output snippets.
Snippet A (side note: client hung and did not continue until ^C):
Code: Select all
Note: Please read the license agreement (fah6 -license). Further
use of this software requires that you have read and accepted this agreement.
8 cores detected
--- Opening Log file [June 6 11:58:42 UTC]
# Linux SMP Console Edition ###################################################
###############################################################################
Folding@Home Client Version 6.24beta
http://folding.stanford.edu
###############################################################################
###############################################################################
Launch directory: /fah/clients/fah
Executable: ./fah6
Arguments: -oneunit -verbosity 9 -forceasm -smp
[11:58:42] - Ask before connecting: No
[11:58:42] - User name: tear (Team 100259)
[11:58:42] - User ID: 1FD229A605CD6A27
[11:58:42] - Machine ID: 3
[11:58:42]
[11:58:42] Loaded queue successfully.
[11:58:42] - Preparing to get new work unit...
[11:58:42] + Attempting to get work packet
[11:58:42] - Will indicate memory of 2013 MB
[11:58:42] - Connecting to assignment server
[11:58:42] Connecting to http://assign.stanford.edu:8080/
[11:58:42] - Autosending finished units... [11:58:42]
[11:58:42] Trying to send all finished work units
[11:58:42] + No unsent completed units remaining.
[11:58:42] - Autosend completed
[11:58:44] Posted data.
[11:58:44] Initial: 43AB; - Successful: assigned to (171.67.108.24).
[11:58:44] + News From Folding@Home: Welcome to Folding@Home
[11:58:44] Loaded queue successfully.
[11:58:44] Connecting to http://171.67.108.24:8080/
[11:58:50] Posted data.
[11:58:50] Initial: 0000; - Receiving payload (expected size: 4842125)
[11:59:05] - Downloaded at ~315 kB/s
[11:59:05] - Averaged speed for that direction ~1264 kB/s
[11:59:05] + Received work.
[11:59:05] + Closed connections
[11:59:05]
[11:59:05] + Processing work unit
[11:59:05] At least 4 processors must be requested.Core required: FahCore_a2.exe
[11:59:05] Core found.
[11:59:05] Working on queue slot 05 [June 6 11:59:05 UTC]
[11:59:05] + Working ...
[11:59:05] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 05 -nocpulock -checkpoint 15 -forceasm -verbose -lifeline 27519 -version 624'
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
[11:59:05]
[11:59:05] *------------------------------*
[11:59:05] Folding@Home Gromacs SMP Core
[11:59:05] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[11:59:05]
[11:59:05] Preparing to commence simulation
[11:59:05] - Ensuring status. Please wait.
[11:59:14] - Assembly optimizations manually forced on.
[11:59:14] - Not checking prior termination.
[11:59:15] - Expanded 4841613 -> 24004881 (decompressed 495.8 percent)
[11:59:15] Called DecompressByteArray: compressed_data_size=4841613 data_size=24004881, decompressed_data_size=24004881 diff=0
[11:59:16] - Digital signature verified
[11:59:16]
[11:59:16] Project: 2671 (Run 3, Clone 82, Gen 42)
[11:59:16]
[11:59:16] Assembly optimizations on if available.
[11:59:16] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=octopus
NNODES=4, MYRANK=1, HOSTNAME=octopus
NNODES=4, MYRANK=2, HOSTNAME=octopus
NNODES=4, MYRANK=3, HOSTNAME=octopus
NODEID=0 argc=20
NODEID=1 argc=20
NODEID=2 argc=20
NODEID=3 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_05.tpr, VERSION 3.3.99_development_20070618 (single precision)
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 '22878 system in water'
10750000 steps, 21500.0 ps (continuing from step 10500000, 21000.0 ps).
[11:59:25] Completed 0 out of 250000 steps (0%)
t = 21000.005 ps: Water molecule starting at atom 95476 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 21000.007 ps: Water molecule starting at atom 46285 can not be settled.
Check for bad contacts and/or reduce the timestep.
-------------------------------------------------------
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 -2147483503. It should have been within [ 0 .. 2312 ]
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 2, will try to stop all the nodes
Halting parallel pro
-------------------------------------------------------
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 -2147483519. It should have been within [ 0 .. 1800 ]
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 2 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_2]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
-------------------------------------------------------
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 -2147483527. It should have been within [ 0 .. 1568 ]
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 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
gram 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 3Code: Select all
Note: Please read the license agreement (fah6 -license). Further
use of this software requires that you have read and accepted this agreement.
8 cores detected
--- Opening Log file [June 6 16:27:21 UTC]
# Linux SMP Console Edition ###################################################
###############################################################################
Folding@Home Client Version 6.24beta
http://folding.stanford.edu
###############################################################################
###############################################################################
Launch directory: /fah/clients/fah
Executable: ./fah6
Arguments: -oneunit -verbosity 9 -forceasm -smp
[16:27:21] - Ask before connecting: No
[16:27:21] - User name: tear (Team 100259)
[16:27:21] - User ID: 1FD229A605CD6A27
[16:27:21] - Machine ID: 3
[16:27:21]
[16:27:22] Loaded queue successfully.
[16:27:22]
[16:27:22] + Processing work unit
[16:27:22] At least 4 processors must be requested.Core required: FahCore_a2.exe
[16:27:22] Core found.
[16:27:22] - Autosending finished units... [June 6 16:27:22 UTC]
[16:27:22] Working on queue slot 05 [June 6 16:27:22 UTC]
[16:27:22] Trying to send all finished work units
[16:27:22] + Working ...
[16:27:22] + No unsent completed units remaining.
[16:27:22] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 05 -nocpulock -checkpoint 15 -forceasm -verbose -lifeline 5785 -version 624'
[16:27:22] - Autosend completed
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
[16:27:22]
[16:27:22] *------------------------------*
[16:27:22] Folding@Home Gromacs SMP Core
[16:27:22] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[16:27:22]
[16:27:22] Preparing to commence simulation
[16:27:22] - Ensuring status. Please wait.
[16:27:31] - Assembly optimizations manually forced on.
[16:27:31] - Not checking prior termination.
[16:27:32] - Expanded 4841613 -> 24004881 (decompressed 495.8 percent)
[16:27:32] Called DecompressByteArray: compressed_data_size=4841613 data_size=24004881, decompressed_data_size=24004881 diff=0
[16:27:33] - Digital signature verified
[16:27:33]
[16:27:33] Project: 2671 (Run 3, Clone 82, Gen 42)
[16:27:33]
[16:27:33] Assembly optimizations on if available.
[16:27:33] Entering M.D.
NNODES=4, MYRANK=1, HOSTNAME=octopus
NNODES=4, MYRANK=0, HOSTNAME=octopus
NNODES=4, MYRANK=2, HOSTNAME=octopus
NNODES=4, MYRANK=3, HOSTNAME=octopus
NODEID=2 argc=20
NODEID=0 argc=20
NODEID=1 argc=20
NODEID=3 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_05.tpr, VERSION 3.3.99_development_20070618 (single precision)
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 '22878 system in water'
10750000 steps, 21500.0 ps (continuing from step 10500000, 21000.0 ps).
[16:27:42] Completed 0 out of 250000 steps (0%)
t = 21000.005 ps: Water molecule starting at atom 95476 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 21000.007 ps: Water molecule starting at atom 46285 can not be settled.
Check for bad contacts and/or reduce the timestep.
-------------------------------------------------------
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 -2147483503. It should have been within [ 0 .. 2312 ]
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 2, will try to stop all the nodes
Halting parallel pro
-------------------------------------------------------
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 -2147483519. It should have been within [ 0 .. 1800 ]
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 2 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_2]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
gram 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 -2147483527. It should have been within [ 0 .. 1568 ]
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
[0]0:Return code = 255
[0]1:Return code = 0, signaled with Quit
[0]2:Return code = 255
[0]3:Return code = 255
[16:27:48] CoreStatus = FF (255)
[16:27:48] Sending work to server
[16:27:48] Project: 2671 (Run 3, Clone 82, Gen 42)
[16:27:48] - Error: Could not get length of results file work/wuresults_05.dat
[16:27:48] - Error: Could not read unit 05 file. Removing from queue.
[16:27:48] Trying to send all finished work units
[16:27:48] + No unsent completed units remaining.
[16:27:48] + -oneunit flag given and have now finished a unit. Exiting.- Preparing to get new work unit...
[16:27:48] + Attempting to get work packet
[16:27:48] - Will indicate memory of 2013 MB
[16:27:48] - Connecting to assignment server
[16:27:48] ***** Got a SIGTERM signal (15)
[16:27:48] Connecting to http://assign.stanford.edu:8080/
[16:27:48] Killing all core threads
Folding@Home Client Shutdown.tear
It's still in the system. I got it again today and it idled my Mac for most of the day.