Gromacs je preveden s Intel 2019 i MVAPICH2 2.2 i parametrima:
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" export DEFOPTS="-DGMX_BUILD_MDRUN_ONLY=on -D BUILD_SHARED_LIBS=OFF -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=/usr -DGMX_FFT_LIBRARY=mkl -DGMX_SIMD=None" 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 precision cmake3 -D GMX_DEFAULT_SUFFIX=OFF -D GMX_BINARY_SUFFIX=_d -D GMX_MPI=ON -D GMX_DOUBLE=ON $DEFOPTS |
Dostupne verzije su:
Verzija | Modul |
---|---|
5.1.4 | gromacs/5.1.4 |
2018.3 | gromacs/2018.3 |
Primjer korištenja:
module load gromacs/2018.4 mpirun_rsh -np $NSLOTS -hostfile $TMPDIR/machines mdrun ... |
OBAVEZNO koristiti uz mpisingle, te ne širiti proces na više od 16 jezgri |