On Thu, Feb 13, 2014 at 9:03 AM, Chaitali Chandratre <chaitujo...@gmail.com>wrote:
> Dear Sir, > > Thanks for your reply. > With Change in host_config.h it worked fine. But It needed full Cuda folder > to be copied into > my home area. > > Can we compile gromacs-4.6.4 gpu version with *pgi* compiler? > Seems wildly unlikely to be worthwhile, even if possible. Nvidia would have to make CUDA support it (no idea here), and then it would have to do a decent job of compiling the GROMACS SIMD instrinsics - which it didn't do last time someone tried it. Even trying it would require you to set up your environment so that the C compiler visible to CMake is actually a C compiler, as those errors you got say. Mark I* used below command :* > > ""/cmake-2.8.12.1/bin/cmake -DGMX_FFT_LIBRARY=mkl > -DMKL_LIBRARIES="/path/to/mkl/lib/intel64/" > -DMKL_INCLUDE_DIR="/path/to/mkl/include/intel64/lp64/" -D > CMAKE_INSTALL_PREFIX=/path/to/gromacs-4.6.4-PGI/build-gpu-pgi/ > -DGMX_MPI=ON -DGMX_GPU=ON > > -D*CUDA_HOST_COMPILER=/path/to-pgi/13.4/bin/pgCC*-DCUDA_TOOLKIT_ROOT_DIR=/path/to/CUDA-5.5/ > /path/tok/gromacs-4.6.4-PGI/ > > *It gave below error :* > > -- The C compiler identification is unknown > -- Check for working C compiler: /path/to/13.4/bin/pgCC > -- Check for working C compiler: /path/to/13.4/bin/pgCC -- broken > CMake Error > at /path/to/ > cmake-2.8.12.1/share/cmake-.8/Modules/CMakeTestCCompiler.cmake:61 > (message): > > The C compiler " /path/to/13.4/bin/pgCC" is not able to compile a > simple test program. > It fails with the following output: > Change Dir: /path/to/gromacs-4.6.4-PGI/build-gpu-pgi/CMakeFiles/CMakeTmp > Run Build Command:/usr/bin/gmake "cmTryCompileExec1420923523/fast" > > /usr/bin/gmake -f CMakeFiles/cmTryCompileExec1420923523.dir/build.make > CMakeFiles/cmTryCompileExec1420923523.dir/build > > gmake[1]: Entering directory > /path/to/gromacs-4.6.4-PGI/build-gpu-pgi/CMakeFiles/CMakeTmp' > > > /opt/app/cmake-2.8.12.1/bin/cmake -E cmake_progress_report > /path/to/gromacs-4.6.4-PGI/build-gpu-pgi/CMakeFiles/CMakeTmp/CMakeFiles > 1 > > Building C object > CMakeFiles/cmTryCompileExec1420923523.dir/testCCompiler.c.o > /opt/pgi/linux86-64/13.4/bin/pgCC -o > CMakeFiles/cmTryCompileExec1420923523.dir/testCCompiler.c.o -c > > /path/to/gromacs-4.6.4-PGI/build-gpu-pgi/CMakeFiles/CMakeTmp/testCCompiler.c > > > > > " > /path/to/gromacs-4.6.4-PGI/build-gpu-pgi/CMakeFiles/CMakeTmp/testCCompiler.c", > line 2: catastrophic error: > > #error directive: "The CMAKE_C_COMPILER is set to a C++ > compiler" > # error "The CMAKE_C_COMPILER is set to a C++ compiler" > ^ > > Compilation terminated. > > gmake[1]: *** > [CMakeFiles/cmTryCompileExec1420923523.dir/testCCompiler.c.o] > > > --------------------------------------------------------------------------------------------------------------------------------- > > Can u please tell possible reasons for the same. > > Thanks, > Chaitali > > > > On Tue, Feb 11, 2014 at 6:56 PM, Szilárd Páll <pall.szil...@gmail.com > >wrote: > > > On Tue, Feb 11, 2014 at 6:12 AM, Chaitali Chandratre > > <chaitujo...@gmail.com> wrote: > > > Dear Sir, > > > > > > Below is error message for gromacs-4.6.4 gpu enabled install: > > > > > > --------------------------------------------------------------------------------------------------------------------------- > > > make error : > > > > > > "[chaitalij@gpu4 build-gpu]$ make > > > [ 0%] Building NVCC (Device) object > > > > > > src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o > > > /opt/CUDA-5.5/include/host_config.h(72): catastrophic error: #error > > > directive: -- unsupported ICC configuration! Only ICC 12.1 on Linux > > x86_64 > > > is supported! > > > #error -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64 > > is > > > supported! > > > ^ > > > > The error is right there, explained quite clearly in the above > > message. What you can do is to: > > - complain to NVIDIA AND > > > > - remove the limitation which is mostly a safety measure (AFAIK the > > nvcc + icc 13 is not fully tested and/or compatible) by either editing > > the above mentioned header or if you can't do that (no root access) > > creating a copy of to edit it and appending its path in > > CUDA_NVCC_FLAGS (i.e. adding ";-I/path/to/my/cuda-host-config-h"). > > OR > > - use another compiler, e.g. gcc 4.8 will probably be faster than icc 13. > > > > > CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 > > (message): > > > Error generating > > > > > > path/to/gromacs/gromacs-4.6.4/build-gpu/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 > > > " > > > > > > ------------------------------------------------------------------------------------------------------------------------- > > > > > > Below is config command : > > > > > > ---------------------------------------------------------------------------------------------------------------------- > > > " > > > /path/to/cmake-2.8.12.1/bin/cmake -DGMX_FFT_LIBRARY=mkl > > > -DMKL_LIBRARIES="/path/to//mkl/lib/intel64" > > > -DMKL_INCLUDE_DIR="/path/to//mkl/include" -D > > > CMAKE_INSTALL_PREFIX=/path/to//gromacs-4.6.4/build-gpu/ -DGMX_MPI=ON > > > -DGMX_GPU=ON -DCUDA_HOST_COMPILER=/path/to/intel64/icc > > > -DCUDA_TOOLKIT_ROOT_DIR=/opt/CUDA-5.5/ /path/to/gromacs-4.6.4/ > > > " > > > > > > ------------------------------------------------------------------------------------------------------------------------ > > > Icc details : > > > icc version 13.0.1 (gcc version 4.4.6 compatibility) > > > > > > OpenMM is not available in environment. > > > > > > > > > > > > > > > On Mon, Feb 10, 2014 at 6:15 PM, Szilárd Páll <pall.szil...@gmail.com > > >wrote: > > > > > >> On Mon, Feb 10, 2014 at 1:27 PM, Chaitali Chandratre > > >> <chaitujo...@gmail.com> wrote: > > >> > Dear Sir, > > >> > > > >> > I have question w.r.t gromacs-4.6.4 installation with GPU support. > > >> > I have installed non-GPU vesion(for 4.6.4) and it works fine. > > >> > > > >> > But while compiling with gpu (-DGMX_GPU=ON > > >> > -DCUDA_TOOLKIT_ROOT_DIR=/opt/CUDA-5.5) > > >> > It gives compilation error. The node is having gpu card fermi and > > >> cuda5.5. > > >> > > > >> > Do I need to set some more things? > > >> > > >> Yes, perhaps you could tell us what the error is. :) > > >> > > >> -- > > >> Szilárd > > >> > > >> > > > >> > Thanks. > > >> > > > >> > -- > > >> > With Regards, > > >> > Chaitali > > >> > > > >> > "I know everything happens for a reason...But sometimes I wish I > knew > > >> what > > >> > the reason was !! " > > >> > -- > > >> > 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-usersor > > >> send a mail to gmx-users-requ...@gromacs.org. > > >> -- > > >> 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 gmx-users-requ...@gromacs.org. > > >> > > > > > > > > > > > > -- > > > With Regards, > > > Chaitali > > > > > > "I know everything happens for a reason...But sometimes I wish I knew > > what > > > the reason was !! " > > > -- > > > 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 gmx-users-requ...@gromacs.org. > > -- > > 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 gmx-users-requ...@gromacs.org. > > > > > > -- > With Regards, > Chaitali > > "I know everything happens for a reason...But sometimes I wish I knew what > the reason was !! " > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
