[gmx-developers] Error in parrallel mdrun:" More than 8 graph edges per atom"

Igor Leontyev ileontyev at ucdavis.edu
Sun Oct 26 01:32:27 CEST 2008


Hi, gromacs experts.
I have problem starting parallel simulations on 5 and more cpus:
-------------------------------------------------------
Program mdrun, VERSION 3.3.1
Source code file: mshift.c, line: 91
Fatal error:
More than 8 graph edges per atom (atom 950)
------------------------------------------------------- 
Reported earlier solution "to increase the number 4 on the line 229 of 
mshift.c" is associated with compilation process which is kind of 
complicated for me. Moreover, the solution seems to be irrelevant for my 
case since the problem disappears when simulation is started on 4 cpu. Do 
someone has any idea how to avoid the problem in 16 cpu mdrun without 
recompilation?
       Bellow is log of the successful mdrun on 4 cpus:

################################################

                         :-)  G  R  O  M  A  C  S  (-:

                   Great Red Oystrich Makes All Chemists Sane

                            :-)  VERSION 3.3.1  (-:


      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2006, The GROMACS development team,
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                    :-)  /opt2/gromacs-3.3.1/bin/mdrun  (-:


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------

CPU=  0, lastcg=11941, targetcg=23909, myshift=    3
CPU=  1, lastcg=15926, targetcg= 3959, myshift=    3
CPU=  2, lastcg=19910, targetcg= 7943, myshift=    2
CPU=  3, lastcg=23934, targetcg=11967, myshift=    2
nsb->shift =   3, nsb->bshift=  0
Listing Scalars
nsb->nodeid:         0
nsb->nnodes:      4
nsb->cgtotal: 23935
nsb->natoms:  47813
nsb->shift:       3
nsb->bshift:      0
Nodeid   index  homenr  cgload  workload
     0       0   11952   11942     11942
     1   11952   11955   15927     15927
     2   23907   11952   19911     19911
     3   35859   11954   23935     23935

parameters of the run:
   integrator           = md
   nsteps               = 1000
   init_step            = 0
   ns_type              = Grid
   nstlist              = 20
   ndelta               = 2
   bDomDecomp           = FALSE
   decomp_dir           = 0
   nstcomm              = 1003
   comm_mode            = Angular
   nstcheckpoint        = 1000
   nstlog               = 1000
   nstxout              = 100
   nstvout              = 100
   nstfout              = 0
   nstenergy            = 0
   nstxtcout            = 0
   init_t               = 0
   delta_t              = 0.002
   xtcprec              = 1000
   nkx                  = 52
   nky                  = 60
   nkz                  = 91
   pme_order            = 4
   ewald_rtol           = 1e-05
   ewald_geometry       = 0
   epsilon_surface      = 0
   optimize_fft         = FALSE
   ePBC                 = xyz
   bUncStart            = FALSE
   bShakeSOR            = FALSE
   etc                  = Berendsen
   epc                  = Berendsen
   epctype              = Isotropic
   tau_p                = 0.5
   ref_p (3x3):
      ref_p[    0]={ 1.01325e+00,  0.00000e+00,  0.00000e+00}
      ref_p[    1]={ 0.00000e+00,  1.01325e+00,  0.00000e+00}
      ref_p[    2]={ 0.00000e+00,  0.00000e+00,  1.01325e+00}
   compress (3x3):
      compress[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
      compress[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
      compress[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
   andersen_seed        = 815131
   rlist                = 1
   coulombtype          = PME
   rcoulomb_switch      = 0
   rcoulomb             = 1
   vdwtype              = Cut-off
   rvdw_switch          = 0
   rvdw                 = 1
   epsilon_r            = 1
   epsilon_rf           = 1
   tabext               = 1
   gb_algorithm         = Still
   nstgbradii           = 1
   rgbradii             = 2
   gb_saltconc          = 0
   implicit_solvent     = No
   DispCorr             = No
   fudgeQQ              = 0.8333
   free_energy          = no
   init_lambda          = 0
   sc_alpha             = 0
   sc_power             = 0
   sc_sigma             = 0.3
   delta_lambda         = 0
   disre_weighting      = Conservative
   disre_mixed          = FALSE
   dr_fc                = 1000
   dr_tau               = 0
   nstdisreout          = 100
   orires_fc            = 0
   orires_tau           = 0
   nstorireout          = 100
   dihre-fc             = 1000
   dihre-tau            = 0
   nstdihreout          = 100
   em_stepsize          = 0.01
   em_tol               = 10
   niter                = 20
   fc_stepsize          = 0
   nstcgsteep           = 1000
   nbfgscorr            = 10
   ConstAlg             = Lincs
   shake_tol            = 1e-04
   lincs_order          = 4
   lincs_warnangle      = 30
   lincs_iter           = 1
   bd_fric              = 0
   ld_seed              = 1993
   cos_accel            = 0
   deform (3x3):
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   userint1             = 0
   userint2             = 0
   userint3             = 0
   userint4             = 0
   userreal1            = 0
   userreal2            = 0
   userreal3            = 0
   userreal4            = 0
grpopts:
   nrdf:            101649
   ref_t:           298.15
   tau_t:              0.2
anneal:                        No
ann_npoints:             0
   acc:                  0           0           0
   nfreeze:           Y           Y           Y           N           N 
N
   energygrp_flags[  0]: 0
   efield-x:
      n = 0
   efield-xt:
      n = 0
   efield-y:
      n = 0
   efield-yt:
      n = 0
   efield-z:
      n = 0
   efield-zt:
      n = 0
   bQMMM                = FALSE
   QMconstraints        = 0
   QMMMscheme           = 0
   scalefactor          = 1
qm_opts:
   ngQM                 = 0
Max number of graph edges per atom is 6
Table routines are used for coulomb: TRUE
Table routines are used for vdw:     FALSE
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's:   NS: 1   Coulomb: 1   LJ: 1
System total charge: -0.000
Generated table with 1000 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1000 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1000 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 500 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for 1-4 LJ12.
Tabscale = 500 points/nm

Enabling SPC water optimization for 11938 molecules.

Will do PME sum in reciprocal space.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Parallelized PME sum used.
PARALLEL FFT DATA:
   local_nx:                  13  local_x_start:                   0
   local_ny_after_transpose:  15  local_y_start_after_transpose    0
Removing pbc first time
Done rmpbc
Center of mass motion removal mode is Angular
We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 302278
There are: 11952 Atoms

Constraining the starting coordinates (step -2)

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------


Initializing LINear Constraint Solver
  number of constraints is 5967
  average number of constraints coupled to one constraint is 0.9

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.012234   6702   6703   0.003802
        After LINCS         0.000005   7804   7806   0.000001

Going to use C-settle (4 waters)
wo = 0.888099, wh =0.0559503, wohh = 18.016, rc = 0.075695, ra = 0.00655606
rb = 0.0520322, rc2 = 0.15139, rone = 1, dHH = 0.15139, dOH = 0.09572

Constraining the coordinates at t0-dt (step -1)
   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.001303   7535   7537   0.000163
        After LINCS         0.000026  10529  10532   0.000003

Started mdrun on node 0 Sat Oct 25 17:35:08 2008
Initial temperature: 296.531 K
           Step           Time         Lambda
              0        0.00000        0.00000

Grid: 12 x 14 x 21 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.


   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.061793   7445   7446   0.007589
        After LINCS         0.000032  10529  10532   0.000003

   Energies (kJ/mol)
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
    9.42960e+03    2.53513e+04    1.38929e+03    2.94437e+04    1.19233e+04
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
    1.38451e+05    4.34924e+04   -5.72876e+05   -2.39230e+05   -5.52626e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    1.25294e+05   -4.27332e+05    2.96497e+02   -1.70726e+02

           Step           Time         Lambda
           1000        2.00000        0.00000

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.072407   7445   7446   0.007658
        After LINCS         0.000032   3550   3551   0.000003

   Energies (kJ/mol)
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
    9.31967e+03    2.53570e+04    1.35254e+03    2.94476e+04    1.20265e+04
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
    1.38690e+05    4.33753e+04   -5.74055e+05   -2.39420e+05   -5.53906e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    1.26112e+05   -4.27794e+05    2.98434e+02    5.69840e+01


Total NODE time on node 0: 242.99
Average NODE time: 60.7475
Load imbalance reduced performance to 400% of max
       <======  ###############  ==>
       <====  A V E R A G E S  ====>
       <==  ###############  ======>

   Energies (kJ/mol)
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
    9.28039e+03    2.53419e+04    1.35613e+03    2.93246e+04    1.19887e+04
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
    1.38392e+05    4.33318e+04   -5.73108e+05   -2.39245e+05   -5.53338e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    1.25976e+05   -4.27362e+05    2.98111e+02   -2.69801e+00

          Box-X          Box-Y          Box-Z         Volume   Density (SI)
    6.09850e+00    7.19869e+00    1.08997e+01    4.78511e+02    1.04899e+03
             pV
   -7.77757e+01

   Total Virial (kJ/mol)
    4.16629e+04    3.74690e+02   -3.38657e+02
    3.74799e+02    4.14944e+04    1.74394e+02
   -3.41842e+02    1.75904e+02    4.29355e+04

   Pressure (bar)
    2.41223e+01   -2.06918e+01    2.23237e+01
   -2.06993e+01    4.74897e+01   -6.10837e+00
    2.25447e+01   -6.21320e+00   -7.97060e+01

   Total Dipole (Debye)
   -6.55277e+02   -8.61214e+02    4.17082e+02

       <======  ###############################  ==>
       <====  R M S - F L U C T U A T I O N S  ====>
       <==  ###############################  ======>

   Energies (kJ/mol)
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
    1.55015e+02    2.03651e+02    4.20929e+01    1.22827e+02    7.61767e+01
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
    1.81161e+02    5.82316e+02    7.17480e+02    9.44462e+01    4.40698e+02
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    3.93428e+02    1.45874e+02    9.31012e-01    1.29635e+02

          Box-X          Box-Y          Box-Z         Volume   Density (SI)
    1.23222e-03    1.45343e-03    2.20161e-03    2.89950e-01    6.35630e-01
             pV
    3.73587e+03

   Total Virial (kJ/mol)
    2.75764e+03    1.92974e+03    2.11050e+03
    1.93131e+03    2.94483e+03    2.05791e+03
    2.11304e+03    2.05311e+03    3.31016e+03

   Pressure (bar)
    1.90896e+02    1.36925e+02    1.48015e+02
    1.37042e+02    2.04299e+02    1.43707e+02
    1.48169e+02    1.43367e+02    2.31551e+02

   Total Dipole (Debye)
    9.68668e+01    1.43086e+02    3.27665e+02


       M E G A - F L O P S   A C C O U N T I N G

       Parallel run - timing based on wallclock.
   RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
   T=Tabulated        W3=SPC/TIP3p    W4=TIP4p (single or pairs)
   NF=No Forces

 Computing:                        M-Number         M-Flops  % of Flops
-----------------------------------------------------------------------
 Coul(T)                         646.149375    27138.273750     4.2
 Coul(T) [W3]                      2.543824      317.978000     0.0
 Coul(T) + LJ                   2021.495476   111182.251180    17.3
 Coul(T) + LJ [W3]               219.255641    30257.278458     4.7
 Coul(T) + LJ [W3-W3]            730.391892   279009.702744    43.4
 Outer nonbonded loop            173.047881     1730.478810     0.3
 1,4 nonbonded interactions       31.503472     2835.312480     0.4
 Spread Q Bspline               3063.092032     6126.184064     1.0
 Gather F Bspline               3063.092032    36757.104384     5.7
 3D-FFT                        10296.774488    82374.195904    12.8
 Solve PME                       568.407840    36378.101760     5.7
 NS-Pairs                        394.401556     8282.432676     1.3
 Reset In Box                      2.438463       21.946167     0.0
 Shift-X                          95.603508      573.621048     0.1
 CG-CoM                            1.220685       35.399865     0.0
 Sum Forces                      143.582439      143.582439     0.0
 Bonds                             6.193187      266.307041     0.0
 Angles                           22.014993     3588.443859     0.6
 Propers                           2.389387      547.169623     0.1
 RB-Dihedrals                     25.411386     6276.612342     1.0
 Virial                           47.968921      863.440578     0.1
 Update                           47.860813     1483.685203     0.2
 Stop-CM                           0.047813        0.478130     0.0
 P-Coupling                       47.860813      287.164878     0.0
 Calc-Ekin                        47.908626     1293.532902     0.2
 Lincs                             5.984901      359.094060     0.1
 Lincs-Mat                        31.955580      127.822320     0.0
 Constraint-V                     47.860813      287.164878     0.0
 Constraint-Vir                   41.906343     1005.752232     0.2
 Settle                           11.973814     3867.541922     0.6
-----------------------------------------------------------------------
 Total                                        643418.053697   100.0
-----------------------------------------------------------------------

               NODE (s)   Real (s)      (%)
       Time:    281.000    281.000    100.0
                       4:41
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:     12.882      2.290      0.615     39.028

Detailed load balancing info in percentage of average
Type        NODE:  0   1   2   3 Scaling
---------------------------------------
        Coul(T):399   0   0   0     25%
   Coul(T) [W3]:  0  36 106 256     38%
   Coul(T) + LJ:399   0   0   0     25%
Coul(T) + LJ [W3]:  0  43 126 229     43%
Coul(T) + LJ [W3-W3]:  0 218 135  46     45%
Outer nonbonded loop:172  71  77  78     57%
1,4 nonbonded interactions:400   0   0   0     25%
Spread Q Bspline: 99 101 101  97     98%
Gather F Bspline: 99 101 101  97     98%
         3D-FFT:100 100 100 100    100%
      Solve PME:100 100 100 100    100%
       NS-Pairs:266  56  43  32     37%
   Reset In Box: 99 100  99 100     99%
        Shift-X:100 100 100  99     99%
         CG-CoM:199  66  66  67     50%
     Sum Forces: 99 100  99 100     99%
          Bonds:400   0   0   0     25%
         Angles:400   0   0   0     25%
        Propers:400   0   0   0     25%
   RB-Dihedrals:400   0   0   0     25%
         Virial: 99 100  99 100     99%
         Update: 99 100  99 100     99%
        Stop-CM: 99 100  99 100     99%
     P-Coupling: 99 100  99 100     99%
      Calc-Ekin: 99 100  99 100     99%
          Lincs:400   0   0   0     25%
      Lincs-Mat:400   0   0   0     25%
   Constraint-V: 99 100  99 100     99%
 Constraint-Vir: 57 114 114 113     87%
         Settle:  0 133 133 132     74%

    Total Force:132 133  89  43     74%


    Total Shake: 38 120 120 120     82%


Total Scaling: 75% of max performance

Finished mdrun on node 0 Sat Oct 25 17:39:49 2008
 




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