PBS Pro Quick STart GUIDE
How to prepare a batch job (PDF)
How to prepare a batch job (PDF)
This section presents a few examples regarding jobs' submissions under the CERIT-SC infrastructure.
At first, let us summarize several fundamental principles and suggestions:
At first, check, whether the application you require is available in the CERIT-SC/MetaCentrum infrastructure (see the list of available applications being referenced in the Available Applications section)
Decide, where your job will read the input data from, and where it will save the working and output data
Submit the job via the Torque or PBS Pro submission systems (using the qsub command); do not forget to specify the requirements your job has -- the number of execution nodes, available memory, as well as available application licences.
Most probably, the job will wait for available nodes (or application license) after submission; the reason of job's waiting can be found using the following command, being run on any of the available frontends (see the comment section in the command's output):
The common waiting reasons are:
Log on the CERIT-SC frontend (see the section Infrastructure access):
Copy the job's input data to your home (sub)directory (/storage/.../home/<username>/), available on the frontend.
More inforamtion about storage.
I. Use your favourite text editor for creating a shell script (named, for example, script.sh), which will perform an initialization of the modular system, and which will perform an initialization of the application you want to use (see the section Applications):
II. Instruct your script to transfer the job's input data to a subdirectory of the fast /scratch storage volume (before the computation), and subsequently, to transfer the job's output data and to clean the working directory (after the computation).
Add the following lines at the end of the above script:
a) Shared storage (home via NFS)
b) Network connected storage (without NFS)
Specify the job's resource requirements (number of execution nodes, requested processors, memory, scratch size and
type, application license, etc.) and the maximum job run-time (walltime).
These resource requirements can be specified:
Qsub example:
New select syntax offers more possibilities – chunks usage, submitting requests on specific machine, work with cgroups, request for presence/absence of specific machine feature, ...
Qsub modications: Attention, for better comprehensibility, following
examples aren’t complete. Memory, scratch, walltime ... may not be assigned!
See the man qstat page for a description of all options.
Status of the job (most common):
Q ... queued E ... exiting
R ... running F ... finished
If you need to forcibly terminate/kill any of your job (no matter if already running or just waiting), use the qdel command as follows:
qsub -q default@wagap-pro.cerit-sc.cz
$ qstat -u <username> @wagap-pro.cerit-sc.cz
Qsub assembler: https://metavo.metacentrum.cz/pbsmon2/person
PBSMon web application monitoring jobs: https://metavo.metacentrum.cz/pbsmon2/
Documentation: https://wiki.metacentrum.cz/wiki/
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