Page History

...

Note the use of the %I to create separate output files for each of the slots in the job array. Embarrassingly parallel programs need to know which part of the problem they will work on. If you read through the LSF documentation on jobs arrays, you'll see examples that show how to do this be by constructing separate stdin input files for each job array slot: Handling Input and Output Files which makes use of the %I expansion for job array slots. The page on Passing Arguments on the Command Line discusses how to make use of LSF environment variables that identify the jobindex, however this is tricky and the example which uses a backslash and passes \$LSB_JOB_INDEX does not work when I submit jobs under the bash shell. These environment variables are not defined until the job is launched on the remote host. The most robust way to access them seems to be to read the environment variables LSB_JOBINDEX and LSB_JOBINDEX_END from within your program rather than to try to construct a command line (however I had some success by enclosing the whole command line in "").

...