Main.RunningQUEST History
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!! How to Run [=FAMOUS=] on the [=QUEST=] Cluster
The current "base" [=FAMOUS=] job on quest is %red%xcpsb%% under username ''annette'' on the puma UMUI. This is scientifically equivalent to xbyva, see FAMOUSStandardVersions. By default, the job produces restarts every 6 months and means over annual and decadal periods.
We assume users are accessing the UMUI through puma, see [[http://ncas-cms.nerc.ac.uk/content/view/736/187/|NCAS-CMS]].
The FAMOUS files on quest are installed under the directory @@/exports/gpfsbig/um/[=PUM6=]4/famous@@. The queues at the moment have a limit of 2 days, and after that you will have to resubmit manually, as there is no automatic resubmission.
Submission needs to be done in several stages.
* Submit compile job (runs automatically)
* Submit run job:
** copy files over to quest using umsubmit
** run directly on quest using qsub-um
'''1) Set up your environment on quest'''
* Copy the setvars file to your home directory
->[@
cd $HOME
cp /exports/gpfsbig/um/PUM64/setvars $HOME
ln -s setvars setvars_4.5
@]
* Append to your .profile (or equivalent):
->[@
module add default-infiniband-pgi-251
. $HOME/setvars
@]
Note: If you have already been running on quest, you may have references to the old @@module default-infiniband-pgi@@ in your @@.profile@@ and/or @@setvars@@, so just check that they are consistent.
'''2) Create a job'''
* Copy the job to one of your own folders. Change the user details and DATA_DIR environment variable.
'''3) Compile the job'''
The compilation and the run must be done in separate stages.
* In "Compile Options" in the UMUI, select "compile and build then stop".
* Under "Job resources and re-submission", select "at".
->(I never worry about any of the other options.)
* Submit using umsubmit in the usual way:
->[@
~jeff/bin/umsubmit -h quest-hpc.bris.ac.uk -u USERID -r scp RUNID
@]
I've also found that the SUBMIT button works here.
Compilation output will be sent to @@$HOME/umui_out@@
'''4) Run the job'''
Copy the files over from puma:
* Under "Compile Options", select "Run from existing exec".
* Under "Job resources and re-submission", select "qsub".
* Submit using the SUBMIT button or umsubmit.
Submit the job directly on quest:
* cd to the most recent directory in $HOME/umui_runs
->[@
cd $HOME/umui_runs
ls -lrt
cd ...
@]
* submit the job with:
->[@
~um/bin/qsub-um qsubmit.quest
@]
Job output will be sent to this directory.
Use @@qstat -an@@ to get a summary of the running jobs.
to:
Added lines 1-83:
!! How to Run [=FAMOUS=] on the [=QUEST=] Cluster
The current "base" [=FAMOUS=] job on quest is %red%xcpsb%% under username ''annette'' on the puma UMUI. This is scientifically equivalent to xbyva, see FAMOUSStandardVersions. By default, the job produces restarts every 6 months and means over annual and decadal periods.
We assume users are accessing the UMUI through puma, see [[http://ncas-cms.nerc.ac.uk/content/view/736/187/|NCAS-CMS]].
The FAMOUS files on quest are installed under the directory @@/exports/gpfsbig/um/[=PUM6=]4/famous@@. The queues at the moment have a limit of 2 days, and after that you will have to resubmit manually, as there is no automatic resubmission.
Submission needs to be done in several stages.
* Submit compile job (runs automatically)
* Submit run job:
** copy files over to quest using umsubmit
** run directly on quest using qsub-um
'''1) Set up your environment on quest'''
* Copy the setvars file to your home directory
->[@
cd $HOME
cp /exports/gpfsbig/um/PUM64/setvars $HOME
ln -s setvars setvars_4.5
@]
* Append to your .profile (or equivalent):
->[@
module add default-infiniband-pgi-251
. $HOME/setvars
@]
Note: If you have already been running on quest, you may have references to the old @@module default-infiniband-pgi@@ in your @@.profile@@ and/or @@setvars@@, so just check that they are consistent.
'''2) Create a job'''
* Copy the job to one of your own folders. Change the user details and DATA_DIR environment variable.
'''3) Compile the job'''
The compilation and the run must be done in separate stages.
* In "Compile Options" in the UMUI, select "compile and build then stop".
* Under "Job resources and re-submission", select "at".
->(I never worry about any of the other options.)
* Submit using umsubmit in the usual way:
->[@
~jeff/bin/umsubmit -h quest-hpc.bris.ac.uk -u USERID -r scp RUNID
@]
I've also found that the SUBMIT button works here.
Compilation output will be sent to @@$HOME/umui_out@@
'''4) Run the job'''
Copy the files over from puma:
* Under "Compile Options", select "Run from existing exec".
* Under "Job resources and re-submission", select "qsub".
* Submit using the SUBMIT button or umsubmit.
Submit the job directly on quest:
* cd to the most recent directory in $HOME/umui_runs
->[@
cd $HOME/umui_runs
ls -lrt
cd ...
@]
* submit the job with:
->[@
~um/bin/qsub-um qsubmit.quest
@]
Job output will be sent to this directory.
Use @@qstat -an@@ to get a summary of the running jobs.