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| * [[Torus/Storage|Disk storage policies and advice]]
* [[Torus/Queue|Cluster usage instructions and policies]]
* [[attachment:MPI_Torus.pdf|Stephen Murray's instructions for installing OpenMPI in your account|&do=get]]
| * [[CIBRClusters/Prism/Queue|Running Jobs on the Cluster]]
* [[CIBRClusters/Prism/Storage|Disk storage policies]]
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 6,170,000 CPU-hr of computation annually, however, it is impossible to keep such a cluster fully loaded all of the time, and typical clusters run at ~60-80% of capacity, and allocations reflect this.
CIBR faculty can acquire time allocations on this cluster simply by requesting them via email to firstname.lastname@example.org. Initial allocations of 25,000 CPU-hr do not require any formal application, simply a request. The request must come from the PI, not students/postdocs, as allocations are made on a per-faculty basis, and the professor must decide how to allocate the time among people in his/her lab. Faculty must be members of CIBR to receive free time on the cluster (membership is free). If the initial allocation is exhausted, larger allocations may be possible, depending on usage levels, and the number of requests in that quarter.
Hardware & Software
- 1 Head node for job management
- 1 Storage node for home directories and mid-term data storage with a 40 TB Raid array
- 48 compute nodes, each with:
- 12 cores (dual 6-core CPUs)
- 48 GB of RAM (4 GB/core)
- 2 TB hard drive (1 TB local scratch, 1 TB Lustre)
- 4 additional "bioinformatics" nodes used exclusively for "bioinfo" queue, each with:
- 16 cores (dual 8-core CPUs)
- 256 GB of RAM (16 GB/core)
- 1 80GB SSD hard drive for system use. 7 1TB 2.5" hard drives raid5, mounted as /data1 (high speed local storage).
QDR Infiniband (40 Gb/sec) interconnect between nodes for high-performance MPI & Lustre filesystem
48 TB Lustre scratch filesystem accessible from all nodes, at speeds comparable to a local disk (offline until further notice)
Prism is equipped with a QDR Infiniband interconnect, capable of very high bandwidth transfers between nodes.
The cluster runs CentOS 6, a variant of linux, which is equivalent to RHEL6.
The Torque queuing system with Maui scheduler, basically equivalent to PBS. This is how users submit jobs for execution on the cluster nodes.
OpenMPI is available, and users are free to compile and use other MPI distributions which can take advantage of the available Infiniband interconnect.
- The cluster has a wide range of open-source programs and libraries installed on it as part of the CentOS distribution. Within limits, new packages requested by users can be added.
- There is, at present, no commercial software available on Torus. If you require a specific commercial software package, you may install your
- BCM's Matlab license is not for cluster use, though it is possible to install a license in your own account for use on one node at a time. To do this you need to use PBS in interactive mode. You MUST still use PBS, not directly log in to a node and run matlab.
Detailed Information on Using the Cluster
The cluster is currently maintained by Dwight Noel, who works for the NCMI, and maintains the clusters only part-time. In general, he will be happy to help you and answer your questions, but keep in mind that his effort is being provided as a courtesy to non-NCMI personnel. In general, if you don’t understand something about how to use the cluster effectively, or have any questions/issues, don’t hesitate to email (email@example.com) or Steve Ludtke ( firstname.lastname@example.org ).
SysOp: Dwight Noel email@example.com
Last modified on Feb 22, 2013