Skip to main content

Systems Biology Nero server

Systems Biology has a server that is available for general computing tasks. There is no easily accessible documentation, so these are my notes, for the record


There is a head node and then two nodes, each with 64 cores and 256GByte of RAM. The nodes can be accessed using ssh node003 and ssh node004, which requires that passwordless access using key-based authentication is set up correctly for your account.

Submitting jobs

Nero uses the Torque job scheduler which is the same as that used by the CSC cluster Minerva. Click for documentation.

The key-based authentication must be setup for job submission to work as this allows the nectessary file transfers to take place.

  • qstat -a : Lists all of the jobs
  • qstat -at : When jobs are loaded as an array of jobs this lists the status of each of the individual jobs


The home directory on the head node and the home directory on nodes 3 and 4 used for batch jobs are on different drives, and contain different files. The 'cluster' link from the head node sub directory takes you to the node3/4 home directory, which appears as /home/<username> when logged into the nodes or running a job. This means that .profiles etc need to be set up as appropriate

Toolsets such as gcc

Nero comes with a fairly old set of tools installed (e.g. the 2012 release 4.4.7 version of gcc which does not support C+ 2011). A newer set of tools can be enabled on the head node using

scl enable devtoolset-2 bash

which can be inserted into the .profile. devtoolset-2 is not available on nodes 3 & 4, but code compiled usiing this toolset on the head node appears to run on the other nodes, implying that the necessary shared objects are nevertheless available.

Using svn

The systems svn repository is now hosted on Nero. To checkout a directory from Nero onto nero itself the following works:

svn co svn+ssh://<username>@nero/home/shared/svn/TRegS/software/<path within Repository> <local directory>

Using the full address for Nero causes problems for ssh within svn. To checkout a directory to another plaform (e.g. pc) then use the full IRL for nero, ie

svn co svn+ssh://<username><path within Repository> <local directory>