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[23:04:53]
[23:04:53] *------------------------------*
[23:04:53] Folding@Home Gromacs SMP Core
[23:04:53] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[23:04:53]
[23:04:53] Preparing to commence simulation
[23:04:53] - Ensuring status. Please wait.
[23:05:03] - Looking at optimizations...
[23:05:03] - Working with standard loops on this execution.
[23:05:03] - Files status OK
[23:05:04] - Expanded 4826321 -> 24068061 (decompressed 498.6 percent)
[23:05:04] Called DecompressByteArray: compressed_data_size=4826321 data_size=24068061, decompressed_data_size=24068061 diff=0
[23:05:04] - Digital signature verified
[23:05:04]
[23:05:04] Project: 2671 (Run 35, Clone 80, Gen 21)
[23:05:04]
[23:05:04] Entering M.D.
NNODES=4, MYRANK=3, HOSTNAME=computenode
NNODES=4, MYRANK=1, HOSTNAME=computenode
NNODES=4, MYRANK=2, HOSTNAME=computenode
NNODES=4, MYRANK=0, HOSTNAME=computenode
NODEID=0 argc=20
NODEID=1 argc=20
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.99_development_20090307 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
:-) mdrun (-:
Reading file work/wudata_06.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=2 argc=20
NODEID=3 argc=20
Note: tpx file_version 48, software version 64
NOTE: The tpr file used for this simulation is in an old format, for less memory usage and possibly more performance create a new tpr file with an up to date version of grompp
Making 1D domain decomposition 1 x 1 x 4
starting mdrun '22908 system in water'
5500000 steps, 11000.0 ps (continuing from step 5250001, 10500.0 ps).
[23:05:14] Completed 0 out of 249999 steps (0%)
[23:18:55] Completed 2500 out of 249999 steps (1%)
[23:32:34] Completed 5000 out of 249999 steps (2%)
[23:46:13] Completed 7500 out of 249999 steps (3%)
[23:59:54] Completed 10000 out of 249999 steps (4%)
Step 5260217, time 10520.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007567, max 0.406410 (between atoms 1598 and 1599)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 5260218, time 10520.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 369.582345, max 22653.367188 (between atoms 1604 and 1605)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
1604 1607 91.8 0.1090 115.2658 0.1090
1598 1599 90.1 0.1533 854.5095 0.1090
1600 1602 90.0 0.1089 1.9971 0.1090
1600 1603 119.2 0.1392 12.9478 0.1090
t = 10520.436 ps: Water molecule starting at atom 88384 can not be settled.
Check for bad contacts and/or reduce the timestep.
[00:01:05]
[00:01:05] Folding@home Core Shutdown: INTERRUPTED
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[cli_3]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[0]0:Return code = 102
[0]1:Return code = 0, signaled with Segmentation fault
[0]2:Return code = 0, signaled with Quit
[0]3:Return code = 1
[00:01:09] CoreStatus = 66 (102)
[00:01:09] + Shutdown requested by user. Exiting.***** Got a SIGTERM signal (15)
[00:01:09] Killing all core threads
Folding@Home Client Shutdown.