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The job submission scripts use the flags from both the command line and the .py file ("logical or").
Batch Job Output
Because of a file-locking bug in afs, all output from GPAW should go to nfs. Our fileserver space is at /nfs/slac/g/suncatfs. You should always use the "/nfs" form of that name (the nfs automounter software often refers to it as "/a", but that syntax should not be in any of your scripts).
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