Kurt-Hetrick / CIDR_WES

CIDR's production pipeline for WES and other targeted DNA sequencing projects.
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exclude bigdata-03 #27

Closed Kurt-Hetrick closed 6 years ago

Kurt-Hetrick commented 6 years ago

you're killing me smalls

Kurt-Hetrick commented 6 years ago

The -l should be first! (If qsub works the way qlogin worked for me)

qsub -l h=’! node’ -q prod.q,rnd.q

Kurt-Hetrick commented 6 years ago

done. the comment above actually does not work but, -l 'hostname=!node' does

brmyers commented 6 years ago

heads up, this has burned me before qsub -l h=’! node’ -q prod.q,rnd.q doesn't work because it has apostrophes. -l 'hostname=!node' does work because it's single vertical ticks/ straight quotes

Kurt-Hetrick commented 6 years ago

Thanks,

I did use single quote/non-apostrophe (you'll notice in the #hpc channel they are in single quotes).

the apostrophes are from when I copied from an email and was too lazy to fix it (in here, not in the submission).

qalter -l h='! DellR730-03' -q bigdata.q,c6320.q,lemon.q,prod.q,rnd.q 5868563 unknown resource "DellR730-03"

the problem here is the space b/w the node and ! (which was also in the email)

also the "-l" does not need to come first, but yes, you can use h=! as well as hostname=!

the two biggest things that were wrong in the email are

  1. use of single ticks instead of apostrophes
  2. there is no white space b/w the ! and the node name

qsub -q bigdata.q,c6320.q,lemon.q,prod.q,rnd.q -l 'h=!DellR730-03' test.sh Your job 5877982 ("test.sh") has been submitted

I used qstat -F -q bigdata.q -s r to look at the syntax for resource allocation/request (that's how I came up with hostname).