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using-the-cluster

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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. For each server, we mention the number of CPUs and the year it was commissioned:

Detailed Information

Machine Specifications Uses 1 hour status
taurus116 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.1584620179.txt.gz · Last modified: 2020/03/19 12:16 by jean-baka