[gmx-users] Getting some interesting errors.

Berk Hess gmx3 at hotmail.com
Mon Sep 20 21:38:58 CEST 2010


Could you file a bugzilla?

And what do you mean with "-dlb on"?
on is not an option, the options are: auto, yes, no



Date: Mon, 20 Sep 2010 12:22:18 -0700
From: mustardt at onid.orst.edu
To: gmx-users at gromacs.org
Subject: [gmx-users] Getting some interesting errors.


    Message body

    Running several free energy perturbation (FEP) runs to further understand how I should set up my larger production runs and I keep getting errors that I cannot find in the gmx-user email or anywhere specifically online.




    Error 1:
    I get this error on three of my four runs.The system is a single rna in a water box. Amber03 and tip3p. Two are cyt an the other two are gua. I get through energy minimization (steep) and I fail on positional restriction sd. I can continue on if I turn -dlb on but I get error 2 below.


    Some interactions seem to be assigned multiple times...


    This seemed to occur after a restart of a failed job due to loss of HDD available space. I am trying to reproduce this error.





    Error 2:

    This error only comes up if I turn "-dlb on" in the above step. I get through energy minimisation (steep), positional restraint (sd) and I then fail on step 0 of my production run (sd).


    Getting Loaded...

    Reading file monomer_md.tpr, VERSION 4.5.1 (single precision)

    Starting 2 threads

    Loaded with Money


    Making 1D domain decomposition 2 x 1 x 1


    Back Off! I just backed up dhdl.xvg to ./#dhdl.xvg.1#

    starting mdrun 'Protein in water'

    625000 steps,   2500.0 ps.

    step 0/opt/gridengine/default/spool/compute-0-15/job_scripts/1877: line 50: 28413 Segmentation fault      /home/tjmustard/bin/Gromacs/gromacs-4.5.1-runfolder/bin/g4.5.1-mdrun -v -s monomer_md.tpr -o monomer_md.trr -c monomer_after_pr.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt -dlb no



    Both jobs are running on a linux cluster running SGE. I have had several jobs finish on this cluster with no problems. I am also running a slightly modified 4.5.1 version. The topsort.c file in the source code was missing a line of code and I was getting Improper Dihedral in ip_pert errors. I have run several methane hydration FEP's with very similar results. I am hoping this is a small problem that can be fixed easily.


    Thank you for any assistance,

    TJ Mustard

    Email: mustardt at onid.orst.edu

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