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<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>
<p style="margin: 0px;">TJ Mustard</p>
<p style="margin: 0px;"> </p>
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<br />
On September 28, 2010 at 3:21 AM TJ Mustard <mustardt@onid.orst.edu> wrote:<br />
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<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 http://www.gromacs.org/Documentation/Errors<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: mustardt@onid.orst.edu</p>
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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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