using-the-cluster
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using-the-cluster [2020/03/19 13:20] – [How to Connect to the Cluster] jean-baka | using-the-cluster [2022/05/03 09:17] – aorth | ||
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ILRI's high-performance computing " | ILRI's high-performance computing " | ||
* **hpc**: main login node, " | * **hpc**: main login node, " | ||
- | * **taurus**, **compute2**, **compute04**: used for batch and interactive jobs like BLAST, structure, R, etc (compute04 has lots of disk space under its ''/ | + | * **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**: | + | * **compute03**: |
- | * **compute05**: | + | |
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 [[Using SLURM|SLURM]] so you can learn how to submit jobs to the cluster. | 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 [[Using SLURM|SLURM]] so you can learn how to submit jobs to the cluster. | ||
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===== How to Connect to the Cluster ===== | ===== 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, | + | Connecting to the HPC **is not done through clicking on the "Log In" link** on the top right corner of these wiki pages. |
- | ==== If you are running | + | ==== If you are running |
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:// | 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:// | ||
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==== If you are running Microsoft Windows ==== | ==== If you are running Microsoft Windows ==== | ||
- | If you are running Windows 10, you can access a simple ssh client by [[https:// | + | 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 ===== | ||
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^Machine | ^Machine | ||
- | |taurus|116 GB RAM \\ 64 CPUs | batch and interactive jobs \\ Good for BLAST, structure, R, admixture, etc.|{{https:// | ||
- | |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.|{{https:// | ||
|compute03 | 442 GB RAM \\ 8 CPUs | batch and high-memory jobs \\ Good for genome assembly (mira, newbler, abyss, etc), mothur|{{https:// | |compute03 | 442 GB RAM \\ 8 CPUs | batch and high-memory jobs \\ Good for genome assembly (mira, newbler, abyss, etc), mothur|{{https:// | ||
- | |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:// | |compute05 | 384 GB RAM \\ 48 CPUs \\ 1.6TB scratch | batch jobs \\ Most recent AMD EPYC CPUs, good for BLAST, structure, R, etc |{{https:// | ||
+ | |compute06|256 GB RAM \\ 64 CPUs | batch and interactive jobs \\ Good for BLAST, structure, R, admixture, etc.|{{https:// | ||
+ | |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