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Splitting work into 20 jobs and running with 100 processors using sh
I’m not familiar with the MR protocol, but this line concerns me. Is this on a single box or a cluster? If it’s a single 8-core, shared memory machine, trying to launch 100 copies of Rosetta or Phenix is very likely to hang/kill your box as they all compete for the same 8 cores and the same memory.
Try changing the “nproc = 100” line to something more reasonable for your system and see if that helps.