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

Soren Wacker swacker at ucalgary.ca
Fri Nov 21 19:28:04 CET 2014 

Thanks Mark!

It works using the GNU compiler instead of the intel compiler. 
Now everything works.
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: Friday, November 21, 2014 2:22 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Installing gromacs 5.0.2 single precision with CUDA and MPI ??

On Fri, Nov 21, 2014 at 2:32 AM, Soren Wacker <swacker at ucalgary.ca> wrote:

> 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?
>

Not on the Gromacs end. If your tools are set up correctly then things will
work. First, get a test CUDA+MPI program to work - consult your sysadmins.
You will likely get better performance and have fewer troubles with gcc,
anyway.

Mark

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
> >>
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
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> >>
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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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