One can run a single-column version of the Venus PCM. This is the '''rcm1d''' main program which simply uses the same physics as the 3D PCM but without dynamics, and for a single column. Very useful for some studies and when debugging or developing parametrizations.

== Compilation ==
The main program '''rcm1d''' is compiled using the same compilation script, [[The makelmdz fcm GCM Compilation Script|makelmdz_fcm]], as for the 3D Venus PCM. Nevertheless, there are few modifications:
* the ''-d'' option requires only one argument, the number of vertical levels;
* the main program to compile is ''rcm1d'' rather than ''gcm''.
* Even though the 1d-column version does not need to be run in parallel it should be compiled with option "-parallel mpi" because its outputs are managed by XIOS which requires being compiled with an MPI library (and hence the model should also be compiled with option "-io xios")

So for instance to compile a case for 78 vertical levels one would run something like:
<syntaxhighlight lang="bash">
makelmdz_fcm -arch somearch -p venus -d 78 -parallel mpi -io xios rcm1d
</syntaxhighlight>
which would generate executable <code>rcm1d_78_phyvenus_para.e</code> in the ''bin'' subdirectory.

== Inputs ==
Like the ''gcm'' program, the ''rcm1d'' program needs some inputs to be able to run. The needed files are:
* <code>z2sig.def</code> for the definition of vertical levels;
* <code>traceur.def</code> for the definition of tracers that the user wants the model to run with;
* <code>physiq.def</code> for the definition of parametrizations that the user wants the model to run with;
* <code>run.def</code> and <code>gcm.def</code> files for the run configuration, which are similar to the one for the 3D PCM but in fact mostly not used as parameters there essentially concern dynamics.
* <code>rcm1d.def</code> A dedicated ASCII file adapted to the 1D case. An example <code>rcm1d.def</code> file, is available in <code>LMDZ.VENUS/deftank</code>.

Note that unlike the ''gcm'' program, the ''rcm1d'' program can run without any initial conditions start files (start.nc and startphy.nc); running ''rcm1d'' is as simple as running any serial code, e.g. assuming the executable has been renamed ''rcm1d.e'':
<syntaxhighlight lang="bash">
./rcm1d.e
</syntaxhighlight>
As for the GCM all external input files (apart from start files) are required to be present and available.

When running with chemistry, you will need to initialize the composition. This is done with <code>init_1D.txt</code> file, that contains a first line with labels, then columns with levels (e.g. 78 to 1) / pressure (hPa) / density (g.cm-3) / then all the tracers mole fractions, in the same number and order as in the <code>traceur.def</code> file. Pressure and density are not used.

== Outputs ==

The ''rcm1d'' main program uses the same output system than the 3D PCM. Therefore all outputs are managed by XIOS via xml files in the same way as the GCM.

[[Category:Venus-Model]]

Using Irene Rome

2022-09-21T12:27:43Z

Lebonnois: /* Some useful commands */

This page provides a summary of examples and tools designed to help you get used with the Irene Rome environment. (as of July 2022)

== How to access the cluster ==

For people on the "Atmosphères Planétaires" GENCI project who need to open an account on Irene-Rome, here is the procedure:

* Log on to https://www-dcc.extra.cea.fr/CCFR/ and provide various information about yourself

A few tips:

- chose TGCC

- give your PROFESSIONAL phone number (and not your personal cell phone number)

- name of the project: Atmosphères Planétaires Numéro du Dossier: A0120110391

- Responsable scientifique du projet: M. Ehouarn MILLOUR , ehouarn.millour@lmd.ipsl.fr, 0144275286, Nationalité: Fr

- Responsable sécurité: M. Franck Guyon, franck.guyon@lmd.ipsl.fr, 0144275277, Nationalité: Fr

- IPs & machine names to connect to Irene: 134.157.47.46 (ssh-out.lmd.jussieu.fr) and 134.157.176.129 (ciclad.ipsl.upmc.fr)

- Chose anything you want for the 8 character password

* And then get Ehouarn to sign the form and forward it to Franck for him to sign as well.

* Send the signed form to hotline.tgcc@cea.fr

== Some useful commands ==

* To access the disks of our project on Irene ("Atmosphères Planétaires" GENCI project), add the following line in your .bash_profile file:
(.bash_profile rather than .bashrc, because otherwise scp may not find your files when fetching them from $CCCWORKDIR on irene to your machine)

<syntaxhighlight lang="bash">
module switch dfldatadir/gen10391
</syntaxhighlight>

* To access your work directory (to run your simulations)

<syntaxhighlight lang="bash">
cd /ccc/work/cont003/gen10391/
</syntaxhighlight>

you can also access the work directory with:

<syntaxhighlight lang="bash">
cd $CCCWORKDIR
</syntaxhighlight>

* To access your store directory (to store big data files we are limited in inode number not in filesize! It is recommended to store files of at least 50M, preferably more, e.g. big tar files of 10G or more)
<syntaxhighlight lang="bash">
cd /ccc/work/cont003/gen10391/
</syntaxhighlight>

you can also access the store directory with:

<syntaxhighlight lang="bash">
cd $CCCSTOREDIR
</syntaxhighlight>

* To access the scratch directory
<syntaxhighlight lang="bash">
cd $CCCSCRATCHDIR
</syntaxhighlight>
IMPORTANT: the scratchdir is fast access, very big, BUT regularly automatically purged! If you use it do remember to backup stuff on the WORKDIR or STOREDIR.

The scratch purge policy (from machine.info):
<pre>
* Files not accessed for 60 days are automatically purged
* Symbolic links are not purged
* Directories that have been empty for more than 30 days are removed
</pre>

* To access Irene Interactive Documentation:
<syntaxhighlight lang="bash">
machine.info
</syntaxhighlight>

NB: you can also access the online documentation here: http://www-hpc.cea.fr/tgcc-public/en/html/toc/fulldoc/Introduction.html

* To display infos about project accounting:
<syntaxhighlight lang="bash">
ccc_myproject
</syntaxhighlight>

* To know about user and group disk quota
<syntaxhighlight lang="bash">
ccc_quota -a
</syntaxhighlight>

* To know about how long your passwd will be active:
<syntaxhighlight lang="bash">
ccc_password_expiration
</syntaxhighlight>

* To change passwd:
<syntaxhighlight lang="bash">
passwd
</syntaxhighlight>

== Example of a job to run a GCM simulation ==

=== Mixed openMP / MPI ===

<syntaxhighlight lang="bash">
#!/bin/bash
# Partition to run on:
#MSUB -q rome
# project to run on
#MSUB -A gen10391
# disks to use
#MSUB -m scratch,work,store
# Job name
#MSUB -r run_gcm
# Job standard output:
#MSUB -o run_gcm.%I
# Job standard error:
#MSUB -e run_gcm.%I
# number of OpenMP threads c
#MSUB -c 2
# number of MPI tasks n
#MSUB -n 16
# number of nodes to use N
#MSUB -N 1
# max job run time T (in seconds)
#MSUB -T 3600
# request exculsive use of the node (128 cores)
##MSUB -x

source ../trunk/LMDZ.COMMON/arch.env
export OMP_STACKSIZE=400M
export OMP_NUM_THREADS=2

ccc_mprun -l gcm_32x32x15_phystd_para.e > gcm.out 2>&1

</syntaxhighlight>

=== Pure MPI + long run ===

The most important parameter for mpi-only runs is ''-n''
providing the total number of CPUs
(ideally a multiple of 128, which is the number of CPUs per core).

Runs longer than 1 day are not possible unless
selecting a quality-of-service (QoS) "long"

<syntaxhighlight lang="bash">
#!/bin/bash

# Partition to run on:
#MSUB -q rome
# project to run on
#MSUB -A gen10391
# disks to use
#MSUB -m scratch,work,store
# Job name
#MSUB -r run_wrf
# Job standard output:
#MSUB -o run_wrf.%I
# Job standard error:
#MSUB -e run_wrf.%I
# number of MPI tasks n (total)
#MSUB -n 256
# max job run time T (in seconds)
#MSUB -T 345600
# select quality-of-service
# - test < 30min
# - normal < 1d (default)
# - long < 3d
#MSUB -Q long

#############################

# load the modules used to compile
source arch.env

# clean the logs
rm -rf rsl.*

# create initial state
# -- this is done on a single proc
ideal.exe
mv rsl.error.0000 ideal_rsl.error.0000
mv rsl.out.0000 ideal_rsl.out.0000

# main launch
ccc_mprun -l wrf.exe

</syntaxhighlight>

== Main submission commands ==

* To launch the job script ''run_gcm.job'':
<syntaxhighlight lang="bash">
ccc_msub run_gcm.job
</syntaxhighlight>
* To display information about your jobs:
<syntaxhighlight lang="bash">
ccc_mpp -u $USER
</syntaxhighlight>
* To kill job number ''jobid''
<syntaxhighlight lang="bash">
ccc_mdel jobid
</syntaxhighlight>
* To display infos about project accounting:
<syntaxhighlight lang="bash">
ccc_myproject
</syntaxhighlight>
* To display infos about limits:
<syntaxhighlight lang="bash">
ccc_mqinfo
</syntaxhighlight>
* To display infos about partitions:
<syntaxhighlight lang="bash">
ccc_mpinfo
</syntaxhighlight>

== Extra Tips ==

*If you encounter a quota issue on Irene, first check:

<syntaxhighlight lang="bash">
ccc_quota
</syntaxhighlight>

if you ha "disk quota exceeded error message", this might be because your files/scripts do not have correct right access. To solve this,
use the following command on all your dirs (before tranfering them to Irene):

<syntaxhighlight lang="bash">
chmod -R g+s NAME_OF_DIR
</syntaxhighlight>

== File transfert from Occigen ==
One should use ccfr:
<syntaxhighlight lang="bash">
module load ccfr
</syntaxhighlight>
A list of available machines is given by
<syntaxhighlight lang="bash">
ccfr_ssh -v
</syntaxhighlight>
To log on to Occigen (from Irene):
<syntaxhighlight lang="bash">
ccfr_ssh occigenlogin@cines
</syntaxhighlight>

To copy a file:
<syntaxhighlight lang="bash">
ccfr_cp occigenlogin@cines:remote_dir local_dir
</syntaxhighlight>

== Worth knowing about ==
* The command wget is disabled on Irene, scripts using it will fail...
* Only "https" is allowed (for svn co, git, etc)

[[Category:FAQ]]

In case you reach a quota issue, please use the following command on your directory before sending the data:

<syntaxhighlight lang="bash">
chmod -R g+s NAME_OF_DIR
</syntaxhighlight>