Hack to switch to tea Shell

/bin/tcsh

How to synchronise with sub-processes

In tcsh, to wait for processes on the same node use

wait

Surprisingly simple, eh? Even the defaults seem ok. See man wait.

Run multiple processes on the same node using "&" in the usual way then wait (in the same shell script file as the &) for them to complete (or fail etc.) May need to adjust -n parameter to LSF bsub to increase the number of CPU cores it allocates.

Enabling CUDA

module load cuda

Use module avail to see other packages that module can load for you.

How to prevent it dumping cores

In Tee shell etc

limit coredumpsize 0

(With unix bash use ulimit -c)

By default failing runs can generate huge files containing core dumps. Often the error message give a good enough idea what went wrong so telling Unix not to generate core dumps saves time.

Problems with LSF

`bpeek: No match.`

bpeek 72890[1]
bpeek: No match.

This is an error with the unix shell command line interpreter rather than bpeek. The work around is to simply wrap the argument to bpeek inside double quotes:

bpeek "72890[1]"

Potentially useful Batch Environment Variables

HOST
LSB_BATCH_JID=70590[1]
LSB_JOBID=70590
LSB_JOBNAME=allgenes[1-1]
LSB_HOSTS=
LSB_JOBFILENAME
LSB_JOBINDEX=55
LSB_JOBINDEX_STEP=1
LSB_JOBINDEX_END=100
LSB_OUTPUTFILE=xtrain2nd_1

Article in SIGEvolution. (Slides).
Technical report on using initial experiences of Emerald RN/12/08.

Created 9 June 2012 by W.Langdon (last update 11 Feb 2013).