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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 id="stopSpelling">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>
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<p style="">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>
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<p style="">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>
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Some interactions seem to be assigned multiple times...<br>
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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>
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<p style="">Error 2:</p>
<p style="">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>
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<p style="">Getting Loaded...<br>
Reading file monomer_md.tpr, VERSION 4.5.1 (single precision)<br>
Starting 2 threads<br>
Loaded with Money<br>
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Making 1D domain decomposition 2 x 1 x 1<br>
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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>
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<p style="">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>
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<p style="">Thank you for any assistance,</p>
<p style="font-family: monospace; white-space: nowrap;">TJ Mustard<br>
Email: mustardt@onid.orst.edu</p>
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