Run a parallel job in the batch system

Author: J. Ghattas
Last revision: 2020/03/03

First prepare a run directory following the how to How to run a simple test case with ORCHIDEE. Link also the executable for XIOS:

ln -s ../modipsl/bin/xios_server_prod.exe .

Secondly, prepare according to the examples below, a job file corresponding to computer environment and the choice of parallelization and submit it.

irene skylake at TGCC

#!/bin/ksh
#MSUB -r test             # name of the job
#MSUB -o Script_Output    # name of output file for standard messages
#MSUB -e Script_Output    # name of output file for error messages
#MSUB -eo
#MSUB -n 32               # Request number of cores
#MSUB -T 1800             # Time limit in seconds
#MSUB -q skylake
#MSUB -m store,work,scratch
#MSUB -A gen6328          # Set your project id. Most people working with
#                         # ORCHIDEE at LSCE belong to project gen6328


## Go to current folder and execute the model
cd ${BRIDGE_MSUB_PWD}


## Source same modules as used during compilation. See examples below depending on the configurations used.
# For ORCHIDEE_3 and more recent offline versions or coupled v6.2 and more recent versions:
#source ../modipsl/config/ORCHIDEE_OL/ARCH/arch-X64_IRENE.env
#source ../modipsl/config/LMDZOR_v6/ARCH/arch-X64_IRENE.env
# For ORCHIDEE_2_0, 2_1, 2_2 and coupled models v6.1.x:
# source /ccc/cont003/home/igcmg/igcmg/MachineEnvironment/irene/env_irene


## Create a run_file to be used to lauch with XIOS in server mode
# Note: 31+1 should be equal the number set in the header. For example, if you set 16 in the header, set 15 for orchidee and keep 1 for xios. 
#       If you want to run LMDZ, change orchidee_ol_prod into the name for the lmdz executable.
rm -f run_file
echo "31 ./orchidee_ol_prod" > run_file
echo "1 ./xios_server_prod.exe " >> run_file
chmod +x run_file


## Launch the executables
/usr/bin/time ccc_mprun -E-K1  -f ./run_file

Submit the job to the queue with the command

ccc_msub Myjobname

Check the status of the job by

ccc_mstat

or by

ccc_mstat -u mylogin

Read more here about job headers at irene: ​https://forge.ipsl.fr/igcmg_doc/wiki/Doc/ComputingCenters/TGCC/Irene#Irenejobheaders

Jean-Zay at IDRIS

See job examples here: ​https://forge.ipsl.fr/igcmg_doc/wiki/Doc/ComputingCenters/IDRIS/JeanZay#ExampleofajobtostartanexecutableinaParallelenvironnement

obelix at LSCE MPI

See job example here: ​https://forge.ipsl.fr/igcmg_doc/wiki/Doc/ComputingCenters/LSCE#ExampleofparallelMPIjob

Ciclad and ClimServ at IPSL ESPRI-mesocenter

See job example here: ​https://forge.ipsl.fr/igcmg_doc/wiki/Doc/ComputingCenters/ESPRImesocenter#ExampleofjobforaMPIexecutable