[gmx-users] gromacs 4.6.4 query
Mark Abraham
mark.j.abraham at gmail.com
Fri Feb 14 00:07:20 CET 2014
On Thu, Feb 13, 2014 at 9:03 AM, Chaitali Chandratre
<chaitujoshi at 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.szilard at gmail.com
> >wrote:
>
> > On Tue, Feb 11, 2014 at 6:12 AM, Chaitali Chandratre
> > <chaitujoshi at gmail.com> wrote:
> > > Dear Sir,
> > >
> > > Below is error message for gromacs-4.6.4 gpu enabled install:
> > >
> >
> ---------------------------------------------------------------------------------------------------------------------------
> > > make error :
> > >
> > > "[chaitalij at 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.szilard at gmail.com
> > >wrote:
> > >
> > >> On Mon, Feb 10, 2014 at 1:27 PM, Chaitali Chandratre
> > >> <chaitujoshi at 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-request at gromacs.org.
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> posting!
> > >>
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> > >>
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> > >> send a mail to gmx-users-request at 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
> > >
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> > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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> > posting!
> >
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> >
>
>
>
> --
> 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
>
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