Ceci est une ancienne révision du document !
Version | Compilateur | Interconnexion | chemin d'accès | OS | modèle de configuration |
---|---|---|---|---|---|
6.12.3 | gnu-4.6.3 | Infiniband | /softs/Abinit/6.12.3/openmpi-1.4.5-gnu-4.6.3 | Centos 5 | N/A |
6.12.3 | intel-12.0.084 | Infiniband | /softs/Abinit/6.12.3/openmpi-1.4.3-intel-12.0.084 | Centos 5 | N/A |
7.2.1 | gnu-4.7.2 | Infiniband | /softs/Debian7/Abinit/7.2.1/x86_64 | Debian 7 | /usr/local/modeles/Abinit-7.2.1-fulldebian7.sh |
7.6.4 | gnu-4.7.2 | Infiniband | /applis/PSMN/debian7/Abinit/7.6.4/full-debian7 | Debian 7 | modulefile Abinit/7.6.4 |
Pour utiliser les modulefiles, consulter Environment Modules
qsub 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
/softs/Debian7/Abinit/7.2.1/x86_64
,
modèle + module-env OK.
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
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
/applis/PSMN/debian7/Abinit/7.6.4/full-debian7
, module-env OK.