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CIBR and other shared clusters

CIBR and a number of specific faculty have sponsored the purchase of several clusters managed for shared use by faculty. CIBR faculty may request moderate allocations for free, as a benefit of CIBR membership (which is free). Those requiring larger resources or dedicated time can participate in the purchase of future cluster equipment, and will get access to corresponding resources for the life of the cluster.

The 4 clusters currently in operation are:

Name	Cores	Storage	Purchased	Free CIBR Access	Paid Access	Notes
sphere.grid.bcm.edu	960	60 TB + 80 TB	2015	25,000 CPU-hr/qtr	Chiu, Barth, Guan, Waterland
prism.grid.bcm.edu	704	63+88 TB	2013	25,000 CPU-hr/qtr	Chiu, Barth, Wensel, Ludtke, Guan
torus.grid.bcm.edu	576+64	40+48+25 TB	2011-2012	10,000 CPU-hr/qtr	Chiu, Ludtke, Barth	Has 4 special 'bioinformatics' nodes with 16 cores and dedicated high performance storage. Temporarily offline for reinstallation
asterix.grid.bcm.edu	180+42 GPUs	10 TB	2009-2011	None	Ludtke, Chiu	GPUs, special projects, NCMI personnel can contact Dr. Ludtke
Store	-	350 TB Raid6x2	2013	upon request	-	Reliable storage (backed up RAID6) for inactive data which will still be needed on the clusters. This storage array is available upon request to users of any of the clusters, but is accessible only from the clusters to discourage people for using it for general lab backup purposes. Please note that the primary active storage on each cluster is NOT backed up in any way. It is a RAID6 volume, which gives it good reliability, but every 4-5 years we experience some sort of failure.

Each cluster has independent user accounts, as different faculty contributed different amounts to each. Please click on one of the links above for detailed policies and procedures for each cluster

All of the clusters run some version of CentOS Linux. We do not provide any commercial software, but most standard open-source tools are installed, and users are welcome to install commercial or free software within their own accounts. BCM's site license for Matlab is usable on the cluster, but must be installed/licensed in the user's account. Contact Larry Mayran about this for details. We may also be able to install other software system-wide, if you have such a need, please ask.

Details on some of the open-source software we have made available for users is maintained on the Software page.

There is a CIBR Cluster Google Group/Mailing List (https://groups.google.com/forum/#!forum/cibrcluster) which is used for announcements of outages, problems, policy changes, etc. We strongly recommend all CIBR Cluster users join.

In manuscripts, grant proposals, presentations, and other publications, please acknowledge the assistance from the CIBR Center by including a statement similar to the following: "We gratefully acknowledge the assistance and computing resources provided by the CIBR Center for Computational and Integrative Biomedical Research of Baylor College of Medicine in the completion of this work."

CIBR recently hosted a Mini-Workshop on cluster computing. The slides can be downloaded here: workshop2015.pdf

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-The 5 clusters currently in operation are:
||'''Name'''||'''Cores'''||'''Storage'''||'''Purchased'''||'''CIBR Access'''||'''Other Access'''||'''Notes'''||
+The 4 clusters currently in operation are:
||'''Name'''||'''Cores'''||'''Storage'''||'''Purchased'''||'''Free CIBR Access'''||'''Paid Access'''||'''Notes'''||
||[[CIBRClusters/Sphere|sphere.grid.bcm.edu]]||960||60 TB + 80 TB||2015||25,000 CPU-hr/qtr||Chiu, Barth, Guan, Waterland || ||
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-||[[CIBRClusters/Torus|torus.grid.bcm.edu]]||576+64||40+48+25 TB||2011-2012||10,000 CPU-hr/qtr||Chiu, Ludtke, Barth||Has 4 special 'bioinformatics' nodes with 16 cores and dedicated high performance storage||
||[[CIBRClusters/Gauss|gauss.grid.bcm.edu]]||632||48 TB||2007-2010||None||Ludtke, Chiu, Lichtarge, Milosavljevic, Barth|| ||
+||[[CIBRClusters/Torus|torus.grid.bcm.edu]]||576+64||40+48+25 TB||2011-2012||10,000 CPU-hr/qtr||Chiu, Ludtke, Barth||Has 4 special 'bioinformatics' nodes with 16 cores and dedicated high performance storage. <<BR>>Temporarily offline for reinstallation||
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+||[[CIBRClusters/Store|Store]]|| - || 350 TB Raid6x2 || 2013 || upon request || - || Reliable storage (backed up RAID6) for inactive data which will still be needed on the clusters. This storage array is available upon request to users of any of the clusters, but is accessible only from the clusters to discourage people for using it for general lab backup purposes. Please note that the primary active storage on each cluster is NOT backed up in any way. It is a RAID6 volume, which gives it good reliability, but every 4-5 years we experience some sort of failure. ||
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+All of the clusters run some version of CentOS Linux. We do not provide any commercial software, but most standard open-source tools are installed, and users are welcome to install commercial or free software within their own accounts. BCM's site license for Matlab is usable on the cluster, but must be installed/licensed in the user's account. Contact Larry Mayran about this for details.  We may also be able to install other software system-wide, if you have such a need, please ask.

Details on some of the open-source software we have made available for users is maintained on the [[CIBRClusters/Software|Software page]].

There is a CIBR Cluster Google Group/Mailing List (https://groups.google.com/forum/#!forum/cibrcluster) which is used for announcements of outages, problems, policy changes, etc. We strongly recommend all CIBR Cluster users join.

'''In manuscripts, grant proposals, presentations, and other publications, please acknowledge the assistance from the CIBR Center by including a statement similar to the following:'''
"We gratefully acknowledge the assistance and computing resources provided by the CIBR Center for Computational and Integrative Biomedical Research of Baylor College of Medicine in the completion of this work."

----
CIBR recently hosted a Mini-Workshop on cluster computing. The slides can be downloaded here: [[attachment:workshop2015.pdf]]