[gmx-users] Strange program behavior after first checkpoint is created

[Braden Kelly]

Hello,

I am trying to do a NPT simulation.

The simulation works fine up to the first time the program outputs to the log file. In the first 15 minutes it does about 100,000 steps (timestep of 0.002).

Subsequently every future output (every 30 minutes? but usually every 15 minutes...) is only 10 additional steps, and the energy.edr file is maxed at 200 ps worth of data. Energies are supposed to be output to the log file every 10000 steps, and it does this until the first checkpoint, but then stops doing this after.

Below is the (truncated to keep this message below 50 kb) logfile which has the strange output. mdp file can be added at request!

Any suggestions?

Log file opened on Fri May 10 04:25:34 2019
Host: cp2328  pid: 31051  rank ID: 0  number of ranks:  4
                      :-) GROMACS - gmx mdrun, 2016.3 (-:

[ Text removed by myself to save space]

Using 4 MPI processes
Using 6 OpenMP threads per MPI process

There are: 8550 Atoms
Initial temperature: 298.79 K

Started mdrun on rank 0 Fri May 10 04:25:34 2019
           Step           Time
              0        0.00000

   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
    7.13848e+03    5.68151e+00    1.50447e+03    1.39242e+03    2.64359e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
   -1.15632e+04   -4.58414e+02   -2.61474e+04    9.31295e+03    7.62085e+03
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
    2.14268e+04    2.90477e+04    2.98841e+02   -5.11304e+01   -2.47658e+03
   Constr. rmsd
    2.81648e-06

DD  step 9 load imb.: force 52.0%


step 20 Turning on dynamic load balancing, because the performance loss due to load imbalance is 4.9 %.


step 1600 Turning off dynamic load balancing, because it is degrading performance.

Atom distribution over 4 domains: av 2137 stddev 107 min 1981 max 2236
DD  step 9999 load imb.: force  1.5%

           Step           Time
          10000       20.00000

   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
    2.14436e+04    1.02672e+02    4.40377e+03    2.24342e+03    2.64718e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
   -1.88094e+04   -7.63518e+02   -2.82876e+04    2.46700e+03    9.27179e+03
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
    2.14203e+04    3.06921e+04    2.98750e+02   -1.41841e+02   -7.96508e+02
   Constr. rmsd
    2.79491e-06

DD  step 19999 load imb.: force  0.3%

           Step           Time
          20000       40.00000

   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
    2.14024e+04    1.09156e+02    4.54557e+03    2.33020e+03    2.65011e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
   -1.91004e+04   -7.76677e+02   -2.83510e+04    2.37177e+03    9.03215e+03
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
    2.12079e+04    3.02401e+04    2.95788e+02   -1.46773e+02    1.33427e+03
   Constr. rmsd
    2.68412e-06

DD  step 29999 load imb.: force  2.0%

           Step           Time
          30000       60.00000

   Energies (kJ/mol)
[removed energies here to save space]

DD  step 39999 load imb.: force  1.5%

           Step           Time
          40000       80.00000

   Energies (kJ/mol)
[removed energies here to save space]


DD  step 49999 load imb.: force  0.7%

           Step           Time
          50000      100.00000

   Energies (kJ/mol)
[removed energies here to save space]


DD  step 59999 load imb.: force  2.4%

           Step           Time
          60000      120.00000

[removed energies here to save space]


DD  step 69999 load imb.: force  1.2%

           Step           Time
          70000      140.00000

[removed energies here to save space]

DD  step 79999 load imb.: force  2.5%

           Step           Time
          80000      160.00000

   Energies (kJ/mol)
[removed energies here to save space]

DD  step 89999 load imb.: force  0.6%

           Step           Time
          90000      180.00000

   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
    2.14768e+04    1.10657e+02    4.54865e+03    2.25242e+03    2.64878e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
   -1.94511e+04   -7.75846e+02   -2.84338e+04    2.27748e+03    8.49301e+03
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
    2.09442e+04    2.94372e+04    2.92109e+02   -1.46459e+02   -7.91727e+02
   Constr. rmsd
    2.69166e-06

DD  step 99999 load imb.: force  1.0%

           Step           Time
         100000      200.00000

   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
    2.16605e+04    1.19725e+02    4.59460e+03    2.29392e+03    2.64847e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
   -1.94911e+04   -7.82499e+02   -2.85735e+04    2.16233e+03    8.46864e+03
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
    2.15452e+04    3.00139e+04    3.00492e+02   -1.48981e+02    3.07955e+02
   Constr. rmsd
    2.83274e-06

Writing checkpoint, step 100670 at Fri May 10 04:40:35 2019

Writing checkpoint, step 100680 at Fri May 10 05:13:33 2019

Writing checkpoint, step 100690 at Fri May 10 05:43:55 2019

[removed to save space]

Writing checkpoint, step 100840 at Fri May 10 12:32:07 2019

Writing checkpoint, step 100850 at Fri May 10 12:56:43 2019


Braden