| Les deux révisions précédentesRévision précédenteProchaine révision | Révision précédente |
| documentation:tools:software:abinit [2020/06/12 08:59] – [Abinit] ltaulell | documentation:tools:software:abinit [2025/03/12 14:14] (Version actuelle) – supprimée ltaulell |
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| ====== Abinit ====== | |
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| <note warning>update needed</note> | |
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| ^ 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 | | |
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| Pour utiliser les modulefiles, consulter [[documentation:tools:modules|Environment Modules]] | |
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| ===== Site officiel ===== | |
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| * http://www.abinit.org | |
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| ====== Script de soumission (exemple) ====== | |
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| * Pour les files d'attente du cluster Equip@méso, avec /scratch commun glusterfs | |
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| ''qsub parexemple.sh'' | |
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| <code bash 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 | |
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| HOMEDIR=$SGE_O_WORKDIR | |
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| ## charge l'env | |
| source /usr/share/modules/init/bash | |
| module use /applis/PSMN/Modules | |
| module load Base/psmn | |
| module load Abinit/7.6.4 | |
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| HOSTFILE=$TMPDIR/machines | |
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| cd $HOMEDIR | |
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| mpirun -np $NSLOTS -hostfile $HOSTFILE abinit-mpi < in.file > out.log | |
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| </code> | |
| ====== Doc admin-sys PSMN ====== | |
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| ===== build -mnative abinit 7.2.1 / openmpi 1.4.5 / gcc 4.7.2 / Debian7 ===== | |
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| :!: pose problème avec les librairies netcdf pré-installées sur l'OS | |
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| <code> | |
| apt-get purge libnetcdf-dev netcdf-dbg libetsf-io-dev libhdf4-alt-dev libnetcdf-dev netcdf-dbg | |
| </code> | |
| |
| <code bash> | |
| 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 | |
| </code> | |
| |
| <note warning>marche pas</note> | |
| ===== build -mnative abinit 7.2.1 / openmpi 1.6.4 / gcc 4.7.2 / Debian7 ===== | |
| |
| :!: pose problème avec les librairies netcdf pré-installées sur l'OS | |
| |
| <code> | |
| apt-get purge libnetcdf-dev netcdf-dbg libetsf-io-dev libhdf4-alt-dev libnetcdf-dev netcdf-dbg | |
| </code> | |
| |
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| <code bash> | |
| 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 | |
| </code> | |
| |
| <note warning>marche pas</note> | |
| ===== build -mgeneric sse4a abinit 7.2.1 / full Debian7 (openmpi 1.4.5 / gcc 4.7.2 + libs) ===== | |
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| :!: pose problème avec les libetsf-io pré-installées sur l'OS | |
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| <code> | |
| apt-get purge etsf-io libetsf-io-dev | |
| </code> | |
| |
| <code bash> | |
| 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 | |
| </code> | |
| |
| <note tip>build OK sur dl165comp, | |
| cible ''/softs/Debian7/Abinit/7.2.1/x86_64'', | |
| modèle + module-env OK.</note> | |
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| ===== build -mgeneric sse4a abinit 7.6.4 / full Debian7 (openmpi 1.4.5 / gcc 4.7.2 + libs) ===== | |
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| * build sequentiel | |
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| <code bash> | |
| mkdir tmp-seq | |
| cd tmp-seq | |
| source /usr/local/modeles/set_debian7-clean.sh | |
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| 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 | |
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| make mj4 | |
| </code> | |
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| * build openmpi | |
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| <code bash> | |
| mkdir tmp-mpi | |
| cd tmp-mpi | |
| source /usr/local/modeles/set_debian7-clean.sh | |
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| 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" | |
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| make mj4 | |
| </code> | |
| |
| <note tip>build OK sur dl175comp, | |
| cible ''/applis/PSMN/debian7/Abinit/7.6.4/full-debian7'', module-env OK.</note> | |
