[gmx-users] Installing gromacs 5.0.2 single precision with CUDA and MPI ??

Soren Wacker swacker at ucalgary.ca
Fri Nov 21 02:32:58 CET 2014 

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: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Wednesday, November 19, 2014 6:08 PM
To: gmx-users at gromacs.org
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: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abraham at gmail.com]
> 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 <swacker at ucalgary.ca> 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
>>
>>
>> --
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--
==================================================

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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