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 multithread | gromacs/5.1.4-mvapich22-double | |
| 2018.3 | gromacs/2018.3 |
Primjer korištenja:
| Code Block |
|---|
module load gromacs/2018.4
mpirun_rsh -np $NSLOTS -hostfile $TMPDIR/machines mdrun ... |
| Warning |
|---|
OBAVEZNO koristiti uz mpisingle, te ne širiti proces na više od 16 jezgri |
Gromacs multithread je preveden s Intel 2019 i MVAPICH2 2.2 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="-DGMX_BUILD_MDRUN_ONLY=on-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 BUILD_SHARED_LIBS=OFF GMX_MPI=OFF -D GMX_DOUBLE=OFF $DEFOPTS . # avx2 single precision export DEFOPTS="-DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DGMX_X11=ON -DCMAKE_C_FLAGS_RELEASE= -DCMAKE_CXX_FLAGS_RELEASE= -DCMAKE_INSTALL_PREFIX=/usrapps/gromacs/5.1.4/intel-single/avx2 -DGMX_FFT_LIBRARY=mkl -DGMX_SIMDGPU=Noneoff" export CC=mpicc export CXX=mpicxx export F77=mpif77 export F90=mpif90 export FC=mpif90 # single precision cmake3 -D GMX_MPI=ON -D GMX_DOUBLE=ON $DEFOPTS # double precisioncmake3 -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_BINARY_SUFFIX=_dMPI=OFF -D GMX_MPIDOUBLE=ON $DEFOPTS -D GMX_DOUBLE=ON $DEFOPTS |
Dostupne verzije su:
...
. # 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 |
...
Primjer korištenja:
| Code Block |
|---|
module load gromacs/2018.4
mpirun_rsh -np $NSLOTS -hostfile $TMPDIR/machines mdrun ... |
| Warning |
|---|
OBAVEZNO koristiti uz mpisingle, te ne širiti proces na više od 16 jezgri/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 |