I tried both, with the same result. I can compile gromacs 5.0.2 as non-MPI version using cuda 5.5 and intel 12.1.4. But, it is not working together with MPI 1.6.5 nor 1.6.2
Is there anything else to consider when compiling with cuda and mpi? The error messages do not tell me much: icc: command line warning #10006: ignoring unknown option '-dumpspecs' icc: command line warning #10006: ignoring unknown option '-dumpspecs' icc: command line error: no files specified; for help type "icc -help" icc: command line error: no files specified; for help type "icc -help" CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:206 (message): Error generating $HOME/Install_Software/gromacs-5.0.2/builds/gromacs_5p0p2_intel1214_sharedfftw3_openmp_sse41_mpi_single/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o Thanks Soren ________________________________________ From: [email protected] [[email protected]] on behalf of Justin Lemkul [[email protected]] Sent: Wednesday, November 19, 2014 6:08 PM To: [email protected] Subject: Re: [gmx-users] Installing gromacs 5.0.2 single precision with CUDA and MPI ?? On 11/19/14 8:01 PM, Soren Wacker wrote: > Which gromacs version would you recommend then?? Are you installing 5.0.2, as the subject line states, or 5.0-rc1, as your install directory name implies? If you're not actually installing 5.0.2, that's the one you should be installing. -Justin > Soren > > > ________________________________________ > From: [email protected] > [[email protected]] on behalf of Mark Abraham > [[email protected]] > Sent: Wednesday, November 19, 2014 4:43 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Installing gromacs 5.0.2 single precision with CUDA > and MPI ?? > > On Thu, Nov 20, 2014 at 12:08 AM, Soren Wacker <[email protected]> wrote: > >> Hi, >> >> another question: >> Is it possible to install gromacs 5.0.2 with CUDA and MPI? >> > > Yes, but you should use a compiler version that is supported by your CUDA > version, and not try to install release candidate versions Gromacs. ;-) > > Mark > > >> Since, when I try to generate mdrun_mpi everything seems to work fine until >>> make install >> >> then I get some cryptic error messages. >> >> Some details first: >> ------ >> Intel(R) Xeon(R) CPU X5550 @ 2.67GHz >> # Set up environment to work with the Intel 12.1.4 compilers >> >> openmpi/1.6.5 >> intel/2011-sp1.10.319 (intel 12.1.4 or 12.1.0 compiler) >> cuda/6.0 (also tried cuda 5.5) >> >>> mpicc -v >> icc version 12.1.4 (gcc version 4.4.7 compatibility) >> >> input commands: >> CC=mpicc \ >> CXX=mpiCC \ (also tried mpicxx) >> cmake ${SOURCE_DIR} \ >> -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} \ >> -DFFTWF_INCLUDE_DIR=$FFTWSINGLE/include \ >> -DFFTWF_LIBRARY=$FFTWSINGLE/lib/libfftw3f.a \ >> -DCMAKE_PREFIX_PATH="/global/software/boost/gcc" \ >> -DCMAKE_PREFIX_PATH="$FFTWSINGLE" \ >> -DGMX_BUILD_MDRUN_ONLY=ON \ >> -DGMX_MPI=on \ >> -DGMX_SIMD="SSE4.1" >> -------- >> >> >> >> >> Here the output: >> >> -- Configuring done >> -- Generating done >> -- Build files have been written to: >> /home/@USER/Install_Software/gromacs/builds/gromacs_50rc1_intel1214_sharedfftw3_openmp_sse41_mpi_single >> Scanning dependencies of target git-version-info >> Scanning dependencies of target mdrun_objlib >> [ 0%] Generating git version information >> [ 1%] [ 1%] [ 1%] Building CXX object >> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o >> Building C object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o >> Building CXX object >> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.cpp.o >> warning #13000: could not open message catalog file: diagsc.cat >> warning #13000: could not open message catalog file: diagsc.cat >> warning #13000: could not open message catalog file: diagsc.cat >> [ 1%] Built target git-version-info >> [ 1%] Building CXX object >> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/runner.cpp.o >> warning #13000: could not open message catalog file: diagsc.cat >> [ 1%] Building CXX object >> src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o >> [ 1%] [ 1%] Building NVCC (Device) object >> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_cudautils.cu.o >> Generating baseversion-gen.c >> [ 1%] warning #13000: could not open message catalog file: diagsc.cat >> Building NVCC (Device) object >> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_copyrite_gpu.cu.o >> icc: command line warning #10006: ignoring unknown option '-dumpspecs' >> icc: command line error: no files specified; for help type "icc -help" >> CMake Error at libgromacs_generated_cudautils.cu.o.cmake:206 (message): >> Error generating >> >> /home/@USER/Install_Software/gromacs/builds/gromacs_50rc1_intel1214_sharedfftw3_openmp_sse41_mpi_single/src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_cudautils.cu.o >> >> >> make[2]: *** >> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_cudautils.cu.o] >> Error 1 >> make[2]: *** Waiting for unfinished jobs.... >> icc: command line warning #10006: ignoring unknown option '-dumpspecs' >> icc: command line error: no files specified; for help type "icc -help" >> CMake Error at libgromacs_generated_copyrite_gpu.cu.o.cmake:206 (message): >> Error generating >> >> /home/@USER/Install_Software/gromacs/builds/gromacs_50rc1_intel1214_sharedfftw3_openmp_sse41_mpi_single/src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_copyrite_gpu.cu.o >> >> >> make[2]: *** >> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_copyrite_gpu.cu.o] >> Error 1 >> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 >> make[1]: *** Waiting for unfinished jobs.... >> [ 1%] Built target mdrun_objlib >> make: *** [all] Error 2 >> [ 0%] Generating git version information >> [ 0%] Built target git-version-info >> [ 0%] Building NVCC (Device) object >> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_cudautils.cu.o >> icc: command line warning #10006: ignoring unknown option '-dumpspecs' >> icc: command line error: no files specified; for help type "icc -help" >> CMake Error at libgromacs_generated_cudautils.cu.o.cmake:206 (message): >> Error generating >> >> /home/@USER/Install_Software/gromacs/builds/gromacs_50rc1_intel1214_sharedfftw3_openmp_sse41_mpi_single/src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_cudautils.cu.o >> >> >> make[2]: *** >> [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_cudautils.cu.o] >> Error 1 >> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 >> make: *** [all] Error 2 >> Finished installing MPI single-precision version of mdrun at Wed Nov 19 >> 15:34:18 MST 2014 >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to [email protected]. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected]. > -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
