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using-the-cluster
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Table of Contents
Using the Cluster
ILRI's high-performance computing "cluster" is currently composed of 7 dedicated machines:
- hpc: main login node, "master" of the cluster
- taurus, compute2, compute04: used for batch and interactive jobs like BLAST, structure, R, etc (compute04 has lots of disk space under its
/var/scratch) - mammoth: used for high-memory jobs like genome assembly (mira, newbler, abyss, etc)
- compute03: fast CPUs, but few of them
- compute05: batch jobs, has the fastest processors (AMD EPYC)
To get access to the cluster you should talk to Jean-Baka (he sits in BecA). Once you have access you should read up on SLURM so you can learn how to submit jobs to the cluster.
Cluster Organization
The cluster is arranged in a master/slave configuration; users log into HPC (the master) and use it as a "jumping off point" to the rest of the cluster. Here's a diagram of the topology:
Detailed Information
| Machine | Specifications | Uses | 1 hour status |
|---|---|---|---|
| taurus | 116 GB RAM 64 CPUs | batch and interactive jobs Good for BLAST, structure, R, admixture, etc. |  |
| mammoth | 516 GB RAM 8 CPUs | batch and high-memory jobs Good for genome assembly (mira, newbler, abyss, etc) |  |
| compute2 | 132 GB RAM 64 CPUs | batch and interactive jobs Good for BLAST, structure, R, etc. |  |
| compute03 | 442 GB RAM 8 CPUs | batch and high-memory jobs Good for genome assembly (mira, newbler, abyss, etc), mothur |  |
| compute04 | 48 GB RAM 8 CPUs 10TB scratch | batch jobs Good for BLAST, structure, R, etc that need lots of disk space |  |
| compute05 | 384 GB RAM 48 CPUs 1.6TB scratch | batch jobs Most recent AMD EPYC CPUs, good for BLAST, structure, R, etc |  |
Backups
At the moment we don't backup users' data in their respective home folders. We therefore advise users to have their own backups.
using-the-cluster.1584620084.txt.gz · Last modified: 2020/03/19 12:14 by jean-baka
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