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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