After how many steps do you get the error? Do you get the error also with -dlb yes and the environment variable GMX_DLB_FLOP set to 1 or 2?
Roland On Tue, Sep 28, 2010 at 12:54 PM, TJ Mustard <[email protected]> wrote: > 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? > > > > TJ Mustard > > > > On September 28, 2010 at 3:21 AM TJ Mustard <[email protected]> > wrote: > > Hey all, > > > > 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... > > > > > > > > Back Off! I just backed up prlog.log to ./#prlog.log.1# > Getting Loaded... > Reading file monomer_pr.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 pr.edr to ./#pr.edr.1# > starting mdrun 'Protein in water' > 25000 steps, 100.0 ps. > step 900, will finish Mon Sep 27 18:19:07 2010imb F 18% > NOTE: Turning on dynamic load balancing > > step 1600, will finish Mon Sep 27 18:18:42 2010vol 0.92 imb F 1% > A list of missing interactions: > LJC Pairs NB of 278 missing 1 > exclusions of 6966 missing 1 > > ------------------------------------------------------- > Program g4.5.1-mdrun, VERSION 4.5.1 > Source code file: domdec_top.c, line: 173 > > Software inconsistency error: > Some interactions seem to be assigned multiple times > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > > > > > Some settings: > > > > define = -DPOSRES > > dt = 0.004 > nsteps = 25000 > > > > > > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = PME ; = Cutoff > rcoulomb-switch = 0 ; = 0 > rcoulomb = 0.9 ; = 1 > ; Relative dielectric constant for the medium and the reaction field > epsilon_r = 1 ; = 1 > epsilon_rf = 1 ; = 1 > ; Method for doing Van der Waals > vdw-type = Cut-off ; = Cut-off > ; cut-off lengths > rvdw-switch = 0 ; = 0 > rvdw = 1 ; = 1 > ; Apply long range dispersion corrections for Energy and Pressure > DispCorr = No ; = No > ; Extension of the potential lookup tables beyond the cut-off > table-extension = 1 ; = 1 > ; Seperate tables between energy group pairs > energygrp_table = ; = > ; Spacing for the PME/PPPM FFT grid > fourierspacing = 0.12 ; = 0.12 > ; FFT grid size, when a value is 0 fourierspacing will be used > fourier_nx = 0 ; = 0 > fourier_ny = 0 ; = 0 > fourier_nz = 0 ; = 0 > ; EWALD/PME/PPPM parameters > pme_order = 6 ; = 4 > ewald_rtol = 1e-05 ; = 1e-05 > ewald_geometry = 3d ; = 3d > epsilon_surface = 0 ; = 0 > optimize_fft = yes ; = no > > > > > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > ; Temperature coupling > tcoupl = v-rescale ; = No > nsttcouple = -1 ; = -1 > nh-chain-length = 10 ; = 10 > ; Groups to couple separately > tc-grps = RNA SOL ; = > ; Time constant (ps) and reference temperature (K) > tau-t = 0.1 0.1 ; = > ref-t = 300 300 ; = > ; Pressure coupling > Pcoupl = Parrinello-Rahman ; = No > Pcoupltype = Isotropic > nstpcouple = -1 ; = -1 > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > tau-p = 1 ; = 1 > compressibility = 4.5e-5 ; = > ref-p = 1.0 ; = > ; Scaling of reference coordinates, No, All or COM > refcoord_scaling = No ; = No > ; Random seed for Andersen thermostat > andersen_seed = 815131 ; = 815131 > > > > > > gen-vel = yes ; = no > gen-temp = 300 ; = 300 > gen-seed = 173529 ; = 173529 > > > > > > constraints = all-bonds > > > > 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. > > Thank you, > > TJ Mustard > Email: [email protected] > > > > TJ Mustard > Email: [email protected] > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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