roject: 2671 (Run 35, Clone 80, Gen 21) seg fault

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alpha754293
Posts: 383
Joined: Sun Jan 18, 2009 1:13 am

roject: 2671 (Run 35, Clone 80, Gen 21) seg fault

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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.
restarting client...
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