Interactive Jobs

In some cases you may want to run tests on the compute nodes, to validate your scripts.

A good way to do this is to run an LSF job in interactive mode. This way, you can simulate the exact environment in which your code will run. Here are the suggested commands for experimenting at the compute node level with interactive batch submission…

To run in interactive mode, use the -Is flags, with your shell of choice:

bsub -Is bash

Then you can interact on the node…

[hpcadmin@HPC-login ~]$ bsub -Is bash
Job is submitted to default queue .
Waiting for dispatch …
Starting on node069
bash-4.1$ /tools/bioperl-1.6.1/examples/bp_basic.pl
seq is 11 bases long
revcom seq is CTATCTACATG

Since all compute nodes are configured alike, you can test your syntax as it will apply across the cluster.

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