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 and Owens Clusters. The versions currently available at OSC are the following:
| Version | Owens | Pitzer | Notes |
|---|---|---|---|
| 4.0.0-1 | X* | X* |
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 Owens
Set-up
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 Owens 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 1:00:00which 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.Usage on Pitzer
Set-up
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 Owens 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 1:00:00which 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.