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Genepool

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The Genepool system is a cluster dedicated to the DOE Joint Genome Institute's computing needs.  Denovo is a smaller test system for Genepool that is primarily used by NERSC staff to test new system configurations and  software.

Genepool Upcoming Changes

Genepool's Upcoming Changes Genepool will see several important changes in 2017, outlined on this page. Changes to the system will increase system stability, create greater parity between Genepool and other NERSC HPC systems, and enable new tools like Shifter to run there. Users will need to make adjustments to the way that jobs are scheduled, and may need to recompile or make adjustments to accommodate a major OS version upgrade. If you have any questions or would like focused assistance in… Read More »

Getting started

Learn how to log in and get started Read More »

Configuration

The Genepool system will be made up of a heterogeneous collection of nodes to serve the diverse workload of the JGI users. Read More »

User Environment

When users log into Genepool/Phoebe they have the default global homes environment which includes the JGI software and tools. Read More »

Programming

The Genepool system has a rich set of software development tools and build environments. Read More »

Software

Users can access software in /jgi/tools. In the future NERSC will create software modules and details regarding software maintenance and access will be found here. Read More »

Queues and Policies

Learn about the fair share batch scheduler and queues used on Genepool/Phoebe Read More »

Running Jobs

UGE (Formerly Sun Grid Engine) is the batch system used on Genepool and Phoebe, this section will tell you how to run jobs using this system. Read More »

Cluster Statistics

Basic user and group usage statistiscs. Read More »

File storage and I/O

There are 5 main areas on Genepool where users can read, write and store data. This page documents the purpose and performance of each one. Read More »

Data Management

Move your data from Netapps to /project b or /house. Back up and delete data from house! Read More »

Genepool Training and Tutorials

This is a summary page for the trainings and tutorial sessions that have been given at the JGI.  So far we have just posted presentations and talks from 2013, we will work on getting the slides from 2012. Read More »

Websites, databases and cluster services

Regulations and best practices for running and using network services. Read More »

Denovo, the replacement for Genepool

Denovo is the name of the cluster we are using to test the upgrade for Genepool; i.e. it's what Genepool will eventually become. Denovo is production-ready from the viewpoint of system and software as of mid October 2017, and we will be migrating capacity from Genepool to Denovo as fast as circumstances allow. That means that as soon as you transition your pipelines to Denovo and verify that they work, we will move capacity across so you can switch to running on Denovo at the scales you need. Read More »

Cori for JGI

NERSC is pleased to provide compute capacity on its flagship supercomputer, Cori, to JGI users. Burst buffer, Shifter, and all other features available to Haswell Cori nodes are available via a new JGI "quality of service" (QOS). At this time, early access to a specialized partition is being made available to users willing to test and benchmark their software and pipelines. We expect the partition to be available to all JGI users for production use in Jan 2018. If you'd like early access,… Read More »