set cpu alloc & cpu time from the namelist_exp.sh file

scripts/IRENE-AMD_Rome.env

@@ -31,8 +31,8 @@ if [ "${MODEL_OCE}" = "nemo" ] ; then
    export BDY="bdy/tr12_quik/from_obc"
    export DATA="/ccc/work/cont005/ra0542/hourdinc/data"
 elif [ "${MODEL_OCE}" = "croco" ] ; then
-   export INDIR="${WORKDIR}/${CONFIG}/inputs"
-#  export INDIR="/ccc/work/cont005/gen1140/chabertp/can11sen2_croco/inputs"
+#  export INDIR="${WORKDIR}/${CONFIG}/inputs"
+   export INDIR="/ccc/work/cont005/gen1140/hourdinc/ASAP/inputs"
 fi
 
 #-------------------------------------------------------------------------------

scripts/IRENE-AMD_Rome.header

@@ -25,8 +25,8 @@
 ############   CHANGER LA DOC INTEL par AMD
 
 #MSUB -q rome
-#MSUB -n 256         # number of MPI task
-#MSUB -c 1           # number of threads by MPI task (for OPENMP or to reserve more memory)
+#MSUB -n <mpi_task>         # number of MPI task
+#MSUB -c <cpu_per_task>     # number of threads by MPI task (for OPENMP or to reserve more memory)
 # #MSUB -N 4         # number of nodes to use   (better to use -c option to reserve more memory)
 #MSUB -x             # requests exclusive usage of allocated nodes.
 
@@ -37,18 +37,14 @@
 #=======  Reserve Time CPU
 
 #-------  Test Queue
-# #MSUB -Q test        #  1800 s max
-# #MSUB -T 1800        
+#MSUB -Q test        #  put 1800 s max for time
+#MSUB -T <max_cpu_time>       # 14400 s = 4 hours
 
-#------  Production Queue 
+#------  Production Queue for Intel
 # can11sen2cp :  (parent) LLm0=224, MMm0=288, N=50  (children) LLm0=200, MMm0=300, N=50  
 # ~ 07h40mn   for  agrif/pisces |  pdt=400  |  96 cores/ 4 nodes
 # ~ 05h20mn   for  agrif/pisces |  pdt=600  |  96 cores/ 4 nodes
 
-#MSUB -T 14400       # 4 hours
-# #MSUB -T 28800       # 8 hours
-# #MSUB -T 72000       # 20 hours
-
 
 #=======  Various
 #  #MSUB -M mem            # required amount of memory per core in Mo

scripts/IRENE-Intel_Skylake.env

@@ -31,8 +31,8 @@ if [ "${MODEL_OCE}" = "nemo" ] ; then
    export BDY="bdy/tr12_quik/from_obc"
    export DATA="/ccc/work/cont005/ra0542/hourdinc/data"
 elif [ "${MODEL_OCE}" = "croco" ] ; then
-   export INDIR="${WORKDIR}/${CONFIG}/inputs"
-#  export INDIR="/ccc/work/cont005/gen1140/chabertp/can11sen2_croco/inputs"
+#  export INDIR="${WORKDIR}/${CONFIG}/inputs"
+   export INDIR="/ccc/work/cont005/gen1140/hourdinc/ASAP/inputs"
 fi
 
 #-------------------------------------------------------------------------------

scripts/IRENE-Intel_Skylake.header

@@ -23,30 +23,26 @@
 ### skylake      up        79056      96   78650     310    1647       2    1642       3    3750  48   2  24   1
 
 #MSUB -q  skylake
-#MSUB -n 256         # number of MPI task
-#MSUB -c 1           # number of threads by MPI task (for OPENMP or to reserve more memory)
+#MSUB -n <mpi_task>         # number of MPI task
+#MSUB -c <cpu_per_task>     # number of threads by MPI task (for OPENMP or to reserve more memory)
 # #MSUB -N 4         # number of nodes to use   (better to use -c option to reserve more memory)
 #MSUB -x             # requests exclusive usage of allocated nodes.
 
-#MSUB -A  gen1140
+#MSUB -A gen1140
 #MSUB -m work,scratch,store
 
 
 #=======  Reserve Time CPU
 
 #-------  Test Queue
-#MSUB -Q test        #  1800 s max
-#MSUB -T 1800        
+#MSUB -Q test        #  put 1800 s max for time
+#MSUB -T <max_cpu_time>       # 14400 s = 4 hours
 
-#------  Production Queue 
+#------  Production Queue for Intel
 # can11sen2cp :  (parent) LLm0=224, MMm0=288, N=50  (children) LLm0=200, MMm0=300, N=50  
 # ~ 07h40mn   for  agrif/pisces |  pdt=400  |  96 cores/ 4 nodes
 # ~ 05h20mn   for  agrif/pisces |  pdt=600  |  96 cores/ 4 nodes
 
-# #MSUB -T 14400       # 4 hours
-# #MSUB -T 28800       # 8 hours
-# #MSUB -T 72000       # 20 hours
-
 
 #=======  Various
 #  #MSUB -M mem            # required amount of memory per core in Mo

scripts/JEAN-ZAY.cpu_info.sh

@@ -13,7 +13,7 @@ else
    running=true
 fi
 
-printf "\n\nrunning = ${running}\n"
+printf "running = ${running}\n"
 printf "verbose = ${verbose}\n"
 
 
@@ -172,8 +172,8 @@ if [ "$#" == "1" ]; then
 #  Pour un job en cours d'execution :
    if ${running}; then
 
-      printf "\n\n> scontrol show job ${JOBID2}\n\n"
-                    scontrol show job ${JOBID2}
+      printf "\n> scontrol show job ${JOBID2}\n\n"
+                  scontrol show job ${JOBID2}
    
 #     printf "\n\n> sstat  -j ${JOBID2}\n\n"
 #                   sstat  -j ${JOBID2}

scripts/JEAN-ZAY.env

@@ -31,8 +31,8 @@ if [ "${MODEL_OCE}" = "nemo" ] ; then
    export BDY="bdy/tr12_quik/from_obc"
    export DATA="/ccc/work/cont005/ra0542/hourdinc/data"
 elif [ "${MODEL_OCE}" = "croco" ] ; then
-   export INDIR="${WORKDIR}/${CONFIG}/inputs"
-#  export INDIR="/ccc/work/cont005/gen1140/chabertp/can11sen2_croco/inputs"
+#  export INDIR="${WORKDIR}/${CONFIG}/inputs"
+   export INDIR="/gpfswork/rech/eee/reee084/ASAP/inputs"
 fi
 
 #-------------------------------------------------------------------------------

scripts/JEAN-ZAY.header

@@ -28,9 +28,9 @@
 #      "scontrol show job $JOBID"  give all informations about the job (memory, core, node, time... )
 #-------------------------------------------------------------------------------
 
-#SBATCH --ntasks=120            # Total number of mpi task to use
+#SBATCH --ntasks=<mpi_task>            # Total number of mpi task to use
 # #SBATCH --ntasks-per-node=40    # number of mpi task per node
-#SBATCH --cpus-per-task=2       # --cpus-per-task=1              (default) 
+#SBATCH --cpus-per-task=<cpu_per_task>       # --cpus-per-task=1              (default) 
 #SBATCH --hint=nomultithread       # 1 mpi task per core   # for Slurm,  "multithread" = hyperthreading.
 
 # pour avoir plus de mémoire que la mémoire réservée par le nombre de coeur (4Go / coeur)
@@ -54,7 +54,7 @@
 ###SBATCH --qos=qos_cpu-t4 	      #  100h      | 4   nodes = 160 cores
 #SBATCH --qos=qos_cpu-dev             #  2h        | 128 nodes = 5120 cores 
 
-#SBATCH --time=02:00:00        #  max cpu time 
+#SBATCH --time=<max_cpu_time>       #  max cpu time 
  
 
 #-------------------------------------------------------------------------------
@@ -75,6 +75,7 @@ module load intel-compilers/19.0.4
 module load intel-mpi/19.0.4
 module load netcdf-fortran/4.5.2-mpi
 module load netcdf/4.7.2-mpi
+module load hdf5/1.10.5-mpi
 
 
 

scripts/namelist_exp.sh

-
 ############################# from namelist_exp.sh #############################
 #===============================================================================
 #  Namelist for the experiment
@@ -25,6 +24,7 @@ fi
 #-------------------------------------------------------------------------------
 export CONFIG=`pwd | awk -F"/" '{print $(NF-3)}'`
 export TITLE_EXP="Config Afrique du Sud  ASAP S. Pous  ("`date "+%d %m %Y"`" on ${COMPUTER})"
+printf "\n   ${TITLE_EXP}  \n\n"
 
 #-------------------------------------------------------------------------------
 #  Debug Modes
@@ -80,10 +80,14 @@ export USE_BIOLOGY=true
 
 # MPI
 export USE_MPI=true 
-   export NPROC_X=12
-   export NPROC_Y=10
-# adjust the COMPUTER header!!
- 
+if [ ${COMPUTER} == "JEAN-ZAY" ] ; then
+   export NPROC_X=12; export NPROC_Y=10; export CPU_PER_TASK=2
+elif [ ${COMPUTER} == "IRENE-Intel_Skylake" ] ; then
+   export NPROC_X=16; export NPROC_Y=16; export CPU_PER_TASK=2
+elif [ ${COMPUTER} == "IRENE-AMD_Rome" ] ; then
+   export NPROC_X=16; export NPROC_Y=16; export CPU_PER_TASK=2
+fi
+
 # OpenMP
 export USE_OPENMP=false 
    export NPP=4
@@ -93,6 +97,17 @@ export USE_XIOS=false
    export NXIOS=16 #4
    export NXIOSper=-1
  
+# Time CPU run
+if [ ${COMPUTER} == "JEAN-ZAY" ] ; then
+   export time_cpu_run="01:00:00"
+elif [ ${COMPUTER} == "IRENE-Intel_Skylake" ] ; then
+#  export time_cpu_run="01:00:00"
+   export time_cpu_run="00:30:00" # for Queue test max 30'
+elif [ ${COMPUTER} == "IRENE-AMD_Rome" ] ; then
+#  export time_cpu_run="01:00:00"
+   export time_cpu_run="00:30:00" # for Queue test max 30' #### if exists on AMD cpu
+fi
+ 
 # files to save in ascii jobdir after running 
 if [ "${MODEL_OCE}" == "croco" ] ; then 
    export PUT_FILES_OCE="croco.in* out_run.txt croco_cpp.txt listing*"

scripts/submitjob.sh

@@ -87,7 +87,9 @@ cd -
 #-------------------------------------------------------------------------------
 sed -e "s/<exp>/${ROOT_NAME_1}/g" \
     -e "s/<exp_lst>/${listing_root_name}/" \
-    -e "s/<5+agrifz>/$(( 5 + ${AGRIFZ} ))/" \
+    -e "s/<mpi_task>/$(( ${NPROC_X} * ${NPROC_Y} ))/" \
+    -e "s/<cpu_per_task>/${CPU_PER_TASK}/" \
+    -e "s/<max_cpu_time>/${time_cpu_run}/" \
     ./${COMPUTER}.header > HEADER_tmp
     cat HEADER_tmp ./common_definitions.sh ./namelist_exp.sh ./namelist_period.sh ./${COMPUTER}.env job.base.sh > ${JOBDIR_ROOT}/${jobname}
     \rm HEADER_tmp