After how many steps do you get the error?<div><br></div><div>Do you get the error also with -dlb yes and the environment variable GMX_DLB_FLOP set to 1 or 2?</div><div><br></div><div>Roland</div><div><br><div class="gmail_quote">
On Tue, Sep 28, 2010 at 12:54 PM, TJ Mustard <span dir="ltr"><<a href="mailto:mustardt@onid.orst.edu">mustardt@onid.orst.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div>
<p style="margin:0px">Found that if I set the setting of "-dlb no" when running the mdrun it would not fail. How could dynamic load balancing do this?</p>
<p style="margin:0px"> </p><font color="#888888">
<p style="margin:0px">TJ Mustard</p></font><div><div></div><div class="h5">
<p style="margin:0px"> </p>
<div style="margin:5px 0px 5px 0px">
<br>
On September 28, 2010 at 3:21 AM TJ Mustard <<a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a>> wrote:<br>
<br>
<blockquote type="cite" style="margin-left:0px;padding-left:10px;border-left:solid 1px blue">
<p style="margin:0px">Hey all,</p>
<p style="margin:0px"> </p>
<p style="margin:0px">Here is another error that I keep getting. I am trying to "speed up" my md runs with -heavyh and longer time steps. I don't get LINCS errors but I do get this...</p>
<p style="margin:0px"> </p>
<p style="margin:0px"> </p>
<p style="margin:0px"> </p>
<p style="margin:0px">Back Off! I just backed up prlog.log to ./#prlog.log.1#<br>
Getting Loaded...<br>
Reading file monomer_pr.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 pr.edr to ./#pr.edr.1#<br>
starting mdrun 'Protein in water'<br>
25000 steps, 100.0 ps.<br>
step 900, will finish Mon Sep 27 18:19:07 2010imb F 18%<br>
NOTE: Turning on dynamic load balancing<br>
<br>
step 1600, will finish Mon Sep 27 18:18:42 2010vol 0.92 imb F 1%<br>
A list of missing interactions:<br>
LJC Pairs NB of 278 missing 1<br>
exclusions of 6966 missing 1<br>
<br>
-------------------------------------------------------<br>
Program g4.5.1-mdrun, VERSION 4.5.1<br>
Source code file: domdec_top.c, line: 173<br>
<br>
Software inconsistency error:<br>
Some interactions seem to be assigned multiple times<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<span></span></p>
<p style="margin:0px"> </p>
<p style="margin:0px"> </p>
<p style="margin:0px">Some settings:</p>
<p style="margin:0px"> </p>
<p style="margin:0px">define = -DPOSRES</p>
<p style="margin:0px">dt = 0.004<br>
nsteps = 25000</p>
<p style="margin:0px"> </p>
<p style="margin:0px"> </p>
<p style="margin:0px">; OPTIONS FOR ELECTROSTATICS AND VDW<br>
; Method for doing electrostatics<br>
coulombtype = PME ; = Cutoff<br>
rcoulomb-switch = 0 ; = 0<br>
rcoulomb = 0.9 ; = 1<br>
; Relative dielectric constant for the medium and the reaction field<br>
epsilon_r = 1 ; = 1<br>
epsilon_rf = 1 ; = 1<br>
; Method for doing Van der Waals<br>
vdw-type = Cut-off ; = Cut-off<br>
; cut-off lengths <br>
rvdw-switch = 0 ; = 0<br>
rvdw = 1 ; = 1<br>
; Apply long range dispersion corrections for Energy and Pressure<br>
DispCorr = No ; = No<br>
; Extension of the potential lookup tables beyond the cut-off<br>
table-extension = 1 ; = 1<br>
; Seperate tables between energy group pairs<br>
energygrp_table = ; =<br>
; Spacing for the PME/PPPM FFT grid<br>
fourierspacing = 0.12 ; = 0.12<br>
; FFT grid size, when a value is 0 fourierspacing will be used<br>
fourier_nx = 0 ; = 0<br>
fourier_ny = 0 ; = 0<br>
fourier_nz = 0 ; = 0<br>
; EWALD/PME/PPPM parameters<br>
pme_order = 6 ; = 4<br>
ewald_rtol = 1e-05 ; = 1e-05<br>
ewald_geometry = 3d ; = 3d<br>
epsilon_surface = 0 ; = 0<br>
optimize_fft = yes ; = no</p>
<p style="margin:0px"> </p>
<p style="margin:0px"> </p>
<p style="margin:0px">; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>
; Temperature coupling <br>
tcoupl = v-rescale ; = No<br>
nsttcouple = -1 ; = -1<br>
nh-chain-length = 10 ; = 10<br>
; Groups to couple separately<br>
tc-grps = RNA SOL ; =<br>
; Time constant (ps) and reference temperature (K)<br>
tau-t = 0.1 0.1 ; =<br>
ref-t = 300 300 ; =<br>
; Pressure coupling <br>
Pcoupl = Parrinello-Rahman ; = No<br>
Pcoupltype = Isotropic<br>
nstpcouple = -1 ; = -1<br>
; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>
tau-p = 1 ; = 1<br>
compressibility = 4.5e-5 ; =<br>
ref-p = 1.0 ; =<br>
; Scaling of reference coordinates, No, All or COM<br>
refcoord_scaling = No ; = No<br>
; Random seed for Andersen thermostat<br>
andersen_seed = 815131 ; = 815131</p>
<p style="margin:0px"> </p>
<p style="margin:0px"> </p>
<p style="margin:0px">gen-vel = yes ; = no<br>
gen-temp = 300 ; = 300<br>
gen-seed = 173529 ; = 173529</p>
<p style="margin:0px"> </p>
<p style="margin:0px"> </p>
<p style="margin:0px">constraints = all-bonds</p>
<p style="margin:0px"> </p>
<p style="margin:0px">Any help would be appreciated. It also seems to be intermittent as I have 21 identical runs (with different lambda values) and some work and some don't. It also changes every time I run them.</p>
<br>
Thank you,<br>
<p style="font-family:monospace;white-space:nowrap;margin:5px 0px 5px 0px">TJ Mustard<br>
Email: <a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a></p>
</blockquote>
</div>
<p style="margin:0px"> </p>
<p style="font-family:monospace;white-space:nowrap;margin:5px 0px 5px 0px">TJ Mustard<br>
Email: <a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a></p>
</div></div></div>
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