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Shell :

for a in `ls -1 *.pdb`; do ./fud --pdb=$a --command=run --state=-CRYSTAL --element=ion ; done cat //home/*.fxout >> results.out fgrep -v 1 results.out > new.out
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  • elaborate what exact command should be run in parallel? Commented Oct 31, 2017 at 12:25
  • I just need this shell script to run using multiple cores Commented Oct 31, 2017 at 14:25
  • 1
    Maybe you could consider user utility parallel Commented Nov 1, 2017 at 2:17
  • Beware of parsing ls. What does your script do if a .pdb file has a space or newline in the filename? Commented Nov 1, 2017 at 11:29

2 Answers 2

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Consider using GNU Parallel like this:

parallel ./fud —pdb={} —command=run —state=-CRYSTAL —element=ion ::: *.pdb

There’s a great tutorial here.

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Try xargs (-P specifies number of parallel processes to run):

ls -1 *.pdb | xargs -I {} -P8 ./fud --pdb={} --rest-of-switches > result.out
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