Before using LSF ... The Golden rules to batch happiness

1 - ALWAYS try one job interactively first
2 - DO NOT create a .tcshrc file tcsh reads .cshrc file if the other one is missing, batch may start using csh (not tcsh)
3 - Use explicit STAR_LEVELS A batch starts a new shell → The STAR environment is initialized to the site default (pro at the RCF, new at PDSF) In your .cshrc setenv STAR_LEVELS dev Before executing your program using command line setup starver SL03g starpro ...
4 - Avoid using LSF short cut submission command ~~% bsub -q 'some command'~~ (it is the #1 source for user confusion). Use an intermediate shell script (+ rule above)

1 - ALWAYS try one job interactively first