Quest and Kellogg Linux Cluster Downtime, March 22 - 31.
Quest, including the Quest Analytics Nodes, the Genomics Compute Cluster (GCC), the Kellogg Linux Cluster (KLC), and Quest OnDemand, will be unavailable for scheduled maintenance starting at 8 A.M. on Saturday, March 22, and ending approximately at 5 P.M. on Monday, March 31. During the maintenance window, you will not be able to login to Quest, Quest Analytics Nodes, the GCC, KLC, or Quest OnDemand submit new jobs, run jobs, or access files stored on Quest in any way including Globus. For details on this maintenance, please see the Status of University IT Services page.
We strongly encourage all Quest users to review the summary of post-maintenance changes as these changes could immediately impact your workflow after the maintenance.
Quest RHEL8 Pilot Environment
The RHEL8 Pilot Environment is available for use now.
Ahead of the March 2025 Downtime, Quest users have the opportunity to test their software and research workflows on CPU nodes and NVIDIA H100 GPU nodes which are running the new RHEL8 OS. Detailed instructions are available on how to submit jobs for the new Operating System in the Knowledge Base article, RHEL8 Pilot Environment.
RHEL8 Pilot Quest log-in nodes can be access via ssh or FastX through using the hostname login.quest.northwestern.edu. Please note that the new hostname login.quest.northwestern.edu will require the GlobalProtect VPN when outside of the United States.
RHEL8 Pilot Quest Analytics nodes can be access via: rstudio.quest.northwestern.edu, jupyterhub.quest.northwestern.edu, and sasstudio.quest.northwestern.edu.
How to run Parabricks, the licensed GPU version of GATK 4, on the Genomics Compute Cluster on Quest.
NVIDIA’s Clara Parabricks is a licensed GPU version of GATK 4 which runs 10x faster than the open-source CPU version of GATK, and is available to genomics researchers at Northwestern who are members of the Genomics Compute Cluster. To run the CPU version of GATK 4, load the gatk/4.1.0 module. Information on running Parabrick's GPU version of GATK 4 is below.
Checking out Parabricks Licenses
When running Parabricks, your job will require a license for each gpu card it runs on. We have two Parabricks licenses in the Genomics Compute Cluster (GCC). To check out a Parabricks license for your job, include the license directive (-L) in your job submission command:
sbatch -L parabricks:2 <submission_script.sh>
In this example, two Parabricks licenses are being checked out for this job. The scheduler will keep track of checked out licenses and your job will not begin unless licenses are available for it. Run your Parabricks job on two GPU cards, using two Parabricks licenses.
Running Parabricks on Quest
Parabricks requires Python and Singularity to run, so before running Parabricks load the following Quest modules
module load python/anaconda3.6
module load singularity
Parabricks’s pbrun executable is installed in /projects/genomicsshare/software/parabricks_3_6/parabricks/pbrun.
Here’s an example of running the help command, which returns command options for Parabricks:
/projects/genomicsshare/software/parabricks_3_6/parabricks/pbrun --help
Sample submission scripts are in /projects/b1042/Parabricks_Training. Researchers do not have write permissions into that directory so launch these job submission scripts from your own projects directory.
Fastq to Bam example script
cd to your projects directory before submitting this example script:
sbatch -L parabricks:2 /projects/b1042/Parabricks_Training/fq2bam_quest.sh
Deep Variant example script
cd to your projects directory; the output of the deep variant test script will be written to a new sub-directory called “deepvariant”.
sbatch -L parabricks:2 /projects/b1042/Parabricks_Training/dv.sh