using-the-cluster
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using-the-cluster [2016/07/27 12:36] – joguya | using-the-cluster [2020/03/19 14:34] – [Cluster Organization] jean-baka | ||
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====== Using the Cluster ====== | ====== Using the Cluster ====== | ||
- | ILRI's high-performance computing " | + | ILRI's high-performance computing " |
- | * hpc: main login node, " | + | |
- | * taurus, | + | |
- | * mammoth: used for high-memory jobs like genome assembly (mira, newbler, abyss, etc) | + | |
+ | * **compute03**: | ||
+ | * **compute05**: | ||
- | To get access to the cluster you should talk to [[J.Oguya@cgiar.org|James Oguya]] | + | To get access to the cluster you should talk to Jean-Baka |
+ | |||
+ | |||
+ | ===== How to Connect to the Cluster ===== | ||
+ | |||
+ | In order to launch computations on the HPC or even just to view files residing in its storage infrastructure, | ||
+ | |||
+ | ==== If you are running MacOSX (on Apple computers) or any GNU/Linux distribution ==== | ||
+ | |||
+ | Those operating systems are part of the large family of UNIX systems, that almost invariably contain an already-installed SSH client, most often some flavor of the [[https:// | ||
+ | |||
+ | If the above doesn' | ||
+ | |||
+ | |||
+ | ==== If you are running Microsoft Windows ==== | ||
+ | |||
+ | If you are running Windows 10, you can access a simple ssh client by [[https:// | ||
+ | |||
+ | |||
+ | Another option is to [[https:// | ||
+ | * host: '' | ||
+ | * port: leave the default SSH port, i.e. port 22 | ||
+ | * username: your username, as communicated by the person who created your HPC account. | ||
===== Cluster Organization ===== | ===== Cluster Organization ===== | ||
- | The cluster is arranged in a master/ | + | The cluster is arranged in a master/ |
- | {{:ilri-hpc-topology.png?350|}} | + | {{tutorials:hpc_topology_2019_web.png|}} |
==== Detailed Information ==== | ==== Detailed Information ==== | ||
^Machine | ^Machine | ||
- | |taurus|116 GB RAM \\ 64 CPUs | batch and interactive jobs \\ Good for BLAST, structure, R, admixture, etc.|{{http:// | + | |taurus|116 GB RAM \\ 64 CPUs | batch and interactive jobs \\ Good for BLAST, structure, R, admixture, etc.|{{https:// |
- | |mammoth | 516 GB RAM \\ 16 CPUs | batch and high-memory jobs \\ Good for genome assembly (mira, newbler, abyss, etc)|{{http:// | + | |mammoth | 516 GB RAM \\ 8 CPUs | batch and high-memory jobs \\ Good for genome assembly (mira, newbler, abyss, etc)|{{https:// |
- | |compute2| 132 GB RAM \\ 64 CPUs | batch and interactive jobs \\ Good for BLAST, structure, R, etc.|{{http:// | + | |compute2| 132 GB RAM \\ 64 CPUs | batch and interactive jobs \\ Good for BLAST, structure, R, etc.|{{https:// |
- | + | |compute03 | 442 GB RAM \\ 8 CPUs | batch and high-memory jobs \\ Good for genome assembly (mira, newbler, abyss, etc), mothur|{{https:// | |
- | ==== Backups ==== | + | |compute04 | 48 GB RAM \\ 8 CPUs \\ 10TB scratch | batch jobs \\ Good for BLAST, structure, R, etc, that need lots of local disk space (/ |
+ | |compute05 | 384 GB RAM \\ 48 CPUs \\ 1.6TB scratch | batch jobs \\ Most recent AMD EPYC CPUs, good for BLAST, structure, R, etc |{{https:// | ||
+ | ===== Backups | ||
At the moment we don't backup users' data in their respective home folders. We therefore advise users to have their own 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.txt · Last modified: 2023/01/06 06:14 by aorth