Using multiple processer to run the shell script

Question

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

Beware of parsing ls. What does your script do if a .pdb file has a space or newline in the filename? — ghoti
– ghoti, Commented Nov 1, 2017 at 11:29

Mark Setchell · Accepted Answer · 2017-11-01 10:51:41Z

1

Consider using GNU Parallel like this:

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

There’s a great tutorial here.

answered Nov 1, 2017 at 10:51

Mark Setchell

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ADEpt · Accepted Answer · 2017-11-01 00:20:24Z

0

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

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

answered Nov 1, 2017 at 0:20

ADEpt

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