using-the-cluster
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using-the-cluster [2018/02/07 06:32] – [Using the Cluster] aorth | using-the-cluster [2022/05/03 09:17] – aorth | ||
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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, compute2, compute04: used for batch and interactive jobs like BLAST, structure, R, etc | + | * **compute05**, **compute06**: used for batch and interactive jobs like BLAST, structure, R, etc (compute05 and compute06 have the newest AMD EPYC CPUs) |
- | * mammoth: used for high-memory jobs like genome assembly (mira, newbler, abyss, etc) | + | * **compute07**: used for high-memory jobs like genome assembly (mira, newbler, abyss, etc) |
- | * compute03: fast CPUs, but few of them | + | |
- | To get access to the cluster you should talk to [[d.githae@cgiar.org|Dedan Githae]] | + | To get access to the cluster you should talk to Jean-Baka |
+ | |||
+ | |||
+ | ===== How to Connect to the Cluster ===== | ||
+ | |||
+ | Connecting to the HPC **is not done through clicking on the "Log In" link** on the top right corner of these wiki pages. In order to launch computations on the HPC or even just to view files residing in its storage infrastructure, | ||
+ | |||
+ | ==== If you are running Mac OS X (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|}} | + | {{:hpc_topology_2019_web.png|}} |
==== Detailed Information ==== | ==== Detailed Information ==== | ||
^Machine | ^Machine | ||
- | |taurus|116 GB RAM \\ 64 CPUs | batch and interactive | + | |compute03 |
- | |mammoth | + | |compute05 |
- | |compute2| 132 GB RAM \\ 64 CPUs | batch and interactive jobs \\ Good for BLAST, structure, R, etc.|{{http:// | + | |compute06|256 GB RAM \\ 64 CPUs | batch and interactive jobs \\ Good for BLAST, structure, R, admixture, etc.|{{https:// |
- | |compute03 | + | |compute07| 1 TB RAM \\ 8 CPUs | batch and high-memory jobs \\ Good for genome assembly (mira, newbler, abyss, etc)|{{https:// |
===== Backups ===== | ===== 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. | ||
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using-the-cluster.txt · Last modified: 2023/01/06 06:14 by aorth