Code: Select all
[10:26:16] Project: 2671 (Run 52, Clone 43, Gen 82)
[10:26:16]
[10:26:16] Assembly optimizations on if available.
[10:26:16] Entering M.D.
[10:26:25] Run 52, Clone 43, Gen 82)
[10:26:25]
[10:26:25] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=Apollo-Quad-Office
NNODES=4, MYRANK=1, HOSTNAME=Apollo-Quad-Office
NNODES=4, MYRANK=3, HOSTNAME=Apollo-Quad-Office
NNODES=4, MYRANK=2, HOSTNAME=Apollo-Quad-Office
NODEID=0 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_02.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=1 argc=20
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 '22887 system in water'
20750000 steps, 41500.0 ps (continuing from step 20500000, 41000.0 ps).
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090307
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483269. It should have been within [ 0 .. 9464 ]
For more information and tips for trouble shooting please check the GROMACS Wiki at
http://wiki.gromacs.org/index.php/Errors
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090307
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very hi[0]0:Return code = 255
[0]1:Return code = 0, signaled with Quit
[0]2:Return code = 0, signaled with Quit
[0]3:Return code = 255
[10:26:38] CoreStatus = FF (255)
[10:26:38] Sending work to server
[10:26:38] Project: 2671 (Run 52, Clone 43, Gen 82)
[10:26:38] - Error: Could not get length of results file work/wuresults_02.dat
[10:26:38] - Error: Could not read unit 02 file. Removing from queue.
[10:26:38] - Preparing to get new work unit...
[10:26:38] Cleaning up work directory
[10:26:38] + Attempting to get work packet
[10:26:38] - Connecting to assignment server
[10:26:40] - Successful: assigned to (171.67.108.24).
[10:26:40] + News From Folding@Home: Welcome to Folding@Home
[10:26:40] Loaded queue successfully.
[10:26:50] + Closed connections
[10:26:55]
[10:26:55] + Processing work unit
[10:26:55] At least 4 processors must be requested; read 1.
[10:26:55] Core required: FahCore_a2.exe
[10:26:55] Core found.
[10:26:55] Working on queue slot 03 [September 2 10:26:55 UTC]
[10:26:55] + Working ...
[10:26:55]
[10:26:55] *------------------------------*
[10:26:55] Folding@Home Gromacs SMP Core
[10:26:55] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[10:26:55]
[10:26:55] Preparing to commence simulation
[10:26:55] - Ensuring status. Please wait.
[10:27:05] - Looking at optimizations...
[10:27:05] - Working with standard loops on this execution.
[10:27:05] - Files status OK
[10:27:05] - Expanded 1506342 -> 24008597 (decompressed 1593.8 percent)
[10:27:05] Called DecompressByteArray: compressed_data_size=1506342 data_size=24008597, decompressed_data_size=24008597 diff=0
[10:27:06] - Digital signature verified
[10:27:06]
[10:27:06] Project: 2671 (Run 52, Clone 43, Gen 82)
[10:27:06]
[10:27:06] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=Apollo-Quad-Office
NNODES=4, MYRANK=2, HOSTNAME=Apollo-Quad-Office
NNODES=4, MYRANK=3, HOSTNAME=Apollo-Quad-Office
NODEID=2 argc=20
NODEID=3 argc=20
NNODES=4, MYRANK=1, HOSTNAME=Apollo-Quad-Office
NODEID=0 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_03.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=1 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 '22887 system in water'
20750000 steps, 41500.0 ps (continuing from step 20500000, 41000.0 ps).
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090307
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483269. It should have been within [ 0 .. 9464 ]
For more information and tips for trouble shooting please check the GROMACS Wiki at
http://wiki.gromacs.org/index.php/Errors
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090307
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483611. It should have been within [ 0 .. 256 ]
For more information and tips for trouble shooting please check the GROMACS Wiki at
http://wiki.gromacs.org/index.php/Errors
-------------------------------------------------------
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 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_3]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
