add submission script for Jolly Jumper

Author: Francesco Massimo

JJ_submission_script.sh

@@ -0,0 +1,51 @@
+#!/bin/bash
+#PBS -l nodes=1:ppn=24
+#PBS -q default
+#PBS -j oe
+
+#Set the correct modules available (see environment configuration)
+
+. /usr/share/Modules/init/bash
+
+source /usr/share/Modules/init/bash #Set the correct modules available
+unset MODULEPATH; module use /opt/exp_soft/vo.llr.in2p3.fr/modulefiles_el7
+
+#Load compilers
+module load compilers/icc/17.4.196 # for centos7
+module load mpi/openmpi/4.1.1-ib-icc
+module load hdf5/1.10.5-icc-omp4.1.1
+module load python/3.7.0
+module load compilers/gcc/4.9.2
+module load h5py/hdf5_1.10.5-icc-omp4.1.1-py3.7.0
+
+
+export OMPI_CC=icc
+export OMPI_CXX=icpc
+export OMPI_F90=ifort
+export OMPI_F77=ifort
+export OMPI_FC=ifort
+export CC=mpicc
+export CXX=mpicxx
+export FC=mpif77
+
+
+export PS1="\A \u \[\033[01;34m\]\h:\w\[\033[01;31m\] > \[\033[00m\]"
+
+
+
+#Go to current directory
+cd $PBS_O_WORKDIR
+
+# -bind-to-core to fix a given MPI process to a fixed set of cores.
+export OMP_NUM_THREADS=12
+export OMP_SCHEDULE=DYNAMIC
+
+
+export KMP_AFFINITY=granularity=fine,compact,1,0
+
+export PATH=$PATH:/opt/exp_soft/vo.llr.in2p3.fr/GALOP/beck
+
+#Specify the number of sockets per node in -mca orte_num_sockets
+#Specify the number of cores per sockets in -mca orte_num_cores
+mpirun -mca orte_num_sockets 2 -mca orte_num_cores 12  -map-by ppr:1:socket:pe=12 -n 2 -x OMP_NUM_THREADS -x OMP_SCHEDULE ./smilei InputNamelist.py 2>&1 | tee smilei.log
+