[gmx-users] Another error that keeps comming up.

[Roland Schulz]

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 <mustardt at onid.orst.edu> 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 <mustardt at onid.orst.edu>
> 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: mustardt at onid.orst.edu
>
>
>
> TJ Mustard
> Email: mustardt at onid.orst.edu
>
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