https://blake.bcm.edu/emanwiki/ 2026-04-17T02:26:19+00:00 https://blake.bcm.edu/emanwiki/ https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2025-07-05T21:27:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=cibrclusters:cibrclusters_software&rev=1751750827&do=diff Software available on the CIBR Clusters Most tools available on standard Linux installations will be available: * GCC collection * Python * Perl * Ruby * OpenMPI * etc. /usr/local is shared among all of the cluster nodes. So most extra software will be installed within that folder. You can find a lot of available tools simply by checking /usr/local/bin. text/html 2025-07-05T21:19:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=cibrclusters:introduction&rev=1751750365&do=diff Return to the CIBR Cluster Home Page Introduction to Clusters and CIBR Philosophy Glossary & Basic Concepts First, a little terminology. Here is the hierarchy of computing resources on a modern cluster (you may find some disagreement about some of these specific definitions): * Server text/html 2025-07-05T21:22:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=cibrclusters:movingdata&rev=1751750576&do=diff Return to the CIBR Cluster Home Page Moving Data to/from the Clusters Before you can run jobs on the cluster, you will need to first get your data to the cluster. The primary storage on each cluster is designed for temporary use while running jobs, not permanent storage of your data/results, and this cluster storage is not backed up in any way, so there is a measurable risk of total data loss (over a period of years). So, in addition to getting your data TO the cluster, it is also important to… text/html 2025-07-05T21:24:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=cibrclusters:prism&rev=1751750650&do=diff Return to the CIBR Cluster Home Page Prism Overview Prism is a medium-scale high performance linux cluster purchased by a collaborative arrangement between CIBR, and the Chiu, Barth, Wensel, Ludtke and Guan labs. Each group that contributed financially to the purchase of the cluster is entitled to a proportional amount of the overall compute capacity of the cluster. In theory, the cluster can provide up to 6M CPU-hr of computation annually, however, it is impossible to keep such a cluster fu… text/html 2025-07-05T21:24:57+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=cibrclusters:queue&rev=1751750697&do=diff Return to the CIBR Cluster Home Page Batch Queuing System A Batch Queuing System (BQS) manages all of the shared compute resources on a cluster. It allocates processors (and sometimes memory and other resources) to specific jobs in a specific order based on Queuing policies. When you have a job to run on the cluster, you prepare a short script file, describing the resources you need, and the commands to run, then submit it to the BQS. The BQS will then launch the job as soon as the necessary r… text/html 2025-07-05T21:22:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=cibrclusters:slurmqueue&rev=1751750533&do=diff General Policy * Please try to be considerate to other cluster users. * If the cluster is heavily occupied, we request that no single user have more than 240 cores (10 nodes) in the queue (running or waiting). The debug queue is an exception. * text/html 2025-07-05T21:21:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=cibrclusters:sphere&rev=1751750493&do=diff Return to the CIBR Cluster Home Page Sphere Overview Sphere is a medium-scale high performance linux cluster purchased by a collaborative arrangement between CIBR, and the Ludtke, Barth, Waterland and Guan labs. Each group that contributed financially to the purchase of the cluster is entitled to a proportional amount of the overall compute capacity of the cluster. In theory, the cluster can provide up to 6M CPU-hr of computation annually, however, it is impossible to keep such a cluster ful… text/html 2025-07-05T21:23:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=cibrclusters:storage&rev=1751750604&do=diff Return to the CIBR Cluster Home Page Data Storage Each cluster has one or more shared RAID6 arrays as well as scratch storage on each node. User's home folders are on the RAID6 array, and these folders are automounted on any node in the cluster on-demand. This RAID6 storage is NOT BACKED UP IN ANY WAY. While RAID6 storage is inherently more reliable than a normal hard drive, it is far from failure proof, and there is always the risk of hardware failure and TOTAL DATA LOSS. This storage is for… text/html 2025-07-05T21:26:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=cibrclusters:store&rev=1751750794&do=diff Reliable Storage for CIBR Clusters The home folders on all of the CIBR clusters are configured as scratch drives. They are all RAID arrays, and thus have some protection/redundancy, but they are not backed up in any way. That is, there is a significant risk of a failure causing complete data loss. Historically we have encountered an unrecoverable failure of this sort 3 times in ~10 years. That is to say that you should NOT rely on your home folder on the clusters for permanent storage. When yo… text/html 2025-07-05T21:29:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=cibrclusters:torus&rev=1751750988&do=diff Return to the CIBR Cluster Home Page THIS CLUSTER HAS BEEN RETIRED AND NO LONGER EXISTS Torus Policy Important Notice Torus is now operating beyond its end-of-life (ie - it is over 5 years old and out of warranty). Unfortunately it also suffered a severe software issue we have not yet managed to resolve. While we hope to bring it back in operation at some point to offset the load on the other clusters, we cannot guarantee this will happen.