Specify an output file
Use the -o or -oo option to bsub to specify an output file for your batch job. If you do not specify a viable file, the output will be sent via email which when multiplied by the 100s or 1000s can easily overwhelm the mail server.
Use local scratch space
Use local scratch space during the course of your job and copy over the results to the final location when the job finishes. The amount of scratch available varies by machine type, but you can request a host with a certain amount of space with the -R option, e.g. bsub -R "scratch>10" would request a host with 10GB of scratch.
Overview
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