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: r.m.keegan@dl.ac.uk 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
belisama.dl.ac.uk 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
- 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".
#!/bin/bash
#$ -N job_name
#$ -V
#$ -cwd
#$ -o job_name.out
#$ -e job_name.err
./pdbset xyzin input.pdb xyzout output.pdb << eof
FIXBLANK
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
- 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
- CCP4 6.0 including phaser, chooch, mg and coot. Can be found under /usr/local/px/ccp4-6.0.
- CCP4 6.0.1 can be found in /usr/local/ccp4-6.0.1.
- Gnuplot.
- MAFFT sequence alignment program.
- Clustalw sequence alignment program.
- Python version 2.4.2
- Fasta34 and Ssearch34 sequence based search programs.
- 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.
