RPN tools

When using the RPN environment you have access to several tools, some of which are explained below.
You are using this RPN environment on our UQAM servers by default and on Compute Canada clusters after having followed the steps to set up the SSM environment.

A little reminder:
If you reach a "collaboration" web page asking for login and password information, try using 'science' for both.

Job submission

Usually, the way to submit, check, and kill a job depends on the scheduling system and on the way it is installed.
To make your life easier, the RPN environment contains a set of tools that will do all these "adjustments" for you and that you can always get used the same way. They will basically do a "translation" for you.

Submit a job

To submit any job on our UQAM servers, always use the command 'soumet'.
On the Compute Canada clusters it is up to you if you want to use soumet or not.

"Soumet" can only get used to submit shell scripts! If you want to submit anything else, for example an executable, you need to create a script first which executes the executable.
The scripts that will get executed to not know from which directory the job got submitted. Therefore, if you want to run a script in a certain directory, make sure you 'cd' into this directory first!

The command to submit a job/script could look like this:

Where:

'jobname' is the name of the shell script, also called job, you want to submit.

'-t  time_in_seconds' specifies the wallclock in seconds time you acquire for the job. Even if the job is not finished after this time expired the job will get terminated. So better always ask for enough time. However, on larger clusters like Compute Canada clusters jobs asking for more time will be queued longer.
On our UQAM systems the default wallclock time for single CPU/core jobs is 10 days. For multi core jobs the default time is 1 minute.

'-jn  listing_name'  specifies the name of the listing or log file of the job. Everything that would appear on the screen when running the job interactively will now get written into this file. The default listing name is the basename of the job.

'-listing  listing-directory'  specifies the directory in which the listing will get written. The default directory is:
       ~/listings/${TRUE_HOST}
If you want to use the default directory, you should first create the directory ~/listings and then create a symbolic link inside that directory, pointing to a place where you have more space, for example to a directory (that you have to create!) under your data space:

        mkdir -p /dataspace/Listings
        mkdir ~/listings
        ln -s /dataspace/Listings ~/listings/${TRUE_HOST}

Replace 'dataspace' with the full name of your data directory.

'-cpus  number_of_cpus'  specifies the number of cpus you want to use when running the job in parallel using MPI and/or OpenMP. The syntax is the following:  MPIxOpenMP
For example, if you want to use 4 MPI processes and 2 OpenMP processes you would write:  -cpus 4x2
If you want to use pure MPI with MPI=4 processes you would write:  -cpus 4x1  or simply  -cpus 4
If you want to use pure OpenMP with OpenMP=2 processes you would write:  -cpus 1x2
The default is 1x1.

'-mpi'  needs to get added when running a script (or the executable that will get executed within the script) with MPI.

To get more information about the command simply execute:

    soumet -h

Check on jobs

As said above, also the way to check (and kill) jobs depends on the queueing system. Therefore, we created a script called 'qs' which you can find in my ovbin:

    ~winger/ovbin/qs

On our UQAM servers as well as on Beluga (when using the RPN environment) you already have an alias pointing to the above command, called:

    qs

Kill a job

Depending on the machine, this might be an alias again.

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