Merge branch 'develop' of https://dci-gitlab.cines.fr/dci/abs into develop

NEMO/README.md

@@ -11,26 +11,26 @@ Here I describe that this template is not performing any scientific simulation,
 Technical information:
 ----------------------
 
-* website : http://this.url.doesnot.work 
-* Scientific domain : none 
-* Language : C/C++/Fortran/Python
-* Parallelism : MPI + OpenMP
-* GPU acceleration : Yes (CUDA) 
+
+* Scientific domain :climate
+* Language : Fortran
+* Parallelism : MPI + 
+* GPU acceleration : No
 * Scalability : high
-* Vectorization: poor
+* Vectorization: moderate
 
 
 Compilation and simulation:
 ===========================
 
-Here we describe the different phases from the download to the validation of the simulation.
+
 
 Download:
 ---------
 
 Information (if needed) about how to get the sources.
 
-For instance:
+
 ```
 ./download.sh
 ```
@@ -38,17 +38,13 @@ For instance:
 Compile:
 --------
 
-Information (if needed) about how to compile the application. 
-
-For instance:
-
-Compile the code using:
+See
 ```
-source machines/occigen-bdw/env
+
 ./compile.sh
 ```
 
-`machines/occigen-bdw/env` contains the information for compilation (module load gcc openmpi lapack hdf5 ...)
+
 
 Run and validate the simulation:
 --------------------------------

NEMO/machines/irene-amd/batch_small.slurm

+
+#
+#  BENCH launching scripts for Irene
+# Modified for Irene 30/12/2019
+#  To be modified for other machines
+#
+#set -u
+set -x
+#
+cores=2160
+ncore_node=108 # 108 cores used over 128 ( bi-proc 64 cores)
+resolution=1
+dateref=20200210
+timejob=3600
+
+machine=$( hostname | sed -e "s/[0-9]*//g" )
+#
+# number of processes for each executable
+    nproc_exe1=$( echo $cores | bc )
+  (( nproc = $nproc_exe1 ))
+(( nnode = $nproc / $ncore_node ))
+
+nnode=20
+
+[ $nnode -lt 1 ] && nnode=1
+
+nproc5=$( printf "%05d\n" ${nproc_exe1} )
+
+jobname=$HOME/binrun/jobbench
+
+    cat > $jobname << EOF
+#!/bin/bash
+#MSUB -r bench${nproc5}
+#MSUB -m work,scratch
+#MSUB -n ${nproc_exe1}
+#MSUB -N ${nnode}
+#MSUB -T $timejob
+#MSUB -e bench_${resolution}_${nproc5}_%I.eo
+#MSUB -o bench_${resolution}_${nproc5}_%I.eo
+#MSUB -j oe
+#MSUB -x
+#MSUB -q rome
+#MSUB -A tgcc0090
+#==========================================
+set -u
+module load  intel/19.0.5.281
+module load mpi/openmpi/4.0.1
+module load hdf5
+module load  netcdf-c/4.6.0
+module load netcdf-fortran/4.4.4
+#
+set -x
+echo " avant aller dans le repertoire de soumission"
+pwd
+cd \${BRIDGE_MSUB_PWD}/
+pwd
+ls
+#echo $OWN_CCCSCRATCHDIR
+#cd $OWN_CCCSCRATCHDIR
+EXPjob=EXP_${resolution}_${nproc5}_${dateref}
+#
+mkdir -p ${EXPjob}
+cp ${BRIDGE_MSUB_PWD}/tests/BENCH/EXP00/* ${EXPjob}
+ls ${EXPjob}
+
+#rsync -av --exclude="*eo" EXPREF/ \${EXPjob}/
+#rsync -av EXP00/nemo \${EXPjob}/nemo
+cd \${EXPjob}
+ls -la
+
+#jpni=${cores/\**/}
+#jpnj=${cores/?*\*/}
+jpni=45
+jpnj=48
+
+sed -e "s/jpni *=.*/jpni = \${jpni}/" -e "s/jpnj *=.*/jpnj = \${jpnj}/" namelist_cfg_orca${resolution}_like > namelist_cfg
+
+time ccc_mprun -n \${BRIDGE_MSUB_NPROC} ./nemo > jobout_${resolution}_${nproc5}_${dateref}
+
+ls -lrt
+rm -rf *.nc
+cp *  \${BRIDGE_MSUB_PWD}/.
+EOF
+cat $jobname
+
+    ccc_msub $jobname
+