The machine is running Ubuntu 7.10 on an E4300 with 2GB of RAM.
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[19:20:25] Working on Unit 09 [December 15 19:20:25]
[19:20:25] + Working ...
[19:20:25] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 09 -np 4 -checkpoint 30 -verbose -lifeline 8076 -version 602'
[19:20:25]
[19:20:25] *------------------------------*
[19:20:25] Folding@Home Gromacs SMP Core
[19:20:25] Version 2.01 (Wed Aug 13 13:11:25 PDT 2008)
[19:20:25]
[19:20:25] Preparing to commence simulation
[19:20:25] - Ensuring status. Please wait.
[19:20:26] Called DecompressByteArray: compressed_data_size=4839006 data_size=23983821, decompressed_data_size=23983821 diff=0
[19:20:27] - Digital signature verified
[19:20:27]
[19:20:27] Project: 2669 (Run 1, Clone 67, Gen 37)
[19:20:27]
[19:20:27] Assembly optimizations on if available.
[19:20:27] Entering M.D.
[19:20:36] (Run 1, Clone 67, Gen 37)
[19:20:36]
[19:20:37] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=FAHr
NNODES=4, MYRANK=2, HOSTNAME=FAHr
NNODES=4, MYRANK=1, HOSTNAME=FAHr
NNODES=4, MYRANK=3, HOSTNAME=FAHr
NODEID=0 argc=19
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 3.3.99_development_200800503 (-:
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_09.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=1 argc=19
NODEID=2 argc=19
NODEID=3 argc=19
Note: tpx file_version 48, software version 56
Making 1D domain decomposition 1 x 1 x 4
starting mdrun '22884 system'
250000 steps, 500.0 ps.
Step 9250233, time 18500.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009371, max 0.424786 (between atoms 4764 and 4766)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 9250234, time 18500.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000932, max 0.052010 (between atoms 4764 and 4766)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 9250235, time 18500.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005944, max 0.275590 (between atoms 4767 and 4768)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
4767 4768 90.0 0.1010 0.1288 0.1010
Step 9250236, time 18500.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007665, max 0.451738 (between atoms 4764 and 4766)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
4764 4766 90.0 0.1330 0.1582 0.1090
Step 9250237, time 18500.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009280, max 0.508994 (between atoms 4764 and 4766)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 9250238, time 18500.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007285, max 0.432515 (between atoms 4764 and 4766)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
4764 4766 90.0 0.1645 0.1561 0.1090
Step 9250239, time 18500.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 96.256473, max 4497.078125 (between atoms 4761 and 4763)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
4764 4765 123.2 0.1093 13.2382 0.1090
4767 4768 90.0 0.1010 0.1476 0.1010
Step 9250240:
The charge group starting at atom 4763 moved than the distance allowed by the domain decomposition (1.200000) in direction Z
distance out of cell -342.153839
Old coordinates: 6.289 4.341 7.823
New coordinates: 165.649 -320.887 -336.664
Old cell boundaries in direction Z: 5.528 8.538
New cell boundaries in direction Z: 5.490 8.531
-------------------------------------------------------
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 1, will try to stop all the nodes
Halting parallel program mdrun on CPU 1 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_1]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 1
[cli_0]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[22:23:36] - Autosending finished units...