Collaborative Computational Project No. 4
Software for Macromolecular X-Ray Crystallography

Belisama - CCP4 Cluster

This is a quick-guide page to the CCP4 cluster, Belisama. Its a very brief guide to what it is and how to use it. If you would like an account setup for you please contact Ronan (email: or ext: 3701).

About Belisama.....

    In Celtic mythology Belisama was goddess worshipped in Britain. She was connected with lakes and rivers, fire, crafts and light. She was often associated with the rivers Mersey and Ribble in North West England.

About the cluster.....

    The cluster is made up of 9 dual-AMD dual-core Opteron nodes. One master node for submitting and monitoring jobs and 8 compute nodes. They are all running the Suse 9.3 operating system and the job submission is handled by the Sun Grid Engine (SGE) batch queuing system.

Accessing the cluster

    Access to the cluster is by ssh only. To log-on ssh to with your username and password. This will log you on the cluster master node. All of your testing and job submission should be done from here.

Using the cluster

Submitting a job

  1. Batch Jobs: To submit a batch job you need to write a submission script similar to a short shell script. An example of this is give below. To submit the job simply type qsub "script_name".

    #$ -N job_name
    #$ -V
    #$ -cwd
    #$ -o job_name.out
    #$ -e job_name.err       
    ./pdbset xyzin input.pdb xyzout output.pdb << eof

    Some useful switches:
    -N : specifes the job name
    -V : this switch results in the job inheriting the environment of the shell from where it is submitted.
    -cwd : instructs the job to start in the current working directory
    -o : specify file for stdout
    -e : specify file for stderr
    -j y|n : specifies whether or the stdout and stderr streams should be merged
  2. Interactive Jobs: Jobs can also be submitted interactively to the cluster nodes. All stdout and stderr is directed to the submitting terminal unless specified. To submit an interact job simply prefix the job with the qrsh command. This command accepts most of the switches that you can pass to qsub. For example:
    qrsh -V molrep HKLIN mtzin.mtz MODEL input.pdb ....

Monitoring jobs

To view the job queue type qstat. This will list all of the jobs currently running and waiting in the job queue. If run you run qstat -f it will give a more detailed output listing all of the machines and there current status as well as the jobs they are running.

Deleting jobs

To delete a job type qdel "job number". To delete all of your jobs in one go type qdel -all.

Software currently installed

  1. CCP4 6.0 including phaser, chooch, mg and coot. Can be found under /usr/local/px/ccp4-6.0.
  2. CCP4 6.0.1 can be found in /usr/local/ccp4-6.0.1.
  3. Gnuplot.
  4. MAFFT sequence alignment program.
  5. Clustalw sequence alignment program.
  6. Python version 2.4.2
  7. Fasta34 and Ssearch34 sequence based search programs.
  8. MrBUMP 0.3.1 (under CCP4 6.0).

More detailed information....

    If you want more intformation about the cluster and how to use it you can find it in the online manual.