[gmx-users] Problem compiling Gromacs 4.6.3 with CUDA
Hi, I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22. The configuration runs okay and I have made sure that I have set paths correctly. I'm getting errors: $ make [ 0%] Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o icc: command line warning #10006: ignoring unknown option '-dumpspecs' /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message): Error generating /apps/src/gromacs/gromacs-4.6.3/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 Any help would be appreciated. Regards, Ahmed. -- Scanned by iCritical. -- 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] Problem compiling Gromacs 4.6.3 with CUDA
icc and CUDA is pretty painful. I'd suggest getting latest gcc. Mark On Thu, Nov 7, 2013 at 2:42 PM, wrote: > Hi, > > I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22. > > The configuration runs okay and I have made sure that I have set paths > correctly. > > I'm getting errors: > > $ make > [ 0%] Building NVCC (Device) object > src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o > icc: command line warning #10006: ignoring unknown option '-dumpspecs' > /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In > function `_start': > (.text+0x20): undefined reference to `main' > CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message): > Error generating > > /apps/src/gromacs/gromacs-4.6.3/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 > > Any help would be appreciated. > > Regards, > Ahmed. > > -- > Scanned by iCritical. > > -- > 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] Problem compiling Gromacs 4.6.3 with CUDA
Did it a few days ago. Not so much of a problem here. But I compiled everything, including fftw, with it. The only error I got was that I should turn off the separable compilation, and that the user must be in the group video. My settings are (yes, I know it should go better with openmp, but openmp goes horrobly in our cluster, I don't know why): setenv CC "/opt/intel/bin/icc" setenv CXX "/opt/intel/bin/icpc" setenv F77 "/opt/intel/bin/ifort" setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/ mkdir build cd build cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/ make make install cd .. rm -rf build On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham wrote: > icc and CUDA is pretty painful. I'd suggest getting latest gcc. > > Mark > > > On Thu, Nov 7, 2013 at 2:42 PM, wrote: > > > Hi, > > > > I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22. > > > > The configuration runs okay and I have made sure that I have set paths > > correctly. > > > > I'm getting errors: > > > > $ make > > [ 0%] Building NVCC (Device) object > > > src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o > > icc: command line warning #10006: ignoring unknown option '-dumpspecs' > > /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In > > function `_start': > > (.text+0x20): undefined reference to `main' > > CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 > (message): > > Error generating > > > > > /apps/src/gromacs/gromacs-4.6.3/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 > > > > Any help would be appreciated. > > > > Regards, > > Ahmed. > > > > -- > > Scanned by iCritical. > > > > -- > > 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] Problem compiling Gromacs 4.6.3 with CUDA
You will do much better with gcc+openmp than icc-openmp! Mark On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade wrote: > Did it a few days ago. Not so much of a problem here. > > But I compiled everything, including fftw, with it. The only error I got > was that I should turn off the separable compilation, and that the user > must be in the group video. > > My settings are (yes, I know it should go better with openmp, but openmp > goes horrobly in our cluster, I don't know why): > > setenv CC "/opt/intel/bin/icc" > setenv CXX "/opt/intel/bin/icpc" > setenv F77 "/opt/intel/bin/ifort" > setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/ > mkdir build > cd build > cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON > -DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 -DBUILD_SHARED_LIBS=OFF > -DGMX_PREFER_STATIC_LIBS=ON > -DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/ > make > make install > cd .. > rm -rf build > > > On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham >wrote: > > > icc and CUDA is pretty painful. I'd suggest getting latest gcc. > > > > Mark > > > > > > On Thu, Nov 7, 2013 at 2:42 PM, wrote: > > > > > Hi, > > > > > > I'm having trouble compiling v 4.6.3 with GPU support using CUDA > 5.5.22. > > > > > > The configuration runs okay and I have made sure that I have set paths > > > correctly. > > > > > > I'm getting errors: > > > > > > $ make > > > [ 0%] Building NVCC (Device) object > > > > > > src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o > > > icc: command line warning #10006: ignoring unknown option '-dumpspecs' > > > /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In > > > function `_start': > > > (.text+0x20): undefined reference to `main' > > > CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 > > (message): > > > Error generating > > > > > > > > > /apps/src/gromacs/gromacs-4.6.3/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 > > > > > > Any help would be appreciated. > > > > > > Regards, > > > Ahmed. > > > > > > -- > > > Scanned by iCritical. > > > > > > -- > > > 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 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] Problem compiling Gromacs 4.6.3 with CUDA
Really? An what about gcc+mpi? should I expect any improvement? On Thu, Nov 7, 2013 at 6:51 PM, Mark Abraham wrote: > You will do much better with gcc+openmp than icc-openmp! > > Mark > > > On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade >wrote: > > > Did it a few days ago. Not so much of a problem here. > > > > But I compiled everything, including fftw, with it. The only error I got > > was that I should turn off the separable compilation, and that the user > > must be in the group video. > > > > My settings are (yes, I know it should go better with openmp, but openmp > > goes horrobly in our cluster, I don't know why): > > > > setenv CC "/opt/intel/bin/icc" > > setenv CXX "/opt/intel/bin/icpc" > > setenv F77 "/opt/intel/bin/ifort" > > setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/ > > mkdir build > > cd build > > cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON > > -DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 -DBUILD_SHARED_LIBS=OFF > > -DGMX_PREFER_STATIC_LIBS=ON > > -DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/ > > make > > make install > > cd .. > > rm -rf build > > > > > > On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham > >wrote: > > > > > icc and CUDA is pretty painful. I'd suggest getting latest gcc. > > > > > > Mark > > > > > > > > > On Thu, Nov 7, 2013 at 2:42 PM, wrote: > > > > > > > Hi, > > > > > > > > I'm having trouble compiling v 4.6.3 with GPU support using CUDA > > 5.5.22. > > > > > > > > The configuration runs okay and I have made sure that I have set > paths > > > > correctly. > > > > > > > > I'm getting errors: > > > > > > > > $ make > > > > [ 0%] Building NVCC (Device) object > > > > > > > > > > src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o > > > > icc: command line warning #10006: ignoring unknown option > '-dumpspecs' > > > > /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In > > > > function `_start': > > > > (.text+0x20): undefined reference to `main' > > > > CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 > > > (message): > > > > Error generating > > > > > > > > > > > > > > /apps/src/gromacs/gromacs-4.6.3/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 > > > > > > > > Any help would be appreciated. > > > > > > > > Regards, > > > > Ahmed. > > > > > > > > -- > > > > Scanned by iCritical. > > > > > > > > -- > > > > 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 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] Problem compiling Gromacs 4.6.3 with CUDA
On Fri, Nov 8, 2013 at 12:02 AM, Jones de Andrade wrote: > Really? Of course. With openmp gets to use all your cores for PME+bondeds+stuff while the GPU does PP. Any version without openmp gets to use one core per domain, which is bad. > An what about gcc+mpi? should I expect any improvement? > Run how and compared with what? Using an external MPI library within a single node is a complete waste of time compared with the alternatives (thread-MPI, OpenMP, or both). Mark > > > On Thu, Nov 7, 2013 at 6:51 PM, Mark Abraham >wrote: > > > You will do much better with gcc+openmp than icc-openmp! > > > > Mark > > > > > > On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade > >wrote: > > > > > Did it a few days ago. Not so much of a problem here. > > > > > > But I compiled everything, including fftw, with it. The only error I > got > > > was that I should turn off the separable compilation, and that the user > > > must be in the group video. > > > > > > My settings are (yes, I know it should go better with openmp, but > openmp > > > goes horrobly in our cluster, I don't know why): > > > > > > setenv CC "/opt/intel/bin/icc" > > > setenv CXX "/opt/intel/bin/icpc" > > > setenv F77 "/opt/intel/bin/ifort" > > > setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/ > > > mkdir build > > > cd build > > > cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF > > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON > > > -DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 > -DBUILD_SHARED_LIBS=OFF > > > -DGMX_PREFER_STATIC_LIBS=ON > > > -DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/ > > > make > > > make install > > > cd .. > > > rm -rf build > > > > > > > > > On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham > > >wrote: > > > > > > > icc and CUDA is pretty painful. I'd suggest getting latest gcc. > > > > > > > > Mark > > > > > > > > > > > > On Thu, Nov 7, 2013 at 2:42 PM, wrote: > > > > > > > > > Hi, > > > > > > > > > > I'm having trouble compiling v 4.6.3 with GPU support using CUDA > > > 5.5.22. > > > > > > > > > > The configuration runs okay and I have made sure that I have set > > paths > > > > > correctly. > > > > > > > > > > I'm getting errors: > > > > > > > > > > $ make > > > > > [ 0%] Building NVCC (Device) object > > > > > > > > > > > > > > > src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o > > > > > icc: command line warning #10006: ignoring unknown option > > '-dumpspecs' > > > > > /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In > > > > > function `_start': > > > > > (.text+0x20): undefined reference to `main' > > > > > CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 > > > > (message): > > > > > Error generating > > > > > > > > > > > > > > > > > > > > /apps/src/gromacs/gromacs-4.6.3/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 > > > > > > > > > > Any help would be appreciated. > > > > > > > > > > Regards, > > > > > Ahmed. > > > > > > > > > > -- > > > > > Scanned by iCritical. > > > > > > > > > > -- > > > > > 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 mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Ma
Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA
Ok, you convinced me. I'll really give it a try. I'm following this throw the suposition that openMP implementation on intel compilers is not as good as GNU compilers. I already tested intel openMP in our cluster, and it just sucked in comparison to the pure MPI compilation. Let's hope I can make it work together with the IMPI. I don't want to install openmpi as just a user also (did it a long time ago as root, not in limited space). Thanks again! On Fri, Nov 8, 2013 at 9:21 AM, Mark Abraham wrote: > On Fri, Nov 8, 2013 at 12:02 AM, Jones de Andrade >wrote: > > > Really? > > > Of course. With openmp gets to use all your cores for PME+bondeds+stuff > while the GPU does PP. Any version without openmp gets to use one core per > domain, which is bad. > > > > An what about gcc+mpi? should I expect any improvement? > > > > Run how and compared with what? Using an external MPI library within a > single node is a complete waste of time compared with the alternatives > (thread-MPI, OpenMP, or both). > > Mark > > > > > > > > On Thu, Nov 7, 2013 at 6:51 PM, Mark Abraham > >wrote: > > > > > You will do much better with gcc+openmp than icc-openmp! > > > > > > Mark > > > > > > > > > On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade > > >wrote: > > > > > > > Did it a few days ago. Not so much of a problem here. > > > > > > > > But I compiled everything, including fftw, with it. The only error I > > got > > > > was that I should turn off the separable compilation, and that the > user > > > > must be in the group video. > > > > > > > > My settings are (yes, I know it should go better with openmp, but > > openmp > > > > goes horrobly in our cluster, I don't know why): > > > > > > > > setenv CC "/opt/intel/bin/icc" > > > > setenv CXX "/opt/intel/bin/icpc" > > > > setenv F77 "/opt/intel/bin/ifort" > > > > setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/ > > > > mkdir build > > > > cd build > > > > cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF > > > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON > > > > -DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 > > -DBUILD_SHARED_LIBS=OFF > > > > -DGMX_PREFER_STATIC_LIBS=ON > > > > -DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/ > > > > make > > > > make install > > > > cd .. > > > > rm -rf build > > > > > > > > > > > > On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham < > mark.j.abra...@gmail.com > > > > >wrote: > > > > > > > > > icc and CUDA is pretty painful. I'd suggest getting latest gcc. > > > > > > > > > > Mark > > > > > > > > > > > > > > > On Thu, Nov 7, 2013 at 2:42 PM, wrote: > > > > > > > > > > > Hi, > > > > > > > > > > > > I'm having trouble compiling v 4.6.3 with GPU support using CUDA > > > > 5.5.22. > > > > > > > > > > > > The configuration runs okay and I have made sure that I have set > > > paths > > > > > > correctly. > > > > > > > > > > > > I'm getting errors: > > > > > > > > > > > > $ make > > > > > > [ 0%] Building NVCC (Device) object > > > > > > > > > > > > > > > > > > > > > src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o > > > > > > icc: command line warning #10006: ignoring unknown option > > > '-dumpspecs' > > > > > > /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: > In > > > > > > function `_start': > > > > > > (.text+0x20): undefined reference to `main' > > > > > > CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 > > > > > (message): > > > > > > Error generating > > > > > > > > > > > > > > > > > > > > > > > > > > > /apps/src/gromacs/gromacs-4.6.3/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 > > > > > > > > > > > > Any help would be appreciated. > > > > > > > > > > > > Regards, > > > > > > Ahmed. > > > > > > > > > > > > -- > > > > > > Scanned by iCritical. > > > > > > > > > > > > -- > > > > > > 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 do
