| Panel | ||||||
|---|---|---|---|---|---|---|
|
Modulefiles
Na računalnom klasteru Isabella koristi se alat Modulefiles za podršku instalacije više različitih verzija istih programa. Za svaku verziju dostupnog programa pripremljen je modul u kojem je definirano koje varijable okoline se postavljaju prilikom aktivacije modula. Osnovna naredba za rad s Modulefiles je module. Sve izmjene nad varijablama okoline odnose se isključivo za aktivnu sesiju, odnosno za pokrenuti posao. Stoga je module potrebno aktivirati u kod svakog podnošenja posla.
...
| Code Block |
|---|
module load mpi/openmpi3-intel-x86_64 mpirun -np $NSLOTS -machinefile $TMPDIR/machines applikacija |
Abinit
Abinit je preveden s Intel 2019 i MVAPICH2 2.2 i parametrima:
| Code Block |
|---|
export FCFLAGS="-O2 -DLINUX -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -ffree-line-length-0"
export CFLAGS="-O2 -DLINUX -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE"
export CXXFLAGS=$CFLAGS
export CPPFLAGS=$CFLAGS
./configure CC=mpicc CXX=mpicxx FC=mpif90 FCFLAGS="-O2" CFLAGS="-O2" CXXFLAGS="-O2" --with-fc-vendor=intel -with-fft-flavor=fftw3-mkl --with-fft-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core" --with-linalg-flavor=mkl --enable-mpi --with-mpi-prefix=/usr/lib64/mvapich2-intel-2.2 --enable-64bit-flags --disable-debug --with-dft-flavor="none" --with-trio-flavor="none" --enable-mpi-inplace --enable-mpi-ioDostupne verzije su: |
Dostupne verzije su:
...
Primjer korištenja:
| Code Block |
|---|
module load abinit/8.8.4
mpirun_rsh -np $NSLOTS -hostfile $TMPDIR/machines abinit -i input_files |
Abyss
Gaussian
Svim zaposlenicima i suradnicima Sveučilišta u Zagrebu dostupan je Gaussian. Na Isabelli su instalirane tri verzije:
- Gaussian 3
- Gaussian 9 verzija D01
- Gaussian 16 verzija A03
Za Gaussian nisu pripremljeni moduli nego se pokreće pomoću pripremljenih skripti:
- /usr/local/bin/dog03-64
- /usr/local/bin/dog09
- /usr/local/bin/dog16
Bitno: nužno je koristiti paralelne okoline *mpisingle.
| Code Block |
|---|
#!/bin/bash
#$ -N gauss
#$ -cwd
#$ -pe *mpisingle 28
#$ -e error/
#$ -o output/
dog09 ulaz.com |
Gromacs
Quantum Espresso je preveden s Intel 2019 i MVAPICH2 2.2 i parametrima:
| Code Block |
|---|
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:
...
Primjer korištenja:
| Code Block |
|---|
module load gromacs/2018.4
mpirun_rsh -np $NSLOTS -hostfile $TMPDIR/machines mdrun ... |
Quantum Espresso
Quantum Espresso je preveden s Intel 2019 i MVAPICH2 2.2 i parametrima:
| Code Block |
|---|
export LIBMPI=-lmpich
export CC=icc
export CXX=icc
export FC=ifort
export MPIF90=mpif90
export FCFLAGS='-I/opt/intel/mkl/include/intel64/ilp64 -I/opt/intel/mkl/include -I/opt/intel/mkl/include/fftw'
export CFLAGS='-I/opt/intel/mkl/include/intel64/ilp64 -I/opt/intel/mkl/include -I/opt/intel/mkl/include/fftw'
export FFLAGS='-I/opt/intel/mkl/include/intel64/ilp64 -I/opt/intel/mkl/include -I/opt/intel/mkl/include/fftw'
export MPI_LIBS='-L/usr/lib64/mvapich2-intel-2.2/lib -lmpich'
export BLAS_LIBS='-L/opt/intel/mkl/lib/intel64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl'
export LAPACK_LIBS='/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 FFT_LIBS='/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 SCALAPACK_LIBS='/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'
./configure --enable-parallel --with-scalapack=intel |
Dostupne verzije su:
...
quantum-espresso/6.3
Primjer korištenja:
| Code Block |
|---|
module load quantum-espresso/6.3
mpirun_rsh -np $NSLOTS -hostfile $TMPDIR/machines $QE_DIR/pw.x ... |