Pour utiliser les modulefiles, consulter Environment Modules

inlinetoc

• http://www.abinit.org

• Pour les files d'attente du cluster Equip@méso, avec /scratch commun glusterfs

qsub parexemple.sh

parexemple.sh

#!/bin/bash
### shell du job:
#$ -S /bin/bash
### nom du job:
#$ -N pouet
### files d'attente:
#$ -q E5-2670deb64Z
### parallel environnement & nslots
#$ -pe mpi16_debian 48
### charge l'environnement utilisateur pour SGE
#$ -cwd
### exporte les variables d'environnement sur les noeuds d'exécution
#$ -V
 
HOMEDIR=$SGE_O_WORKDIR
 
## charge l'env
source /usr/share/modules/init/bash
module use /applis/PSMN/Modules
module load Base/psmn
module load Abinit/7.6.4
 
HOSTFILE=$TMPDIR/machines
 
cd $HOMEDIR
 
mpirun -np $NSLOTS -hostfile $HOSTFILE abinit-mpi < in.file > out.log

pose problème avec les librairies netcdf pré-installées sur l'OS

apt-get purge libnetcdf-dev netcdf-dbg libetsf-io-dev libhdf4-alt-dev libnetcdf-dev netcdf-dbg

make clean
source /usr/local/modeles/set_debian7-clean.sh
source /usr/local/modeles/openmpi-1.4.5-gnu-4.7.2-debian7.sh
./configure --prefix=/home/login/abinit --enable-mpi --enable-mpi-io --with-mpi-prefix=/softs/openmpi-1.4.5-gnu-4.7.2-debian7 --enable-64bit-flags --enable-fallbacks --disable-debug
make mj4

pose problème avec les librairies netcdf pré-installées sur l'OS

apt-get purge libnetcdf-dev netcdf-dbg libetsf-io-dev libhdf4-alt-dev libnetcdf-dev netcdf-dbg

make clean
source /usr/local/modeles/set_debian7-clean.sh
source /usr/local/modeles/openmpi-1.6.4-gnu-4.7.2-debian7.sh
./configure --prefix=/home/login/abinit --enable-mpi --enable-mpi-io --with-mpi-prefix=/softs/openmpi-1.6.4-gnu-4.7.2-debian7 --enable-64bit-flags --enable-fallbacks --disable-debug
make mj4

pose problème avec les libetsf-io pré-installées sur l'OS

apt-get purge etsf-io libetsf-io-dev

make clean
source /usr/local/modeles/set_debian7-clean.sh
OMPI_CC=/usr/bin/gcc-4.7 OMPI_CXX=/usr/bin/g++-4.7 OMPI_FC=/usr/bin/gfortran-4.7 CFLAGS="-mtune=generic -O2 -msse4a" FCFLAGS="-mtune=generic -ffree-line-length-none" CXXFLAGS="-mtune=generic" FC_LDFLAGS_EXTRA="-fopenmp" CC=mpicc.openmpi CXX=mpic++.openmpi FC=mpif90.openmpi ./configure --prefix=/softs/Debian7/Abinit/7.2.1/x86_64 --enable-mpi --enable-mpi-io --enable-mpi-trace --enable-64bit-flags --enable-gui --enable-netcdf --with-netcdf-libs="-L/usr/lib/ -lnetcdff -lnetcdf" --with-netcdf-incs="-I/usr/include" --enable-bigdft --with-linalg-flavor=custom  --with-linalg-incs="-I/usr/include/atlas" --with-linalg-libs="-L/usr/lib/atlas-base/atlas -llapack -lblas"
make mj4

• build sequentiel

mkdir tmp-seq
cd tmp-seq
source /usr/local/modeles/set_debian7-clean.sh
 
CFLAGS="-mtune=generic -O2 -msse4a" FCFLAGS="-mtune=generic -ffree-line-length-none" CXXFLAGS="-mtune=generic" ../configure --program-suffix="-seq" --prefix=/applis/PSMN/debian7/Abinit/7.6.4/full-debian7 --disable-mpi --enable-64bit-flags --enable-fallbacks --disable-debug
 
make mj4

• build openmpi

mkdir tmp-mpi
cd tmp-mpi
source /usr/local/modeles/set_debian7-clean.sh
 
OMPI_CC=/usr/bin/gcc-4.7 OMPI_CXX=/usr/bin/g++-4.7 OMPI_FC=/usr/bin/gfortran-4.7 CFLAGS="-mtune=generic -O2 -msse4a" FCFLAGS="-mtune=generic -ffree-line-length-none" CXXFLAGS="-mtune=generic" FC_LDFLAGS_EXTRA="-fopenmp" CC=mpicc.openmpi CXX=mpic++.openmpi FC=mpif90.openmpi ../configure --program-suffix="-mpi" --prefix=/applis/PSMN/debian7/Abinit/7.6.4/full-debian7 --enable-connectors --enable-fallbacks --enable-mpi --enable-mpi-io --enable-mpi-trace --enable-64bit-flags --enable-netcdf --with-netcdf-libs="-L/usr/lib/ -lnetcdff -lnetcdf" --with-netcdf-incs="-I/usr/include" --enable-bigdft --with-bigdft-flavor=abinit --with-linalg-flavor=custom  --with-linalg-incs="-I/usr/include/atlas" --with-linalg-libs="-L/usr/lib/atlas-base/atlas -llapack -lblas" --enable-libxc --with-libxc-incs="-I/usr/include" --with-libxc-libs="-L/usr/lib" --disable-debug --enable-scalapack --with-scalapack-libs="-lscalapack -lblacs"
 
make mj4