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using-the-cluster [2016/01/07 16:36]
joguya [Using the Cluster]
using-the-cluster [2019/05/31 14:40] (current)
jean-baka [Using the Cluster]
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 ILRI's high-performance computing "​cluster"​ is currently composed of 4 dedicated machines: ILRI's high-performance computing "​cluster"​ is currently composed of 4 dedicated machines:
   * hpc: main login node, "​master"​ of the cluster   * hpc: main login node, "​master"​ of the cluster
-  * taurus,​compute2:​ used for batch and interactive jobs like BLAST, structure, R, etc+  * taurus, compute2, compute04: used for batch and interactive jobs like BLAST, structure, R, etc
   * 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
 +  * compute04: batch jobs, has lots of disk space in ''/​var/​scratch''​
 +  * compute05: batch jobs, has the fastest processors (AMD EPYC)
  
-To get access to the cluster you should talk to [[a.orth@cgiar.org|Alan Orth]] ​(he sits in Lab 2).  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|}} 
 ==== Detailed Information ==== ==== Detailed Information ====
  
 ^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.|{{http://​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)|{{http://​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.|{{http://​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?​}} | 
 +|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 ===== 
 +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.1452173791.txt.gz · Last modified: 2016/01/07 16:36 by joguya