.6-beta2/build/CMakeFiles/CMakeTmp/testCXXCompiler.cxx catastrophic error: Compiler configuration problem encountered. The expected target architecture compiler is missing (11.1-intel64 != 12.1-intel64) (0): internal error: backend signals compilation aborted for /home/albert/Downloads/gromacs/gromacs-4.6-beta2/build/CMakeFiles/CMakeTmp/testCXXCompiler.cxx (code 4) gmake[1]: Leaving directory `/home/albert/Downloads/gromacs/gromacs-4.6-beta2/build/CMakeFiles/CMakeTmp gmake[1]: *** [CMakeFiles/cmTryCompileExec.dir/testCXXCompiler.cxx.o] Error 4 gmake: *** [cmTryCompileExec/fast] Error 2 CMake will not be able to correctly generate this project. Call Stack (most recent call first): CMakeLists.txt:157 (enable_language) -- Configuring incomplete, errors occurred! -- 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] GPU warnings
> > gcc 4.7.2 is not supported by any CUDA version. > > > > I suggest that you just fix it by editing the include/host_config.h and > changing the version check macro (line 82 AFAIK). I've never had real > problems with using new and officially not supported gcc-s, the version > check is more of a promise from NVIDIA that "we've tested thoroughly > internally and we more or less vouch for thins combination". > > Cheers, > -- > Szilárd > > PS: > Disclamer: I don't take responsibility if your machine goes up in flames! > ;) > > Hi Szilárd,, I tried to compile gromacs-4.6beta1, is this the version you suggested? If not, please indicate how to download the source cause I am confused with all these development versions. Anyway, this is the error I get with 4.6beta1, gcc 4.7.2 and cuda 5: [ 0%] Building NVCC (Device) object src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o /usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../include/c++/4.7.2/ext/atomicity.h(48): error: identifier "__atomic_fetch_add" is undefined /usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../include/c++/4.7.2/ext/atomicity.h(52): error: identifier "__atomic_fetch_add" is undefined 2 errors detected in the compilation of "/tmp/tmpxft_2394_-9_cudautils.compute_30.cpp1.ii". CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:252 (message): Error generating file /home/thomas/Programs/gromacs-4.6-beta1_gnu_cuda5_build/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o gmake[3]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o] Error 1 gmake[2]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 gmake[1]: *** [src/programs/mdrun/CMakeFiles/mdrun.dir/rule] Error 2 gmake: *** [mdrun] Error 2 Unless I am missing something, cuda 5 does not support gcc 4.7.2. 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
