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" majord@mail.biu.ac.il To: "modeller_usage" modeller_usage@salilab.org 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 > > > >