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: [email protected]
[[email protected]] on behalf of Mark Abraham
[[email protected]]
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 <[email protected]> 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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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