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Dostupne verzije su:
| Verzija | Implementacija | Modul | Napomena |
|---|---|---|---|
| 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 | |
| 2018.6 | single precision multithread + Plumed | gromacs/2018.6 | Koristiti isključivo uz *mpisingle |
| 2018.6 | double precision multithread + Plumed | gromacs/2018.6-double | Koristiti isključivo uz *mpisingle |
| 2018.6 | single precision MPI + Plumed | gromacs/2018.6-mvapich22 | |
| 2018.6 | double precision MPI + Plumed | gromacs/2018.6-mvapich22-double | |
| 2018.6 | single precision multithread + GPU + Plumed | gromacs/2018.6-gpu | Koristiti isključivo uz gpusingle |
| 2018.6 | single precision MPI + GPU + Plumed | gromacs/2018.6-mvapich2-gpu | |
| 2020.6 | single precision MPI + OpenMP+ Plumed | gromacs/2020.6 | |
| 2020.6 | double precision MPI +OpenMP + Plumed | gromacs/2020.6-double | |
| 2020.6 | single precision multithread + GPU + Plumed | gromacs/2020.6-gpu | Koristiti isključivo uz gpusingle |
| 2020.6 | single precision MPI + GPU + Plumed | gromacs/2020.6-mvapich22-gpu | |
| 2021.4 | mixed precision MPI + OpenMP + Plumed | gromacs/2021.4-mvapich22 | |
| 2021.4 | double precision MPI + OpenMP + Plumed | gromacs/2021.4-mvapich22-double | |
| 2021.4 | mixed precision multithread + GPU + Plumed | gromacs/2021.4-gpu | Koristiti isključivo uz gpusingle |
| 2021.4 | mixed precision MPI + GPU + Plumed | gromacs/2021.4-mvapich22-gpu |
CPU verzije
Primjer korištenja višedretvene verzije:
...
| Code Block |
|---|
#$ -N gromacs-cpugpu #$ -pe gpu 3 #$ -l cores=6 #$ -cwd module load gromacs/2018.4-mvapich22-gpu mvapich-wrapper-nopin.sh gmx mdrun -ntomp 6 -v -s topol32.tpr -x traj.xtc -cpi state.cpt -append -c conf32.gro |
Instalacija
CPU
Višedretvena verzija Gromacsa je prevedena s Intel 2019 i parametrima:
| Code Block |
|---|
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 |
MPI verzija Gromacsa je preveden s Intel 2019 i MVAPICH 2.2 i parametrima:
| Code Block |
|---|
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 |
|---|
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 2018, MVAPICH 2.2 i CUDA 10.0 i parametrima:
| Code Block |
|---|
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 |