LOCEAN Croco-Agrif-Pisces Projects
Installing Pulsation-tools & launching a test experience
Find below a guide to:
- computer : JEANZAY
- config : BENGUELA_LR
- experience : exp1
Configure your shell environement for Pulsation-tools
Configure your .bashrc
- Copy the file scripts/bash_pulsation in your HOME directory as .bash_pulsation
- Customize the WORKDIR_EXP, SCRATCHDIR_EXP, STOREDIR_EXP directories to suit your environment (the first lines)
- add in your .bashrc the following line:
. .bash_pulsation
- refresh your environment with
. .bashrc
Create the exp directory and download the pulsation-tools environment
- The only directory to be created (The run, output & restart directories are automatically created when running). "wd" is the directory you can backup to keep the full description of all experiments.
mkdir -p ${WORKDIR_EXP}/wd/BENGUELA_LR/exp
cd ${WORKDIR_EXP}/wd/BENGUELA_LR/exp
- Download with gitlab the branch you want (benguela_lr) and name it as you want (exp1).
git clone --branch benguela_lr git@gitlab.in2p3.fr:christophe.hourdin/pulsation-tools.git exp1
Get the netcdf input files, the croco_v2.00_orig code & the xios library
Get the netcdf input files
link to, copy or download the netcdf input files directory for the BENGUELA_LR config
- to link to :
sca # alias cd ${ARCHDIR}
in JEANZAY.env : export2 INDIR="/gpfswork/rech/eee/reee084/BENGUELA_LR/inputs"
in IRENE.env : export2 INDIR="/ccc/work/cont005/gen1140/hourdinc/BENGUELA_LR/inputs"
in DATARMOR.env: export2 INDIR="/home3/datawork/chourdin/BENGUELA_LR/inputs"
- copy or download:
mkdir -p ${WORKDIR_EXP}/BENGUELA_LR
cd ${WORKDIR_EXP}/BENGUELA_LR
in COMPUTER.env : export2 INDIR="${WORKDIR_EXP}/BENGUELA_LR/inputs"
- copy
for JEANZAY : rsync -a /gpfswork/rech/eee/reee084/BENGUELA_LR/inputs .
for IRENE : rsync -a /ccc/work/cont005/gen1140/hourdinc/BENGUELA_LR/inputs .
for DATARMOR : rsync -a /home3/datawork/chourdin/BENGUELA_LR/inputs .
- or download :
if these directories are unreachable, download BENGUELA_LR inputs tar file
Get the croco_v2.00_orig code
link to, copy or download the croco_v2.00_orig code
- to link to :
sca # alias cd ${ARCHDIR}
in JEANZAY.env : export2 CROCO_SOURCE="/gpfswork/rech/eee/reee084/croco_v2.00_orig/OCEAN"
in IRENE.env : export2 CROCO_SOURCE="/ccc/work/cont005/gen1140/hourdinc/croco_v2.00_orig/OCEAN"
in DATARMOR.env: export2 CROCO_SOURCE="/home3/datawork/chourdin/croco_v2.00_orig/OCEAN"
- copy or download:
cd ${WORKDIR_EXP}
in $COMPUTER_NAME.env : export2 CROCO_SOURCE="${WORKDIR_EXP}/croco_v2.00_orig/OCEAN"
- copy
for JEANZAY : rsync -a /gpfswork/rech/eee/reee084/croco_v2.00_orig .
for IRENE : rsync -a /ccc/work/cont005/gen1140/hourdinc/croco_v2.00_orig .
for DATARMOR : rsync -a /home3/datawork/chourdin/croco_v2.00_orig .
- or download :
if these directories are unreachable, download croco_v2.00_orig tar file
Get the xios library
link to, copy or download the xios library
- to link to :
sca # alias cd ${ARCHDIR}
JEANZAY.env : export2 XIOS_DIR="/gpfswork/rech/eee/reee084/XIOS_X64_JEANZAY_trunk_r2219-2021_09_06"
IRENE.env : export2 XIOS_DIR="/ccc/work/cont005/gen1140/hourdinc/XIOS_X64_IRENE_trunk_r2219-2021_09_06"
IRENE-AMD.env : export2 XIOS_DIR="/ccc/work/cont005/gen1140/hourdinc/XIOS_X64_IRENE-AMD_trunk_r2219-2021_09_06"
DATARMOR.env : export2 XIOS_DIR="/home3/datawork/chourdin/XIOS_X64_DATARMOR_trunk_r2219-2021_09_06"
- copy or download:
cd ${WORKDIR_EXP}
in COMPUTER_NAME.env : export2 XIOS_DIR="${WORKDIR_EXP}/XIOS_X64_${COMPUTER}_trunk_r2219-2021_09_06"
- copy
for JEANZAY : rsync -a /gpfswork/rech/eee/reee084/XIOS_X64_JEANZAY_trunk_r2219-2021_09_06 .
for IRENE : rsync -a /ccc/work/cont005/gen1140/hourdinc/XIOS_X64_IRENE_trunk_r2219-2021_09_06 .
for IRENE-AMD : rsync -a /ccc/work/cont005/gen1140/hourdinc/XIOS_X64_IRENE-AMD_trunk_r2219-2021_09_06 .
for DATARMOR : rsync -a /home3/datawork/chourdin/XIOS_X64_DATARMOR_trunk_r2219-2021_09_06 .
- or download :
if these directories are unreachable, download xios library tar file
launching and monitoring the experience
To submit the pre defined first job test (only 2 timesteps)
sca # alias cd ${ARCHDIR}
vi JEANZAY.env # to customize the WORKDIR, SCRATCHDIR, STOREDIR directories to suit your environment
vi JEANZAY.header # to assign you account login
# JEANZAY : #SBATCH --account eee@cpu
# IRENE : #MSUB -A gen1140
# DATARMOR : no account
sc # alias cd ${SCRIPTDIR}
./submitjob.sh # to launch your experience
To follow the run & get the outputs
JEANZAY : squeue -u $(whoami)
IRENE : ccc_mpp -u $(whoami)
DATARMOR : qstat -u $(whoami)
jo # alias cd ${JOBDIR} ascii pulsation-tools outputs directory
exe # alias cd ${EXEDIR} croco running directory
out # alias cd ${OUTDIR} netcdf output files directory
rst # alias cd ${RSTDIR} restart files directory