Working at IDRIS

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1. IDRIS presentation

See: ​http://www.idris.fr/eng

2. IDRIS's machines and file systems

3. How to install your environment at IDRIS

• Find more information about IDRIS on ​http://www.idris.fr/eng/ and for new users here : ​http://www.idris.fr/static/intro/doc_nouvel_utilisateur-eng.html
• Connection to IDRIS is possible with ssh command from a registered machine. All forms are available here : ​http://www.idris.fr/eng/forms/index-forms.html
• ​Scripts environment at IDRIS
• The Ada machine at IDRIS can be used for our configurations. It supports the model execution and post processing.
• Note: the software ​the Tina software installed at IDRIS gives access to hourly, daily and weekly backups of your $HOME files.

It is important to take the time to install a comfortable and efficient environment.

• We recommend to follow the example of the rpsl035 login's environment which is in bash. Don't use the default .bash_profile but use instead the ~rpsl035/.bash_login file. Copy this file to your home and remove the default .bash_profile.

  ryyy999@ada: rm $HOME/.bash_profile
  ryyy999@ada: cp ~rpsl035/.bash_login $HOME/.
  

• This file include /smphome/rech/psl/rpsl035/.atlas_env_ada_intel_2013_0_bash which include
  • The path of the compiling tools fcm and the rebuild tool used to reconstruct files from a parallel model:

    export PATH=/smphome/rech/psl/rpsl035/FCM/bin:$PATH
    

• The modules giving access to libraries and post processing tools needed on our platform.

  module load netcdf (currently netcdf/seq/4.1.3 in interactive mode) 
  module load ferret/6.85
  module load nco/4.4.6
  module load cdo/1.6.5
  

• Avoid messages displayed when connecting on Ada and Ergon. Do the following tests:
  • Make sure that the command rsh ergon pwd returns a unique line with the HOME on Ada.

    ryyy999@ada: rsh ergon pwd
    /arch/home/rech/yyy/ryyy999
    

  • Make sure the copy of a file using rcp works properly in the two directions. The following test transfers the file a containing the date:

    ryyy999@ada: date > a ; rcp a ergon:
    

• Transfers Ada/Ergon must be done with mfget/mfput.
• For esgf/thredds access, use the command mfdods on Ergon. This creates the link (24h after the first time) visible here: ​http://prodn.idris.fr/thredds/catalog/ipsl_public/catalog.html

  # Export a file:
  ryyy999@ergon: mfdods my_file -d pub/ryyy999/my_dir
  
  # Once the access activated, you must do the following to destroy a file:
  ryyy999@ada: mfdods -r /u/DODS/pub/ryyy999/my_dir/my_file
  

4. Accounting

Since 2016, usage of computing time and quotas are printed at beginning of each new session.

***********************************************************************
* Consommation du projet  XXXXX - groupe : XXX                        *
* ada        :       10231 h   (  34.10% de l'allocation )            *
* HOME       :        5394 Mio ( 95%)    - Inodes -     17787 ( 11%)  *
* WORKDIR    :       11018 Gio ( 50%)    - Inodes -   2831719 ( 80%)  *
* Ergon      :      188700 Gio ( 55%)    - Inodes -   6177427 ( 88%)  *
***********************************************************************

To know the computing time used by your group (updated once a day):

plab999@ada:~> cpt 

5. Things to know about file systems

5.1. WORKDIR

• The $WORKDIR Ada is large but it is not saved.
• The $WORKDIR Ada can be extended (20 To for the group for example). The project investigator can ask an extension on the IDRIS's extranet. See: ​http://www.idris.fr/extranet.html or directly from an authorized IP : ​https://extranet.idris.fr/.

5.2. ERGON

• The $HOME Ergon has to be used for archiving big files
• The $HOME Ergon can be extended (300 To for the group for example). The project investigator can ask an extension on the IDRIS's extranet. See: ​http://www.idris.fr/extranet.html or directly from an authorized IP : ​https://extranet.idris.fr/.
  • you can use idrls to know the status of a file stored on ergon. See idrls -?. m means migrated on tape only, - means on disk.

    idrls IGCM/RESTART/IPSLCM6/DEVT/piControl/O1T03V14/*/Restart/*
    M ACCESS     L USER    GROUP         SIZE   MOD_DATE   ACC_DATE   EXP_DATE FILE_NAME
    = ========== = ======== ===== ============ ========== ========== ========== =========
    - -rwxrwxr-x 1  rpslxxx   psl    218188352 09.06.2015 22.01.2016 22.01.2017 IGCM/RESTART/IPSLCM6/DEVT/piControl/O1T03V14/ICE/Restart/O1T03V14_18891231_restart_icemod.nc
    m -rwxrwxr-x 1  rpslxxx   psl   1411362796 09.06.2015 22.01.2016 22.01.2017 IGCM/RESTART/IPSLCM6/DEVT/piControl/O1T03V14/OCE/Restart/O1T03V14_18891231_restart.nc
    

5.3. Quotas

Since 2016, usage and quotas are printed at beginning of each new session.

***********************************************************************
* Consommation du projet  XXXXX - groupe : xxx                        *
* ada        :       10231 h   (  34.10% de l'allocation )            *
* HOME       :        5394 Mio ( 95%)    - Inodes -     17787 ( 11%)  *
* WORKDIR    :       11018 Gio ( 50%)    - Inodes -   2831719 ( 80%)  *
* Ergon      :      188700 Gio ( 55%)    - Inodes -   6177427 ( 88%)  *
***********************************************************************

To check the used space and the size of the HOME, WORKDIR and ERGON:

# Quota HOME
ryyy999@ada: quota_u

# Quota WORKDIR
ryyy999@ada: quota_u -w

# Quota ERGON
ryyy999@ergon: quota_u

5.4. Access

Since january 2017, access to other is prohibited. You have to use idracl to give specific access. Documentation : ​http://www.idris.fr/ada/configuration-droits-acces.html

Exemples to give access to a list of groups to HOME ergon, HOME and WORKDIR ada :

ergon>  for g in yyy zzz ; do echo $g ; idracl  -a -g $g ; done
ada> for g in yyy zzz ; do echo $g ; idracl -w -a -g $g ; idracl  -a -g $g ; done

Verification :

ada> cd ; ls -ld .
drwxr-xr-x+ 24 rxxx003 xxx 8192 Jan 19 12:13 .
ada> idracl -l
 
Liste des logins et groupes autorises a acceder 
 a mon espace /linkhome/rech/xxx/rxxx003 
===============================================
 logins autorises : 
 groupes autorises : yyy zzz 

In case of problems, please contact the IDRIS' assistance.

6. Simulation outputs

Final simulation outputs are stored on Ergon in IGCM_OUT directories. There are also available from Adapp in $ARCHIVE/IGCM_OUT but not directly from Ada.

The IDRIS's esgf/thredds server is accessible from here : ​http://prodn.idris.fr/thredds/catalog/ipsl_public/catalog.html

7. About Password

At IDRIS, you have a unique password for all computers. Password have to be changed one time per year. The command to change your password is passwd . You receive a mail 2 weeks before password expiration.

8. The IDRIS's machines

• Ada for computing part
• Adapp for post-processing part