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using-the-cluster [2018/07/05 09:30]
aorth
using-the-cluster [2019/05/31 14:02]
jean-baka mammoth has 8 CPUs, not 16. fixed that.
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   * mammoth: used for high-memory jobs like genome assembly (mira, newbler, abyss, etc)   * mammoth: used for high-memory jobs like genome assembly (mira, newbler, abyss, etc)
   * compute03: fast CPUs, but few of them   * compute03: fast CPUs, but few of them
 +  * compute04: batch jobs, has lots of disk space in ''/​var/​scratch''​
  
-To get access to the cluster you should talk to [[d.githae@cgiar.org|Dedan Githae]] ​(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.
  
 ===== Cluster Organization ===== ===== 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: 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:
-{{:​ilri-hpc-topology.png?​350|}} +{{:​infrastructure-2018-fs8.png|}}
-{{:​infrastructure-2018-fs8.png?350|}}+
  
 ==== Detailed Information ==== ==== Detailed Information ====
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 ^Machine ​          ​^Specifications ​               ^Uses                 ^1 hour status ​  ^ ^Machine ​          ​^Specifications ​               ^Uses                 ^1 hour status ​  ^
 |taurus|116 GB RAM \\ 64 CPUs | batch and interactive jobs \\ Good for BLAST, structure, R, admixture, etc.|{{https://​hpc.ilri.cgiar.org/​ganglia/​graph.php?​g=load_report&​z=medium&​c=compute&​h=taurus&​m=os_name&​r=hour&​s=descending&​hc=4&​mc=2&​.gif?​}} | |taurus|116 GB RAM \\ 64 CPUs | batch and interactive jobs \\ Good for BLAST, structure, R, admixture, etc.|{{https://​hpc.ilri.cgiar.org/​ganglia/​graph.php?​g=load_report&​z=medium&​c=compute&​h=taurus&​m=os_name&​r=hour&​s=descending&​hc=4&​mc=2&​.gif?​}} |
-|mammoth | 516 GB RAM \\ 16 CPUs | batch and high-memory jobs \\ Good for genome assembly (mira, newbler, abyss, etc)|{{https://​hpc.ilri.cgiar.org/​ganglia/​graph.php?​g=load_report&​z=medium&​c=compute&​h=mammoth&​m=os_name&​r=hour&​s=descending&​hc=4&​mc=2&​.gif?​}} |+|mammoth | 516 GB RAM \\ CPUs | batch and high-memory jobs \\ Good for genome assembly (mira, newbler, abyss, etc)|{{https://​hpc.ilri.cgiar.org/​ganglia/​graph.php?​g=load_report&​z=medium&​c=compute&​h=mammoth&​m=os_name&​r=hour&​s=descending&​hc=4&​mc=2&​.gif?​}} |
 |compute2| 132 GB RAM \\ 64 CPUs | batch and interactive jobs \\ Good for BLAST, structure, R, etc.|{{https://​hpc.ilri.cgiar.org/​ganglia/​graph.php?​g=load_report&​z=medium&​c=compute&​h=compute2&​m=os_name&​r=hour&​s=descending&​hc=4&​mc=2&​.gif?​}} | |compute2| 132 GB RAM \\ 64 CPUs | batch and interactive jobs \\ Good for BLAST, structure, R, etc.|{{https://​hpc.ilri.cgiar.org/​ganglia/​graph.php?​g=load_report&​z=medium&​c=compute&​h=compute2&​m=os_name&​r=hour&​s=descending&​hc=4&​mc=2&​.gif?​}} |
 |compute03 | 442 GB RAM \\ 8 CPUs | batch and high-memory jobs \\ Good for genome assembly (mira, newbler, abyss, etc), mothur|{{https://​hpc.ilri.cgiar.org/​ganglia/​graph.php?​g=load_report&​z=medium&​c=compute&​h=compute03&​m=os_name&​r=hour&​s=descending&​hc=4&​mc=2&​.gif?​}} | |compute03 | 442 GB RAM \\ 8 CPUs | batch and high-memory jobs \\ Good for genome assembly (mira, newbler, abyss, etc), mothur|{{https://​hpc.ilri.cgiar.org/​ganglia/​graph.php?​g=load_report&​z=medium&​c=compute&​h=compute03&​m=os_name&​r=hour&​s=descending&​hc=4&​mc=2&​.gif?​}} |
 +|compute04 | 48 GB RAM \\ 8 CPUs \\ 10TB scratch | batch jobs \\ Good for BLAST, structure, R, etc that need lots of disk space |{{https://​hpc.ilri.cgiar.org/​ganglia/​graph.php?​g=load_report&​z=medium&​c=compute&​h=compute04&​m=os_name&​r=hour&​s=descending&​hc=4&​mc=2&​.gif?​}} | 
 +|compute05 | 384 GB RAM \\ 48 CPUs \\ 1.6TB scratch | batch jobs \\ Most recent AMD EPYC CPUs, good for BLAST, structure, R, etc |{{https://​hpc.ilri.cgiar.org/​ganglia/​graph.php?​g=load_report&​z=medium&​c=compute&​h=compute05&​m=os_name&​r=hour&​s=descending&​hc=4&​mc=2&​.gif?​}} |
 ===== 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.
  
using-the-cluster.txt · Last modified: 2019/05/31 14:40 by jean-baka