RE: amber-developers: Testing Parallel

From: Lachele Foley <>
Date: Mon, 14 Apr 2008 19:54:04 -0400

Another good idea. I tried that, too (first, actually...). The result is:

[lachele.keats ~]$ setenv DO_P '/blah -o \"blah\" -blahblah'
[lachele.keats ~]$ echo $DO_P
/blah -o \"blah\" -blahblah

The scheduler didn't like that any better.

Granted, I might have missed a permutation, but I tried lots of varieties. Double in, single out. Single in, double out. Backslashes, no backslashes.

I even tried:

setenv DO_PARALLEL '/opt/scali/bin/scasub -qsparams {"-W} {block=true"} -mpimon -network gm0,smp -np 2 -npn 2'

...and a few variations on that, which echo correctly, but still give "qsub: script file:: No such file or directory". Soooo... I guess the scali wrapper (scasub) is generating a temporary file somewhere that it deletes after. And, somehow, having the quote mark in the environment variable messes with that or with qsub's ability to see the file (or something). And, after making a few more steps toward debugging it, I remind myself that it isn't my code... My guess is that the issue is in the scali wrapper or perhaps how qsub interprets arguments and isn't about the shell at all.

:-) Lachele
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
----- Original Message -----
From: Ross Walker
Sent: Mon,
14 Apr 2008 18:07:02 -0400
Subject: RE: amber-developers: Testing Parallel
> Hi Lachele
> > And, if anyone can explain how to make the quote marks work 
> > in the environment variable, I'm curious.
> Try escaping them with backslashes:
> [15:06][caffeine:0.32][rcw:~]$ export foo="foobar"
> [15:06][caffeine:0.27][rcw:~]$ echo $foo
> foobar
> [15:06][caffeine:0.25][rcw:~]$ export foo="\"foobar\""
> [15:06][caffeine:0.21][rcw:~]$ echo $foo              
> "foobar"
> All the best
> Ross
> /\
> \/
> |\oss Walker
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
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Received on Fri Apr 18 2008 - 21:19:23 PDT
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