Working on Ada

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1. IDRIS users' manual

• See: ​http://www.idris.fr/eng/ada/ for ada : computing server
• See: ​http://www.idris.fr/eng/adapp/ for adapp : pre-post-treatment
• See: ​http://www.idris.fr/eng/ergon/ for ergon : file server

2. Commands to manage jobs on ada

• The job's time limit is measured in real time, for example 1 hour on 32 procs accounts for 32 hours. Be careful not to have too much time on 1 processor.
• llsubmit --> submit a job
• llcancel --> cancel a job
• llq -u login --> indicates all jobs in the queue or running for the login login
• Trick: parameterize the llq display to see the job names

  llq -u $(whoami) -f %jn %id %st %c %dq %h -W
  

• Post-mortem : idrjar , idrjar -l -j #jobid#, to obtain detailed information: memory, real time, efficiency,...
• Example of idrjar output :

  ada > idrjar
  |----------------------------------------------|
  |--- IDRIS/CNRS. Version du 18 mars 2015 ---|
  |----------------------------------------------|
  
  Sorties concernant l'identifiant rpslxxx pour la période du
          ==> 01 juin 2013 au 19 juin 2013
  
  
   Owner   Job Name        JobId      Queue tEse  tCpu   #T   (%)   S
  ------- ----------- --------------- ----- ---- ------ --- ------- -
  rpslxxx ADA337      ada338.290170.0 c32t2  133   1232  32   28.95 C
  rpslxxx ADA337      ada338.290333.0 c32t2 5425 165141  32   95.13 C
  rpslxxx PACKDEBUG   ada338.290610.0 t2      11      2   1   18.18 C
  rpslxxx ADA337      ada338.290438.0 c32t2 5471 166878  32   95.32 C
  rpslxxx PACKRESTART ada338.290611.0 t2     182     25   1   13.74 C
  rpslxxx REBUILDWRK  ada338.290612.0 t2    1577    503   1   31.90 C
  rpslxxx PACKOUTPUT  ada338.290730.0 t2     114     43   1   37.72 C
  

3. Example of a job to start an executable in MPI

Here is an example of a simple job to start an executable orchidee_ol (or gcm.e commented). The input files and the executable must be in the directory before starting the executable.

#!/bin/ksh
# ######################
# ##   ADA IDRIS   ##
# ######################
# Query's name
# @ job_name = test
# Job type
# @ job_type = parallel
# Standard output file
# @ output = Script_Output_test.$(jobid)
# Error output file (the same)
# @ error = Script_Output_test.$(jobid)
# Number of requested processes
# @ total_tasks = 8
# max. CPU time per MPI process hh:mm:ss
# @ wall_clock_limit = 1:00:00
# Number of task OpenMP/pthreads per MPI process
### @ parallel_threads = 4
# End of header
# @ queue

poe ./orchidee_ol
#poe ./gcm.e

4. Information on Ergon files from Adapp

Ergon files are visible from Adapp. Use $ARCHIVE to reach Ergon files on Adapp. $ARCHIVE is /arch/home/rech/lab/plabxxx on Adapp. All Unix command are available on Adapp to provides information on Ergon files.

5. Job Header for MPI - MPI/OMP with libIGCM

5.1. Forced model

5.1.1. MPI

To launch a job on XXX MPI tasks

#!/bin/ksh
# ######################
# ##   ADA IDRIS   ##
# ######################
# Job name 
# @ job_name = MyJob
# Job type
# @ job_type = parallel
# Standard output file name
# @ output = Script_Output_MyJob.000001
# Error output file name
# @ error = Script_Output_MyJob.000001
# Total number of tasks
# @ total_tasks = XXX
# @ environment = "BATCH_NUM_PROC_TOT=XXX"
# Maximum CPU time per task hh:mm:ss
# @ wall_clock_limit = 1:00:00
# End of the header options
# @ queue

5.1.2. hybrid MPI-OMP

Hybrid version are only available with _v6 configurations

To launch a job on XXX MPI tasks and YYY threads OMP on each task

• first you need to modify your config.card

  ATM= (gcm.e, lmdz.x, XXXMPI, YYYOMP)
  

• second you need to modify your job header

  #!/bin/ksh
  # ######################
  # ##   ADA IDRIS   ##
  # ######################
  # Job name 
  # @ job_name = MyJob
  # Job type
  # @ job_type = parallel
  # Standard output file name
  # @ output = Script_Output_MyJob.000001
  # Error output file name
  # @ error = Script_Output_MyJob.000001
  # Total number of tasks
  # @ total_tasks = XXX
  # @ environment = "BATCH_NUM_PROC_TOT=XXX*YYY"
  # Maximum CPU time per task hh:mm:ss
  # @ wall_clock_limit = 1:00:00
  # Specific option for OpenMP parallelization: Number of OpenMP threads per MPI task
  # @ parallel_threads = YYY
  # End of the header options
  # @ queue
  

5.2. Coupled model

5.2.1. MPI

To launch a job on XXX (32) MPI tasks. 5 for NEMO, 1 for oasis and 26 MPI tasks for LMDZ by default for IPSLCM5A.

#!/bin/ksh
# ######################
# ##  ADA       IDRIS ##
# ######################
# Job name 
# @ job_name = MyCoupledJob
# Job type
# @ job_type = parallel
# Standard output file name
# @ output = Script_Output_MyCoupledJob.000001
# Error output file name
# @ error = Script_Output_MyCoupledJob.000001
# Total number of tasks
# @ total_tasks = 32
# @ environment = "BATCH_NUM_PROC_TOT=32"
# Maximum CPU time per task hh:mm:ss
# @ wall_clock_limit = 1:00:00
# End of the header options
# @ queue

5.2.2. hybrid MPI-OMP

Hybrid version are only available with _v6 configurations

To launch a job on XXX (24) MPI tasks and YYY (2) threads OMP for LMDZ, ZZZ (7) MPI tasks for NEMO and SSS (1) XIOS servers :

• first you need to modify your config.card. On ada, this is working for IPSLCM6_rc0 (IPSLCM6A_VLR) :

  ATM= (gcm.e, lmdz.x, 24MPI, 2OMP)
  SRF= ("" ,"" )
  SBG= ("" ,"" )
  OCE= (opa, opa.xx  , 7MPI)
  ICE= ("" ,"" )
  MBG= ("" ,"" )
  CPL= ("", "" )
  IOS= (xios_server.exe, xios.x, 1MPI)
  

• second you need to modify your job header

  #!/bin/ksh
  # ######################
  # ##   ADA IDRIS   ##
  # ######################
  # Job name 
  # @ job_name = MyCoupledJob
  # Job type
  # @ job_type = parallel
  # Standard output file name
  # @ output = Script_Output_MyCoupledJob.000001
  # Error output file name
  # @ error = Script_Output_MyCoupledJob.000001
  # Total number of tasks
  # @ total_tasks = 32
  # @ environment = "BATCH_NUM_PROC_TOT=56"
  # Maximum CPU time per task hh:mm:ss
  # @ wall_clock_limit = 1:00:00
  # Specific option for OpenMP parallelization: Number of OpenMP threads per MPI task
  # @ parallel_threads = 2
  # End of the header options
  # @ queue
  

6. Specificities libIGCM on Ada

At IDRIS and for Ada, output files are 'packed' using libIGCM_v2, i.e. they are grouped by periods (in general 1 year) using the command tar or ncrcat for NetCDF output files.

This option implies that files must be temporarily stored on the $WORKDIR space, which means that a large storage is needed (at least 20 To).

The diagram below details all jobs including pack_debug, pack_restart and pack_output as well as the directories those jobs are using. Note that the files are temporarily stored in the $WORKDIR/IGCM_OUT directories before being grouped and sent on Ergon in the IGCM_OUT directories.

You will obtain annual output files with 12 monthly values in the Output/MO directory if you put PeriodLength=1M and PackFrequency=1Y in config.card. This is the default grouping period of most configurations but you can of course change it.

What you must remember:

• The tool RunChecker.job is meant to help you monitoring your simulations. It offers a synthetic view of the different post processing jobs' status.
• The tool clean_latestPackperiod.job is meant to help you clean until the last successfully computed pack period.
• If you detect anomalies and must rerun part of the simulation, you will have to make new complete pack periods (e.g. filling a gap by running 1 month of simulation is out of the question).
• The restart files are stored and grouped on Ergon in the directory IGCM_OUT/.../RESTART
• The different output text-files are stored and grouped on Ergon in the directory IGCM_OUT/.../DEBUG
• The listings for pack-jobs outputs stay on Ada in the directory $WORKDIR/IGCM_OUT/.../Out
• If you put the SpaceName=TESTparameter in config.card the pack jobs will not be started and your simulation will be stored in the WORKDIR/IGCM_OUT directory. This can be very useful for short tests.

To learn more about this Section, you can read the documentation on Simulation and post-processing and on Monitor, debug and relaunching.

Finally, in case of panic, visit us or send your questions to the list platform-users.

7. Specificities for Adapp

• Adapp is dedicated to pre and post-treatment.
• Note that Ergon files are visible in read only mode through $ARCHIVE.
  • 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.

    cd $ARCHIVE
    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
    

• Use largely Adapp for analyses and interactive work
• Adapp is free of charge

7.1. IDRIS users' manual for adapp

• See: ​http://www.idris.fr/eng/adapp/ for adapp : pre-post-treatment

7.2. Header for adapp job

A post-treatment jobs includes these header lines :

# @ job_type = serial
# @ requirements = (Feature == "prepost")