Clara Parabricks

Clara Parabricks is a powerful toolkit designed for genomic analysis. It is primarily designed for GPU computation.

Availability and Restrictions

Versions

Clara Parabricks is available on Pitzer Cluster. The versions currently available at OSC are the following:

Version	Pitzer	Notes
4.0.0-1	X*

* Current default version

You can use module spider clara-parabricks to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

Clara-Parabricks is available to all OSC users. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

Open source

Usage

Usage on Pitzer

Set-up

To load the module for the default version of Parabricks, which initializes your environment for the Clara-Parabricks application, use module load clara-parabricks. To select a particular software version, use module load clara-parabricks/version. For example, use module load clara-parabricks/4.0.0-1 to load Parabricks version 4.0.0-1; and use module help clara-parabricks/4.0.0-1 to view details, such as, compiler prerequisites, additional modules required for specific executables, the suffixes of executables, etc.; some versions require specific prerequisite modules, and such details may be obtained with the command module spider clara-parabricks/version.

Batch Usage

When you log into Pitzer you are actually connected to a login node. To access the compute nodes, you must submit a job to the batch system for execution. Batch jobs can request multiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info.

Interactive Batch Session

For an interactive batch session, one can run the following command:

sinteractive -A <project-account> -N 1 -n 28 -t 1:00:00

which gives you one node with 28 cores (-N 1 -n 28), with 1 hour (-t 1:00:00). You may adjust the numbers per your need.