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Are SCRATCHDIR directories backed up somewhere?

Scratch directories are not backed up in any way.

The data my, however, still be available after the job ends if you did not delete the content of scratch directory manually. The data may persist for several days on the node until automated cleanup script removes them.

If the content of scratchdir was deleted by the batch script, or if the node experienced a hardware failure, the data are not retrievable in any way.