[gmx-users] gromacs 4.6.4 query
Chaitali Chandratre
chaitujoshi at gmail.com
Thu Feb 13 09:03:36 CET 2014
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?
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-users or
> >> 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!
> >>
> >> * 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-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
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>
--
With Regards,
Chaitali
"I know everything happens for a reason...But sometimes I wish I knew what
the reason was !! "
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