Sounds like you do not have the same environment when running jobs
interactively and through the queue. I am not familiar with NQS, does
"#QSUB -s /bin/sh" mean you run your jobs under the bourne shell? If you can
change this to tcsh you may get the proper environment (assuming MODELLER
environment variables are defined in your .cshrc file), MODELLER relies on
environment variables to find its libraries. Another test is to print out
the values of environment variables (the ones relevant to MODELLER) from
within a job to see if in fact they are undefined.
Best,
Roberto
--
Roberto Sanchez, Assistant Professor
Structural Biology Program, Department of Physiology & Biophysics and
Institute for Computational Biomedicine, Mount Sinai School of Medicine
Box 1677, 1425 Madison Avenue, New York, NY 10029
phone +1 (212) 659 8648, fax +1 (212) 849 2456
http://physbio.mssm.edu/~sanchez/
----- Original Message -----
From: "Dan Thomas Major" <>
To: "modeller_usage" <>
Sent: Wednesday, May 08, 2002 6:59 AM
Subject: Modeller in queue
> Hi,
> I was wondering if anyone has experience using Modeller through a queue.
>
> I'm trying to run Modeller6v1 using the NQS queueing system on an
> Origin2000 machine (SGI).
> I get the following error:
>
> sys-2 : UNRECOVERABLE error on system request
> No such file or directory
>
> Encountered during an OPEN of unit 11
> Fortran unit 11 is not connected
> IOT Trap
> /usr/spool/nqe/spool/scripts/++1qK++++27+++[6]: 399544 Abort(coredump)
>
> I manage to run Modeller interactively on the same machine.
> Attached is the NQS script used:
>
> #QSUB -s /bin/sh
> #QSUB -l mpp_p=1
> #QSUB -lt 172800
> #QSUB -lm 100MB
>
> /usr/home/chem/majord/bin/modeller/modeller6v1/bin/mod6v1_iris4d
> refine-loops3.top > refine-loops3.log
>
> Sincerely,
> Dan
>
>
> --
> Dan Thomas Major (at Dr. B. Fischer's lab)
> Bar-Ilan University
>
> Phone: 972-3-5317785
> Fax: 972-3-5348730
>
>
>
>