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CHPC - Research Computing Support for the University

In addition to deploying and operating high performance computational resources and providing advanced user support and training, CHPC serves as an expert team to broadly support the increasingly diverse research computing needs on campus. These needs include support for big data, big data movement, data analytics, security, virtual machines, Windows science application servers, protected environments for data mining and analysis of protected health information, and advanced networking. Visit our Getting Started page for more information.

Change in use of /scratch/local on compute nodes

Effective Tuesday July 21 on lonepeak

posted 7 July 2020

Access permissions to /scratch/local will be set such that users will no longer be able to created directories in the top level /scratch/local directory. Instead, as part of the slurm job prolog (before the job is started), a job level directory,  /scratch/local/$USER/$SLURM_JOB_ID , will be created.   After the end of the job, in the slurm job epilog, this job level directory will be removed.

Once we confirm there are no issues on lonepeak, we will make the same change on the other clusters (kingspeak, notchpeak, ash and redwood)


Summer 2020 CHPC Presentation Schedule


CHPC DOWNTIME: 6/9/2020 at 8am - and windows servers (Narwhal, Beehive) and the community MySQL server

Posted May 27th, 2020

CHPC DOWNTIME: Network upgrade - Wednesday, May 20 7:30 to ~8 am

Posted May 14th, 2020

Arbiter  now running on redwood general Interactive nodes

Posted May 5th, 2020

CHPC DOWNTIME - Science DMZ outage Monday May 4th at 4am

Posted May 1st, 2020

CHPC OUTAGE - /scratch/general/lustre

Posted April 24th, 2020

CHPC ANNOUNCEMENT: Change in Lonepeak Access

Posted: March 31st, 2020

2020 Spring CHPC Newsletter

CHPC ANNOUNCEMENT: CHPC staff working remotely

New PE scratch space - /scratch/general/pe-nfs1

News History...

rock pigeon genomics

Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia)

By Carson Holt, Michael Campbell, David A. Keays, Nathaniel Edelman, Aurélie Kapusta, Emily Maclary, Eric T. Domyan, Alexander Suh, Wesley C. Warren, Mark Yandell, M. Thomas P. Gilbert, and Michael D. Shapiro, Shapiro Lab, Department of Biology

Intensive selective breeding of the domestic rock pigeon (Columba livia) has resulted in more than 350 breeds that display extreme differences in morphology and behavior (Levi 1986; Domyan and Shapiro 2017). The large phenotypic differences among different breeds make them a useful model for studying the genetic basis of radical phenotypic changes, which are more typically found among different species rather than within a single species.

In genetic and genomic studies of C. livia, linkage analysis is important for identifying genotypes associated with specific phenotypic traits of interest (Domyan and Shapiro 2017); however, short scaffold sizes in the Cliv_1.0 draft reference assembly (Shapiro et al. 2013) hinder computationally-based comparative analyses. Short scaffolds also make it more difficult to identify structural changes, such as large insertions or deletions, that are responsible for traits of interest (Domyan et al. 2014; Kronenberg et al. 2015). 

Here we present the Cliv_2.1 reference assembly and an updated gene annotation set. The new assembly greatly improves scaffold length over the previous draft reference assembly, and updated gene annotations show improved concordance with both transcriptome and protein homology evidence.

Read the full article as it appears in G3.

System Status

General Environment

last update: 2020-07-14 12:23:02
General Nodes
system cores % util.
kingspeak 708/832 85.1%
notchpeak 2848/3164 90.01%
lonepeak 2676/2676 100%
Owner/Restricted Nodes
system cores % util.
ash 3240/7360 44.02%
notchpeak 5654/5676 99.61%
kingspeak 5603/5684 98.57%
lonepeak 416/416 100%

Protected Environment

last update: 2020-07-14 12:20:03
General Nodes
system cores % util.
redwood 28/408 6.86%
Owner/Restricted Nodes
system cores % util.
redwood 1232/3944 31.24%

Cluster Utilization


Last Updated: 7/7/20