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Cluster 2.0

Intro

How old cluster installation was superseded by the so-called cluster2.0. You access cluster2.0 just by ssh to login1 (141.80.186.21). login2 is currently not available for normal users.

Main differences

  • Base OS is now Ubuntu10.4 instead of Suse Linux Enterprise 10
  • programs formerly installed in /usr/local can now be found in /usr/local_old CAUTION: These are not compiled for Ubuntu. They may or may not work. This is only for your convenience until these programs are available in /usr/local/
  • All fileservers are mounted using NFS4 now. This should provide some speed benefits. 
  • GridEngine is now "Univa GridEngine 8.0" some options and output formats may have changed.
  • The number of queues is reduced now. "standard" and "standard-big" are now collapsed into one queue "standard". Same goes for "high" and "high-big". Job go to bignodes depending on resource requests.
  • The log file on the nodes is located at /var/spool/sge/<node_name>/messages

New GE features

  • qsub now supports the option -tc limiting the number of concurrently running taks for array jobs.

Software already installed

name
description version
installation source
location
additional information
R  language and environment for statistical computing and graphic 2.13.1 distribution package


bioConductor
R library for analysis and comprehension of genomic data

2.2 (?)

R source package
/usr/local/lib/R

boost  multi-purpose C libraries 1.40.0.1 distribution package

graphviz  graph visualization programs 2.20.2
distribution package

bioruby
Ruby library for bioinformatics 1.4.0.2
distribution package

OLB
Illumina OfflineBaseCaller
1.9.0
1.9.3
source packages
/usr/local/OLB-1.9.0
/usr/local/OLB-1.9.3

CASAVA
Consensus Assessment of Sequence and Variation 1.8.1
source package
/usr/local/CASAVA_v1.8.1

samtools
tools for the Sequence Alignment/Map format 0.1.17
precompiled package /usr/local/samtools-0.1.17
shogun
Large Scale Machine Learning Toolbox
0.0.1
distribution package


bowtie
ultrafast, memory-efficient short read aligner 0.12.7
precompiled package /usr/local/bowtie-0.12.7
cufflinks
Transcript assembly, differential expression, and differential regulation for RNA-Seq
1.0.3
precompiled package /usr/local/cufflinks-1.0.3
tophat
fast splice junction mapper for RNA-Seq reads 1.3.1
precompiled package /usr/local/tophat-1.3.1
SHRiMP
software package for aligning genomic reads against a target genome 2.2.0
precompiled package
/usr/local/SHRiMP_2_2_0/
http://compbio.cs.toronto.edu/shrimp/
bedTools
utilities for comparing genomic features
2.16.2
source package
/usr/local/bin
https://code.google.com/p/bedtools/#BEDTools_Summary

Compare to Installed software for cluster1.0 installed software.

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