Table of Contents

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 show ime_modula

Tip
Svaki znanstveni softver koji je besplatan dostupan je akademskoj i znanstvenoj zajednici. Korisnici mogu zatražiti zahtjev za njegovu instalaciju putem kontakta isabella@srce.hr.

Prevodioci

Intel

U tablici su navedene dostupne verzije Intel prevodioca prevodilaca i pripadni moduli. Preporuča se korištenje najnovije verzije - Intel 2019.

Verzija	Modul
Intel 2019	intel/2019
Intel 2018	intel/2018
Intel 2017	intel/2017

MPI

Za prevođenja pograma koriste se:

icc - prevodilac za C
ifort - prevodilac za Fortran.

Instalirane su i matematičke knjižnice Intel MKL (engl. Math Kernel Library) koje se nalaze u $MKLROOT. Upute za korištenje knjižnica: MKL Developer Guide. Parametri za prevođenje u paralelnih aplikacija u Fortranu:

Code Block

export FFLAGS="-i8 -I${MKLROOT}/include/intel64/ilp64 -I${MKLROOT}/include"
export FCFLAGS=$FFLAGS
export LIBS="${MKLROOT}/lib/intel64/libmkl_blas95_ilp64.a ${MKLROOT}/lib/intel64/libmkl_lapack95_ilp64.a -L${MKLROOT}/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"

Koristan link za prevođenje aplikacija s korištenjem knjižnica Intel MKL: Intel MKL link advisor.

Intel oneAPI

Dostupne verzije Intel oneAPI prevodilacaU U tablici su navedene dostupne verzije knjižnica MPI Intel oneAPI prevodilaca i pripadni moduli. Preporuča se korištenje verzija pripremljenih s Intel prevodiocimanajnovije verzije - Intel 2019.

Verzija

Prevodilac

	Modul

MVAPICH2 2.0GNU 4.8.5

mpi/mvapich2-2.0-x86_64

mpi/mvapich2-x86_64

MVAPICH2 2.2GNU 4.8.5mpi/mvapich2-2.2-x86_64MVAPICH2 2.0Intel 2019

mpi/mvapich2-intel-2.0-x86_64

mpi/mvapich2-intel-x86_64

MVAPICH2 2.2Intel 2019mpi/mvapich2-intel-2.2-x86_64OpenMPI 1.10GNU 4.8.5mpi/openmpi-x86_64OpenMPI 3.0GNU 4.8.5mpi/openmpi3-x86_64OpenMPI 1.10Intel 2019mpi/openmpi-intel-x86_64OpenMPI 2.1Intel 2017openmpi21-intel-x86_64OpenMPI 3.0Intel 2019mpi/openmpi3-intel-x86_64

MVAPICH2

Primjer pokretanja aplikacije prevedene s MVAPICH2 2.2:

Code Block
module load mpi/mvapich2-intel-2.2-x86_64 mpirun_rsh -np $NSLOTS -hostfile $TMPDIR/machines applikacija

OpenMPI

Primjer pokretanja aplikacije prevedene s OpenMPI 3:

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:

...

Intel oneAPI Compilers 2022

2022.0.2

Za prevođenja pograma koriste se:

icc - Intel(R) C++ Compiler Classic
icpc - Intel(R) C Compiler Classic
ifort - Intel(R) Fortran Compiler Classic
icx - Intel(R) oneAPI C Compiler
icpx - Intel(R) oneAPI C++ Compiler
ifx - Intel(R) Fortran Compiler
dpcpp - Intel(R) oneAPI DPC++ (Data Parallel C++)

Primjer:

Code Block
module load oneAPI/intel-oneapi-compilers-2022.0.2 icx --version

GCC

Različite verzije GNU C i C++ prevodilaca su na klaster instalirane iz Software Collections repozitorija.

U tablici su navedene dostupne verzije GNU C i C++ prevodilaca i pripadni moduli.

Verzija	Modul
GCC 7.3.1	gcc/7
GCC 8.2.1	gcc/8
GCC 9.3.1	gcc/9

Primjer:

Code Block

title	GCC 8

module load gcc/8
gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/opt/rh/devtoolset-8/root/usr --mandir=/opt/rh/devtoolset-8/root/usr/share/man --infodir=/opt/rh/devtoolset-8/root/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --with-default-libstdcxx-abi=gcc4-compatible --enable-plugin --enable-initfini-array --with-isl=/builddir/build/BUILD/gcc-8.2.1-20180905/obj-x86_64-redhat-linux/isl-install --disable-libmpx --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 8.2.1 20180905 (Red Hat 8.2.1-3) (GCC)

PGI

Dostupan je i PGI Community Edition Version 19.10 prevodioc.

Verzija	Modul
PGI Community Edition Version 19.10	pgi/19.10

Za prevođenja pograma koriste se:

pgcc - prevodilac za C
pgc++ - prevodilac za C++
pgfortran - prevodilac za Fortran.

Primjer:

Code Block

title	PGI 19.10

module load pgi/19.10
pgcc --version
pgc++ --version
pgfortran --version

NVIDIA HPC SDK

Knjižnice i prevodioci za NVIDIA GPU-ove. Više informacija možete pronaći na adresi: https://developer.nvidia.com/hpc-sdk.

	Verzija	Modul
NVIDIA HPC SDK	20.7	nvhpc/20.7
	21.5	nvhpc/21.5
	22.2	nvhpc/22.2
NVIDIA HPC SDK bez prevodioca	20.7	nvhpc-byo-compiler/20.7
	21.5	nvhpc-byo-compiler/21.5
	22.2	nvhpc-byo-compiler/22.2
NVIDIA HPC SDK bez MPI	20.7	nvhpc-nompi/20.7
	21.5	nvhpc-nompi/21.5
	22.2	nvhpc-nompi/22.2

Za prevođenja pograma koriste se:

nvc - prevodilac za C
nvc++ - prevodilac za C++
nvfortran - prevodilac za Fortran.

MPI

U tablici su navedene dostupne verzije knjižnica MPI i pripadni moduli. Preporuča se korištenje verzija pripremljenih s Intel prevodiocima.

Verzija	Prevodilac	Modul
MVAPICH2 2.0	GNU 4.8.5	mpi/mvapich2-2.0-x86_64 mpi/mvapich2-x86_64
MVAPICH2 2.2	GNU 4.8.5	mpi/mvapich2-2.2-x86_64
MVAPICH2 2.3	GNU 4.8.5	mpi/mvapich23-x86_64
MVAPICH2 2.0	Intel 2017	mpi/mvapich2-intel2017-2.0-x86_64 mpi/mvapich2-intel2017-x86_64
MVAPICH2 2.2	Intel 2017	mpi/mvapich2-intel2017-2.2-x86_64
MVAPICH2 2.2	Intel 2017, CUDA 9.0	mpi/mvapich2-intel2017-cuda90-2.2-x86_64
MVAPICH2 2.0	Intel 2018	mpi/mvapich2-intel2018-x86_64 mpi/mvapich2-intel2018-2.0-x86_64
MVAPICH2 2.2	Intel 2018	mpi/mvapich2-intel2018-2.2-x86_64
MVAPICH2 2.2	Intel 2018, CUDA 10.0	mpi/mvapich2-intel2018-cuda-2.2-x86_64
MVAPICH2 2.0	Intel 2019	mpi/mvapich2-intel-2.0-x86_64 mpi/mvapich2-intel-x86_64
MVAPICH2 2.2	Intel 2019	mpi/mvapich2-intel-2.2-x86_64
MVAPICH2 2.2	Intel 2019, CUDA 10.1	mpi/mvapich2-intel2019-cuda101-2.2-x86_64
OpenMPI 1.10	GNU 4.8.5	mpi/openmpi-x86_64
OpenMPI 3.0	GNU 4.8.5	mpi/openmpi3-x86_64
OpenMPI 3.1	GNU 4.8.5	mpi/openmpi31-x86_64
OpenMPI 4.1	GNU 4.8.5	mpi/openmpi41-x86_64
OpenMPI 1.10	Intel 2019	mpi/openmpi-intel-x86_64
OpenMPI 1.10	Intel 2019, CUDA 10.0	mpi/openmpi-intel-cuda-x86_64
OpenMPI 2.1	Intel 2017	openmpi21-intel-x86_64
OpenMPI 3.0	Intel 2019	mpi/openmpi3-intel-x86_64
OpenMPI 3.0	Intel 2019, CUDA 10.0	mpi/openmpi3-intel-cuda-x86_64
OpenMPI 3.1	Intel 2019	mpi/openmpi31-intel-x86_64
OpenMPI 4.1	Intel 2019	mpi/openmpi41-intel-x86_64
OpenMPI 3.1	PGI Community Edition Version 19.10	mpi/openmpi31-pgi-x86_64
Intel MPI 2021.5	Intel MPI 2021	oneAPI/intel-oneapi-mpi-2021.5.1

MVAPICH2

Primjer pokretanja aplikacije prevedene s MVAPICH2 2.2:

Code Block
module load mpi/mvapich2-intel-2.2-x86_64 mpirun_rsh -np $NSLOTS -hostfile $TMPDIR/machines -export-all applikacija

OpenMPI

Primjer pokretanja aplikacije prevedene s OpenMPI 3:

Code Block
module load mpi/openmpi3-intel-x86_64 mpirun -np $NSLOTS -machinefile $TMPDIR/machines applikacija

Intel MPI

Primjer pokretanja aplikacije prevedene s Intel MPI:

Code Block
module load oneAPI/intel-oneapi-mpi-2021.5.1 mpirun -np $NSLOTS -hosts applikacija

Korisničke aplikacije

Informacije o korisničkim aplikacijama koje održava Srce možete pronaći na stranicama:

Children Display

Primjer korištenja:

Code Block
module load abinit/8.8.4 mpirun_rsh -np $NSLOTS -hostfile $TMPDIR/machines abinit -i input_files

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.

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:

...

Space shortcuts

Page tree

Versions Compared

Old Version 18

New Version Current

Key

Modulefiles

Prevodioci

Intel

MPI

Intel oneAPI

MVAPICH2

OpenMPI

Abinit

GCC

PGI

NVIDIA HPC SDK

MPI

MVAPICH2

OpenMPI

Intel MPI

Korisničke aplikacije

Gaussian

Gromacs

Quantum Espresso

Space shortcuts

Page tree

Page History

Versions Compared

Old Version 18

New Version Current

Key

Modulefiles

Prevodioci

Intel

MPI

Intel oneAPI

MVAPICH2

OpenMPI

Abinit

GCC

PGI

NVIDIA HPC SDK

MPI

MVAPICH2

OpenMPI

Intel MPI

Korisničke aplikacije

Gaussian

Gromacs

Quantum Espresso