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Na klasteru su instalirane varijante programskog paketa Gromacs u serijskoj višedretvenoj i paralelnoj MPI izvedbi za CPU (klasični procesori) i GPU (grafički procesori).
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Verzija | Implementacija | Modul | Napomena |
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5.1.4 | single precision multithread | gromacs/5.1.4 | Koristiti isključivo uz *mpisingle |
5.1.4 | double precision multithread | gromacs/5.1.4-double | Koristiti isključivo uz *mpisingle |
5.1.4 | single precision MPI | gromacs/5.1.4-mvapich22 | |
5.1.4 | double precision MPI | gromacs/5.1.4-mvapich22-double | |
2018.4 | single precision multithread | gromacs/2018.4 | Koristiti isključivo uz *mpisingle |
2018.4 | double precision multithread | gromacs/2018.4-double | Koristiti isključivo uz *mpisingle |
2018.4 | single precision MPI | gromacs/2018.4-mvapich22 | |
2018.4 | double precision MPI | gromacs/2018.4-mvapich22-double | |
2018.4 | single precision multithread + GPU | gromacs/2018.4-gpu | Koristiti isključivo uz gpusingle |
2018.4 | single precision MPI + GPU | gromacs/2018.4-mvapich2-gpu |
CPU verzije
Primjer korištenja multithread višedretvene verzije:
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#$ -pe *mpisingle 8
module load gromacs/5.1.4
gmx mdrun -nt $NSLOTS -nice 0 -v -c conf30.gro -s topol30.tpr -px pullx30.xvg -pf pullf30.xvg -g md30.log -e ener30.edr -x traj30.xtc -cpi state.cpt -append |
Warning | ||
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Gromacs verzija 5.1.4 zahtijeva parametar "-nice 0", kod novijih verzija taj parametar nije potreban. |
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Code Block |
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#$ -pe *mpifull 56 module load gromacs/2018.4 mpirun_rsh -np $NSLOTS -hostfile $TMPDIR/machines -export-all gmx mdrun -ntomp 1 -v -c conf30.gro -s topol30.tpr -px pullx30.xvg -pf pullf30.xvg -g md30.log -e ener30.edr -x traj30.xtc -cpi state.cpt -append |
GPU verzije
Primjer korištenja višedretvene verzije:
Code Block |
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#$ -pe gpusingle 4
module load gromacs/2018.4-gpu
cuda-wrapper.sh gmx mdrun -nt $NSLOTS -v -c conf30.gro -s topol30.tpr -px pullx30.xvg -pf pullf30.xvg -g md30.log -e ener30.edr -x traj30.xtc -cpi state.cpt -append |
Warning | ||
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Aplikacija ( |
Primjer korištenja MPI verzije:
Code Block |
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#$ -pe *gpu 8
module load gromacs/2018.4-mvapich22-gpu
mvapich-wrapper.sh gmx mdrun -ntomp 1 -v -c conf30.gro -s topol30.tpr -px pullx30.xvg -pf pullf30.xvg -g md30.log -e ener30.edr -x traj30.xtc -cpi state.cpt -append |
Warning | ||
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Aplikacija (gmx) u paralelnoj izvedbi se mora pozivati s mvapich-wrapper.sh! |
Instalacija
CPU
Višedretvena verzija Gromacsa je prevedena Gromacs multithread je preveden s Intel 2019 i parametrima:
Code Block |
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module load intel export CC=icc export CXX=icc export F77=ifort export F90=ifort export FC=ifort export CFLAGS="-O3 -I/opt/intel/mkl/include/intel64/ilp64 -I/opt/intel/mkl/include -I/opt/intel/mkl/include/fftw" export LIBS="-O3 /opt/intel/mkl/lib/intel64/libmkl_blas95_ilp64.a /opt/intel/mkl/lib/intel64/libmkl_lapack95_ilp64.a -L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl" # avx single precision export DEFOPTS="-DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DCMAKE_C_FLAGS_RELEASE= -DCMAKE_CXX_FLAGS_RELEASE= -DCMAKE_INSTALL_PREFIX=/apps/gromacs/5.1.4/intel-single/avx -DGMX_FFT_LIBRARY=mkl -DGMX_SIMD=AVX_256 -DGMX_GPU=off" cmake3 -D GMX_DEFAULT_SUFFIX=OFF -D GMX_MPI=OFF -D GMX_DOUBLE=OFF $DEFOPTS . # avx2 single precision export DEFOPTS="-DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DCMAKE_C_FLAGS_RELEASE= -DCMAKE_CXX_FLAGS_RELEASE= -DCMAKE_INSTALL_PREFIX=/apps/gromacs/5.1.4/intel-single/avx2 -DGMX_FFT_LIBRARY=mkl -DGMX_GPU=off" cmake3 -D GMX_DEFAULT_SUFFIX=OFF -D GMX_MPI=OFF -D GMX_DOUBLE=OFF $DEFOPTS . # avx double precision export DEFOPTS="-DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DCMAKE_C_FLAGS_RELEASE= -DCMAKE_CXX_FLAGS_RELEASE= -DCMAKE_INSTALL_PREFIX=/apps/gromacs/5.1.4/intel-double/avx -DGMX_FFT_LIBRARY=mkl -DGMX_SIMD=AVX_256 -DGMX_GPU=off" cmake3 -D GMX_DEFAULT_SUFFIX=OFF -D GMX_MPI=OFF -D GMX_DOUBLE=ON $DEFOPTS . # avx2 double precision export DEFOPTS="-DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DCMAKE_C_FLAGS_RELEASE= -DCMAKE_CXX_FLAGS_RELEASE= -DCMAKE_INSTALL_PREFIX=/apps/gromacs/5.1.4/intel-double/avx2 -DGMX_FFT_LIBRARY=mkl -DGMX_GPU=off" cmake3 -D GMX_DEFAULT_SUFFIX=OFF -D GMX_MPI=OFF -D GMX_DOUBLE=ON $DEFOPTS . # install make make install |
Gromacs MPI verzija Gromacsa je preveden s Intel 2019 i MVAPICH 2.2 i parametrima:
Code Block |
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module load mpi/mvapich2-intel-2.2-x86_64
export CC=mpicc
export CXX=mpicxx
export F77=mpif77
export F90=mpif90
export FC=mpif90
export CFLAGS="-O3 -I/opt/intel/mkl/include/intel64/ilp64 -I/opt/intel/mkl/include -I/opt/intel/mkl/include/fftw"
export LIBS="-O3 /opt/intel/mkl/lib/intel64/libmkl_blas95_ilp64.a /opt/intel/mkl/lib/intel64/libmkl_lapack95_ilp64.a -L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"
# avx single precision
export DEFOPTS="-DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DCMAKE_C_FLAGS_RELEASE= -DCMAKE_CXX_FLAGS_RELEASE= -DCMAKE_INSTALL_PREFIX=/apps/gromacs/5.1.4/mvapich2-intel-2.2/avx -DGMX_FFT_LIBRARY=mkl -DGMX_SIMD=AVX_256 -DGMX_GPU=off"
cmake3 -D GMX_DEFAULT_SUFFIX=OFF -D GMX_MPI=ON -D GMX_DOUBLE=OFF $DEFOPTS .
# avx2 single precision
export DEFOPTS="-DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DCMAKE_C_FLAGS_RELEASE= -DCMAKE_CXX_FLAGS_RELEASE= -DCMAKE_INSTALL_PREFIX=/apps/gromacs/5.1.4/mvapich2-intel-2.2/avx2 -DGMX_FFT_LIBRARY=mkl -DGMX_GPU=off"
cmake3 -D GMX_DEFAULT_SUFFIX=OFF -D GMX_MPI=ON -D GMX_DOUBLE=OFF $DEFOPTS .
# avx double precision
export DEFOPTS="-DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DCMAKE_C_FLAGS_RELEASE= -DCMAKE_CXX_FLAGS_RELEASE= -DCMAKE_INSTALL_PREFIX=/apps/gromacs/5.1.4/mvapich2-intel-2.2-double/avx -DGMX_FFT_LIBRARY=mkl -DGMX_SIMD=AVX_256 -DGMX_GPU=off"
cmake3 -D GMX_DEFAULT_SUFFIX=OFF -D GMX_MPI=ON -D GMX_DOUBLE=ON $DEFOPTS .
# avx2 double precision
export DEFOPTS="-DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DCMAKE_C_FLAGS_RELEASE= -DCMAKE_CXX_FLAGS_RELEASE= -DCMAKE_INSTALL_PREFIX=/apps/gromacs/5.1.4/mvapich2-intel-2.2-double/avx2 -DGMX_FFT_LIBRARY=mkl -DGMX_GPU=off"
cmake3 -D GMX_DEFAULT_SUFFIX=OFF -D GMX_MPI=ON -D GMX_DOUBLE=ON $DEFOPTS .
# install
make
make install |
GPU
Višedretvena verzija Gromacsa je prevedena s Intel 2018 i Cuda 10.0 i parametrima:
Code Block |
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module load intel/2018
module load cuda/10-0
export CC=icc
export CXX=icc
export F77=ifort
export F90=ifort
export FC=ifort
export CFLAGS="-O3 -I/opt/intel/mkl/include/intel64/ilp64 -I/opt/intel/mkl/include -I/opt/intel/mkl/include/fftw"
export LIBS="-O3 /opt/intel/mkl/lib/intel64/libmkl_blas95_ilp64.a /opt/intel/mkl/lib/intel64/libmkl_lapack95_ilp64.a -L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"
# avx2 single precision
export DEFOPTS="-DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DCMAKE_C_FLAGS_RELEASE= -DCMAKE_CXX_FLAGS_RELEASE= -DCMAKE_INSTALL_PREFIX=/apps/gromacs/2018.4/intel-single-gpu/avx2 -DGMX_FFT_LIBRARY=mkl -DGMX_SIMD=AVX2_256 -DGMX_GPU=on"
cmake3 -D GMX_DEFAULT_SUFFIX=OFF -D GMX_MPI=OFF -D GMX_DOUBLE=OFF $DEFOPTS .
# install
make
make install |
MPI verzija Gromacsa je preveden s Intel 2019 i MVAPICH 2.2 i parametrima:
Code Block |
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module load mpi/mvapich2-intel2018-2.2-x86_64-cuda
export CC=mpicc
export CXX=mpicxx
export F77=mpif77
export F90=mpif90
export FC=mpif90
export CFLAGS="-O3 -I/opt/intel/mkl/include/intel64/ilp64 -I/opt/intel/mkl/include -I/opt/intel/mkl/include/fftw"
export LIBS="-O3 /opt/intel/mkl/lib/intel64/libmkl_blas95_ilp64.a /opt/intel/mkl/lib/intel64/libmkl_lapack95_ilp64.a -L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"
# avx2 single precision
export DEFOPTS="-DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DCMAKE_C_FLAGS_RELEASE= -DCMAKE_CXX_FLAGS_RELEASE= -DCMAKE_INSTALL_PREFIX=/apps/gromacs/2018.4/mvapich2-intel-2.2-gpu/avx2 -DGMX_FFT_LIBRARY=mkl -DGMX_SIMD=AVX2_256 -DGMX_GPU=on"
cmake3 -D GMX_DEFAULT_SUFFIX=OFF -D GMX_MPI=ON -D GMX_DOUBLE=OFF $DEFOPTS .
# install
make
make install |
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