{{{
#!html
Working on TGCC
}}}
----
[[PageOutline(1-3,Table of contents,,numbered)]]
# TGCC presentation #
http://www-hpc.cea.fr/en/complexe/tgcc.htm
# TGCC's machines and file systems #
[[Image(wiki:DocBenvBtgcc:TGCC_avril2016.jpg, 360px)]]
# How to install your environment on TGCC #
* More information on the open-access website: http://www-hpc.cea.fr/en/complexe/tgcc.htm
* Online access to the machines' users manual (you will need a TGCC login and password): https://www-tgcc.ccc.cea.fr/ .
* Online access to technical issues and news : https://www-tgcc.ccc.cea.fr/en/news/index.html
* The available TGCC's machine is currently '''curie''' (Bull Sandybridge).
* Note: the '''$HOME/.snapshot''' directory contains hourly, daily, and weekly backups of your $HOME files.
[[NoteBox(note,It is important to take the time to install a comfortable and efficient environment., 600px)]]
We suggest the user to use the p86ipsl login's environment (in bash) as an example (copy the `~p86ipsl/.bashrc_curie` and the `~p86ipsl/.bash_profile` files in your home). You can complete the .bashrc file to create your favorite environment (alias, module load ...)
{{{
#!sh
ryyy999@curie: cp ~p86ipsl/.bashrc_curie ~/.
ryyy999@curie: cp ~p86ipsl/.bash_profile ~/.
}}}
WARNING : if you have a ~/.profile file, it's better to remove it to avoid any problem during the execution of a simulation with libIGCM
In this environment is specified:
* the path to the compiler tool `fcm` and to the `rebuild` tool which recombines output files from a parallel model:
{{{
export PATH=~p86ipsl/fcm/bin:~p86ipsl/rebuild/src_X64_CURIE/modipsl_v2_2_2_netcdf4.2/bin/rebuild:$PATH
}}}
* the load of modules giving access to computing or post processing libraries and tools needed on our platform (done in ~p86ipsl/.atlas_env_netcdf4.3.3.1_hdf5_parallel_curie_ksh). The revision numbers may change, currently (June 2015) following modules are loaded for computing :
{{{
module load ghostscript/9.04
module load ferret/6.9.3
module load gsl/1.14
module load netcdf/4.3.3.1_hdf5_parallel
module load cdo/1.6.7
module load imagemagick/6.7.4
module load nco/4.4.8
}}}
# Project and computing needs #
* To find out the computing time used by the projects you are involved in (daily update):
{{{
#!sh
ryyy999@curie: ccc_myproject
}}}
* When you will create a job you need to specify in the header the project from which you will use computing time:
{{{
#!sh
#MSUB -A genxxx
}}}
# About file systems #
## Quotas ##
To check the available and used storage capacities of `HOME`, `SCRATCH`, `CCCWORKDIR` and `CCCSTOREDIR`:
{{{
#!sh
ryyy999@curie: ccc_quota
}}}
On the curie machine this command will also return the space used by scratch (a specificity of the curie machine).
This command has been improved and gives a lot of information : quotas and usage of shared space, type and duration of exception.
## SCRATCHDIR ##
The `$SCRATCHDIR`directory is often cleaned and only files that are less than 40 days are stored.
## CCCWORKDIR ##
The `$CCCWORKDIR` directory corresponds to the `$WORKDIR` directory on curie. It is large but its content is not backed up. Don't forget to do a backup (tar) for important directories.
## CCCSTOREDIR ##
To manipulate the files in /ccc/store a few commands are useful:
{{{
#!sh
# Demigrate a list of files on CCCSTOREDIR, see also "ccc_hsm -h"
ccc_hsm get $CCCSTOREDIR/FILE1 $CCCSTOREDIR/FILE2 ...
# Demigrate recursively the files from a CCCSTOREDIR directory, see also "ccc_hsm -h"
ccc_hsm get -r $CCCSTOREDIR/DIRECTORY
# Find out the used space on CCCSTOREDIR
cd $CCCSTOREDIR ; find . -printf "%y %s %p \n" | \
awk '{ SUM+=$2 } END {print "SUM " SUM/1000000 " Mo " SUM/1000000000 " Go" }'
# or use --apparent-size with du :
du -sh --apparent-size
}}}
## ccc_home command to know directory complete pathname ##
ccc_home could help you to find directory complete pathname for an other user or for you .
{{{
>ccc_home -h
ccc_home: Print the path of a user directory (default: home directory).
usage: ccc_home [ -H | -s | -t | -W | -A | -G | -a] [-u user]
[-h, --help]
-H, --home : (default) print the home directory path ($HOME)
-s, -t, --scratch : print the scratch directory path ($SCRATCHDIR)
-W, --cccwork : print the CCC work directory path ($CCCWORKDIR)
-A, --cccstore : print the CCC store directory path ($CCCSTOREDIR)
-G, --cccgenostore : print the CCC genostore directory path ($CCCGENOSTOREDIR)
-a, --all : print all paths
-u user : show paths for the specified user instead of the current user
-h, --help : display this help and exit
> ccc_home -A -u ryyy999
/ccc/store/cont003/dsm/ryyy999
}}}
## Storage spaces available from ESGF/THREDDS ##
To store a file for the first time on esgf/thredds, you must ask for esgf/thredds write access by mail to the TGCC hotline access : `hotline.tgcc@cea.fr`.
{{{
On Curie :
/ccc/work/cont003/dods/public/login
/ccc/store/cont003/dods/public/login
On a server web
http://esgf.extra.cea.fr/thredds/catalog/work/catalog.html
http://esgf.extra.cea.fr/thredds/catalog/store/catalog.html
}}}
# Specific file systems for CMIP6 #
For gencmip6 project, and only for it, 3 more file systems and 4 more directories are available. Phase 1 have been installed in april 2016. Phase 2 and Phase 3 will come later in 2017 and 2018.
To use them, in interactive mode, you have to do : {{{module load datadir/gencmip6}}}.
Since libIGCM_v2.8.1, if you set your project to gencmip6/devcmip6, they are automatically used in place of usual HOME, CCCWORKDIR, CCCSTOREDIR and SCRATCHDIR : {{{module switch dfldatadir dfldatadir/gencmip6}}} called from libIGCM.
## GENCMIP6_HOME ##
* 50 TB
* gencmip6 group quota
* dedicated to sources and scripts
* strongly recommanded for CMIP6 sources and simulations scripts
* regular snapshot are taken by the system. See $GENCMIP6_HOME/.snapshot
{{{
... /.snapshot : ls -l
total 44
drwxr-sr-x. 13 xxx gencmip6 4096 Dec 17 09:47 daily.2017-02-07_0010
drwxr-sr-x. 13 xxx gencmip6 4096 Dec 17 09:47 daily.2017-02-08_0010
drwxr-sr-x. 13 xxx gencmip6 4096 Dec 17 09:47 hourly.2017-02-08_0905
drwxr-sr-x. 13 xxx gencmip6 4096 Dec 17 09:47 hourly.2017-02-08_1005
drwxr-sr-x. 13 xxx gencmip6 4096 Dec 17 09:47 hourly.2017-02-08_1105
drwxr-sr-x. 13 xxx gencmip6 4096 Dec 17 09:47 hourly.2017-02-08_1205
drwxr-sr-x. 13 xxx gencmip6 4096 Dec 17 09:47 hourly.2017-02-08_1305
drwxr-sr-x. 13 xxx gencmip6 4096 Dec 17 09:47 hourly.2017-02-08_1405
drwxr-sr-x. 13 xxx gencmip6 4096 Dec 17 09:47 snapshot_for_backup.76
drwxr-sr-x. 13 xxx gencmip6 4096 Dec 17 09:47 weekly.2017-01-29_0015
drwxr-sr-x. 13 xxx gencmip6 4096 Dec 17 09:47 weekly.2017-02-05_0015
}}}
## GENCMIP6_CCCWORKDIR ##
* 2.5 PB in phase 1, 7 PB in phase 2
* gencmip6 group quota
* dedicated to small output files (ATLAS, MONITORING)
* available through https://esgf.extra.cea.fr following work_thredds
* no backup
## GENCMIP6_CCCSTOREDIR ##
* 2.5 PB in phase 1, 7 PB in phase 2 and 14 PB on tape in phase 3
* gencmip6 group quota
* dedicated to large (more than 1GB) output files (Output, Analyse)
* available through https://esgf.extra.cea.fr following store_thredds
* linked with HSM (tapes)
## GENCMIP6_SCRATCHDIR ##
* same file system as GENCMIP6_CCCWORKDIR
* used during batch execution (RUN_DIR) and erased at the end of the execution
* regular cleaning after 40 days
# End-of-job messages #
To receive the end-of-job messages sent by the job itself: end of simulation, error,... you must specify your address in the $`HOME/.forward` file.
# Simulation outputs #
Final simulation outputs are stored in `$CCCSTOREDIR/IGCM_OUT` and on `$CCCWORKDIR/IGCM_OUT` regarding the `ATLAS` and `MONITORING` directories.
The esgf/thredd server on TGCC are available via:
* http://esgf.extra.cea.fr/thredds, click on store, click on your login or directly : http://esgf.extra.cea.fr/thredds/catalog/sotre/YOURLOGIN/catalog.html and ATM (or an other component) for `Analyse` files (TS or SE)
* http://esgf.extra.cea.fr/thredds, click on work, click on your login or directly : http://esgf.extra.cea.fr/thredds/catalog/work/YOURLOGIN/catalog.html for `ATLAS` and `MONITORING`
# About password #
ccc_password_expiration helps you to know expiration date of your password. Currently password have to be changed one time per year.
{{{
> ccc_password_expiration
Password for xxxxx@USERS-CCRT.CCC.CEA.FR: PPPPPPPPPP
Your password will expire in 70 days on Fri Nov 22 08:42:59 2013
> ccc_password_expiration -h
Usage: ccc_password_expiration [username[@realm]]
}}}
# The TGCC's machines #
* [wiki:DocBenvBtgccAcurie Curie]