Ubuntu 8.04
6.24 with -smp 8 -verbosity 9 -advmethods
core version 2.01
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[18:06:20] Completed 155008 out of 250000 steps (62%)
[18:11:07] Completed 157508 out of 250000 steps (63%)
[18:15:50] Completed 160008 out of 250000 steps (64%)
[18:20:36] Completed 162508 out of 250000 steps (65%)
[18:25:22] Completed 165008 out of 250000 steps (66%)
Step 19415958, time 38831.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.056375, max 1.843163 (between atoms 5579 and 5581)
Step 19415958, time 38831.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.029260, max 1.843163 (between atoms 5579 and 5581)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
5579 5581 90.0 0.1090 0.3099 0.1090
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
5579 5581 90.0 0.1090 0.3099 0.1090
5576 5577 90.0 0.1090 0.2778 0.1090
Step 19415959, time 38831.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.108131, max 69.803444 (between atoms 5579 and 5581)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
5579 5581 90.0 0.3099 7.7176 0.1090
Step 19415959, time 38831.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.378295, max 69.803444 (between atoms 5579 and 5581)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
5579 5581 90.0 0.3099 7.7176 0.1090
5569 5570 90.0 0.1010 0.2150 0.1010
5576 5577 90.0 0.2778 0.3789 0.1090
t = 38831.922 ps: Water molecule starting at atom 110713 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Step 19415960:
The charge group starting at atom 5581 moved than the distance allowed by the domain decomposition (1.200000) in direction X
distance out of cell -15.704895
Old coordinates: 0.628 4.004 11.131
New coordinates: -15.705 4.169 0.643
Old cell boundaries in direction X: 0.000 5.089
New cell boundaries in direction X: 0.000 5.271
-------------------------------------------------------
Program mdrun, VERSION 3.3.99_development_200800503
Source code file: domdec.c, line: 2644
Fatal error:
A charge group move too far between two domain decomposition steps
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 3, will try to stop all the nodes
Halting parallel program mdrun on CPU 3 out of 8
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_3]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
[18:27:10]
[18:27:10] Folding@home Core Shutdown: INTERRUPTED
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[cli_1]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_2]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_7]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[19:33:44] - Autosending finished units... [February 2 19:33:44 UTC]
[19:33:44] Trying to send all finished work units
[19:33:44] + No unsent completed units remaining.
[19:33:44] - Autosend completed
