Running simulations with ORCHIDEE-CNP

Experiments with ORCHIDEE usually require a set consisting of two and more simulations: a simulation to equilibrate the biogeochemical cycles to the boundary conditions of the initial state (e.g. pre-industrial conditions) & a second simulation restarting from the first one which consists of simulation of the historic period (pre-industrial to period of interest). We have template folders for these and additional types of simualtions available. Please get in touch with your supervisor regarding the templates.

MIND: The exact setup depends on your objectives. Here we only provide a general template which works for most applications. Please get in touch with your supervisor to design a simulation setup suited for your application.

1.1 Copy a configuration folder

cd ../../config/ORCHIDEE_OL/

cp -fr TEMPLATE MY_EXPERIMENT

cd MY_EXPERIMENT.SPIN/

Replace TEMPLATE with the name of template folder and MY_EXPERIMENT with your experiment name.

1.2 adjust the config.card

Follow the instructions for the ORCHIDEE trunk version. To select the correct driving dataset in the COMP/*.card file get in touch with your supervisors.

On obelix, specify the path to the directory you want to have the output using this variable

ARCHIVE=YOURPATH

Replace YOURPATH with the path you want.

1.3 Create the Job file

../../libIGCM/ins_job

The command creates a Job file named Job_ followed by the JobName? from config.card

1.4 Adjust the Job file

Besides the modifications described for the trunk version of ORCHIDEE (see there), some additional changes need to be done when using the ORCHIDEE-CNP version. We report here only the CNP specific changes, for the others see documents of the main version (e.g. training course).

1.4.1 enhance the computational efficiency

Replace

IGCM_comp_GetInputBoundaryFiles 

With

IGCM_comp_GetInputBoundaryFiles "ln" 

Replace

IGCM_comp_GetInputRestartFiles  

With

IGCM_comp_GetInputRestartFiles "ln"

1.4.2 Setting paths on obelix

On obelix, specify the running directory to minimize the risk of model crashes. (If the default directory (scratch) is used the model regularly crashes as the disc runs full often as it is not properly purged ).

RUN_DIR_PATH=YOURPATH

Replace YOURPATH with the path you want. Mind, with the current libIGCM the RUN_DIR_PATH is deleted when the simulations finishes, thus you need to assign unique folders for each of your simulations, e.g. by adding a random number using $$

RUN_DIR_PATH=/home/surfaceX/userX/RUN_DIR_$$

1.5 submit the job

This is more or less similar to ORCHIDEE trunk & you find more information there.

on obelix ( we might need to source the right modules, but in any case you need to have the modules required for ORCHIDEE in ~/.profile ; see preparation on the how to install ORCHIDEE-CNP page) :

source ../ARCH/arch.env
qsub Job_ID

Replace ID with the simulation name (JobName? in config.card). To monitor or delete jobs you can use qstat or qdel The commands are well described online.

Other machines use different command to handle jobs. Please see the documentation of the main version of ORCHIDEE.

1.6 restart / rerun a job after crash

It is important that you stick to the libIGCM regulations. The libIGCM of ORCHIDEE-CNP uses them same toolset as the trunk version of ORCHIDEE. You can also delete run.card, run.card.bak as well as the experiment folder in the archive folder if you want to start from scratch. To avoid headaches, it is recommended to always delete all file which you want to redo , for example in the experiment output in IGCM_OUT, etc