Passing arguments on the command line
The environment variable LSB_JOBINDEX is used as a substitution string to support passing job array indices on the command line. When the job is dispatched, LSF sets LSB_JOBINDEX in the execution environment to the job array index of the current job. LSB_JOBINDEX is set for all jobs. For non-array jobs, LSB_JOBINDEX is set to zero.
To use LSB_JOBINDEX, all the input files must be named consistently and with a variable part that
corresponds to the indices of the job array. For
example:
input.1, input.2, input.3, ..., input.NYou must escape LSB_JOBINDEX with a backslash, \, to prevent the shell interpreting
bsub from expanding the variable. For example, the following command submits a
job array of 1000 jobs whose input files are named input.1,
input.2, input.3, ..., input.1000 and
located in the current working directory. The executable is being passed an argument that specifies
the name of the input
files:
bsub -J "myArray[1-1000]" myJob -f input.\$LSB_JOBINDEX