1. Working on ESPRI mesocenter: Ciclad and Climserv

For several years, all the IPSL infrastructure is federated as the ​ESPRI mesocenter.

In this infrastructure there are:

• Ciclad: an IPSL computing cluster located on the Jussieu campus (Paris, France), which hosts mostly modeling data (such as CORDEX, CMIP...)
• ClimServ: an IPSL computing cluster located at Polytechnique (Palaisseau, France), which hosts mostly observation data.

The both clusters have the same software and some file systems are cross-mounted, thus libIGCM is used in the same way on both clusters. The shared account, located at Ciclad, is used also at ClimServ. The documentation below is mainly written for Ciclad but the same can be applied for ClimServ.

1.1. General information

1.1.1. Documentation

Quick documentation could be found ​here (only in French for now).

For mesocenter details about ​computation on Ciclad and !ClimServ

hotline : ​meso-support (at) ipsl.fr

1.1.2. The machines and file systems

The front-end machine can be accessed via ciclad.jussieu.ipsl.fr.

Output files written by libIGCM are stored by default in /data/yourlogin/IGCM_OUT at Ciclad and in /homedata/yourlogin/IGCM_OUT at ClimServ.

1.1.3. Shared account

The repository for shared files are found in /prodigfs/ipslfs/igcmg/IGCM.

Read more: Repository for shared files and shared tools

1.1.4. Individual account

You must belong to the igcmg users' group. Use following command to check to which groups you belong:

id -a

1.1.5. How to define your environment

To set up ferret and FAST tools and to load the modules needed for compilation of LMDZ, ORCHIDEE and XIOS, add the following line in your login file (e.g. ${HOME}/.bashrc) :

. /home/igcmg/.atlas_env_ciclad_ksh

To receive the end-of-job messages returned by the job itself (e.g. end of simulation, error,...) you must specify your email address in the file ${HOME}/.forward.

1.2. Compiling at Ciclad and ClimServ

When installing ​modipsl, the default compiler at Ciclad and ClimServ is set to ifort. In modipsl/util/AA_make.gdef this corresponds to the target ifort_CICLAD. The same target is used for both Ciclad and Climserv. The corresponding arch files for compiling with fcm are named arch-ifort_CICLAD.fcm and arch-ifort_CICLAD.path. Other compilers exist at Ciclad and ClimServ but they have not been tested with all models.

Note that the following message from the script ins_make which installs the makefiles is correct both for Ciclad and ClimServ:

Installation of makefiles, scripts and data for ifort_CICLAD

Following forced configurations have been tested at Ciclad with the ifort compiler:

• NEMO forced mode
• ORCHIDEE offline
• LMDZOR_v6

The coupled models IPSLCM5 or IPSLCM6 have not been tested at Ciclad.

To be checked before compilation

• Make sure following libraries are loaded in the terminal: intel/15.0.6.233 openmpi/1.4.5-ifort netcdf4/4.2.1.1-ifort (use "module liste" to see loaded modules). If this is not the case, load them as follow (use 1 of 2 options) :

  source /home/igcmg/.atlas_env_ciclad_ksh
  # or
  module unload intel openmpi netcdf4
  module load intel/15.0.6.233 openmpi/1.4.5-ifort netcdf4/4.2.1.1-ifort
  

• If you use an older version than revision 1039 on the trunk XIOS, then update compile options as follow :

  cd modeles/XIOS/arch
  svn update -r 1039
  

• Verify that the option --netcdf_lib netcdf4_seq is set on the line with make_xios in config/xxxx/Makefile. Otherwise modify to have as follow :

  xios :
          (cd  ../../modeles/XIOS ; ./make_xios  --netcdf_lib netcdf4_seq \
  --prod --arch ${FCM_ARCH} --job 8 ; cp bin/xios_server.exe ../../bin/. ; )
  

1.2.1. Older versions

To compile at Ciclad/ClimServ you need LMDZ5/trunk rev 2133 or later, ORCHIDEE/trunk rev 2375 or later, XIOS branchs/xios-1.0 rev 604 or XIOS/trunk, libIGCM_v2.7 or later. Some modifications might be needed :

• Compiling XIOS using netcdf sequential. For this add in modipsl/config/AA_make : --netcdf_lib netcdf4_seq on the line make_xios as follow:

  (cd  ../../modeles/XIOS ; ./make_xios --netcdf_lib netcdf4_seq  --prod --arch ${FCM_ARCH} --job 8 ; cp bin/xios_server.exe ../../bin/. ; )
  

• To use older versions of LMDZ, add following 2 lines in the end of modipsl/models/LMDZ/arch/arch-ifort_CICLAD.path:

  XIOS_INCDIR=$LMDGCM/../XIOS/inc
  XIOS_LIBDIR=$LMDGCM/../XIOS/lib
  

• LMDZOR_v5, LMDZ_v5, LMDZOR_v5.2 : The versions of LMDZ and ORCHIDEE are too old in these configurations. They can be used but the arch* files needs to be added. Do following
  • update for LMDZ: cd modipsl/modeles/LMDZ/arch; svn -r 2449 update
  • update for ORCHIDEE only in LMDZOR_v5.2 : cd modipsl/modeles/ORCHIDEE/arch ; svn -r 3171 update
  • update for XIOS: cd modipsl/modeles/XIOS/arch; svn -r 1039 update

1.3. libIGCM at Ciclad and ClimServ

libIGCM can be used since tag libIGCM_v2.6 . The options MONITORING, PACK and ATLAS is not implemeted for Ciclad and ClimServ.

The memory needs to be adapted or added in the job's heading section. For LMDZOR resolution 144x142x79 the following seems to be needed, adjust if needed more, in this example using 31MPIx1OMP for the gcm and 1MPI for xios server:

#PBS -l nodes=1:ppn=32
#PBS -l mem=60gb
#PBS -l vmem=200gb

For LMDZOR resolution 96x95x39 the following is enough:

#PBS -l mem=6gb
#PBS -l vmem=30gb

1.3.1. Only MPI

LMDZOR_v6 configuration (LMDZ testing 3114, ORCHIDEE trunk 2724, XIOS branchs/xios-1.0 rev 604, libIGCM_v2.7) has been tested successfully using XIOS with 1 server when running using only MPI. Only the memory needed to be adapted as said above. Note that default compilation for hybrid mode mpi_omp is used also to run with only MPI.

1.3.2. Mixte MPI-OMP

1.3.2.1. Attached mode or using one executable

Add following in the main job but change OMP_NUM_THREADS to the number of threads used in your case :

module load openmpi/1.4.5-ifort
export OMP_STACKSIZE=200M
export OMP_NUM_THREADS=2

1.3.2.2. Server mode or using two executables

Not yet done

1.4. Example of job for a MPI executable

#PBS -S  /bin/bash
#PBS -N  job_mpi8
###PBS -q short
#PBS -j eo
#PBS -l nodes=1:ppn=8
#PBS -l walltime=00:15:00
#PBS -l mem=6gb
#PBS -l vmem=20gb

ulimit -s unlimited
module load netcdf4/4.2.1.1-ifort

# Go to directory where the job was launched
cd $PBS_O_WORKDIR

/usr/lib64/openmpi/1.4.5-ifort/bin/mpirun gcm.e > gcm.out 2>&1

The job is launched with qsub . Use "qstat -u login" to check the queue. Use qdel to cancel a job in queue or running.