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<p style="margin: 0px;">Yes "-dlb no" not on and I will file a bugzilla. Thanks again Berg Hess.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">TJ Mustard<span></span></p>
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<br />
On September 20, 2010 at 8:38 PM Berk Hess <gmx3@hotmail.com> wrote:<br />
<br />
<blockquote type="cite" style="margin-left: 0px; padding-left: 10px; border-left: solid 1px blue;">
Hi,<br />
<br />
Could you file a bugzilla?<br />
<br />
And what do you mean with "-dlb on"?<br />
on is not an option, the options are: auto, yes, no<br />
<br />
Thanks,<br />
<br />
Berk<br />
<br />
<hr />
Date: Mon, 20 Sep 2010 12:22:18 -0700<br />
From: mustardt@onid.orst.edu<br />
To: gmx-users@gromacs.org<br />
Subject: [gmx-users] Getting some interesting errors.<br />
<br />
<p>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.</p>
<p> </p>
<p> </p>
<p> </p>
<p>Error 1:</p>
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.<br />
<br />
Some interactions seem to be assigned multiple times...<br />
<br />
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.<br />
<br />
<br />
<br />
<br />
<p>Error 2:</p>
<p>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).</p>
<p> </p>
<p>Getting Loaded...<br />
Reading file monomer_md.tpr, VERSION 4.5.1 (single precision)<br />
Starting 2 threads<br />
Loaded with Money<br />
<br />
Making 1D domain decomposition 2 x 1 x 1<br />
<br />
Back Off! I just backed up dhdl.xvg to ./#dhdl.xvg.1#<br />
starting mdrun 'Protein in water'<br />
625000 steps,   2500.0 ps.<br />
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</p>
<p> </p>
<p> </p>
<p>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.</p>
<p> </p>
<p>Thank you for any assistance,</p>
<p style="font-family: monospace; white-space: nowrap;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
<br />
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<p style="margin: 0px;"> </p>
<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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