Main issue:
WU tried to run, wouldn't even start processing, aborted.t = 38000.020 ps: Water molecule starting at atom 84613 can not be settled.
Check for bad contacts and/or reduce the timestep.
Code: Select all
[02:44:43] Initial: 40AB; - Successful: assigned to (171.64.65.56).
[02:44:43] + News From Folding@Home: Welcome to Folding@Home
[02:44:43] Loaded queue successfully.
[02:44:43] Connecting to http://171.64.65.56:8080/
[02:44:49] Posted data.
[02:44:49] Initial: 0000; - Receiving payload (expected size: 4844883)
[02:45:02] - Downloaded at ~363 kB/s
[02:45:02] - Averaged speed for that direction ~234 kB/s
[02:45:02] + Received work.
[02:45:02] + Closed connections
[02:45:02]
[02:45:02] + Processing work unit
[02:45:02] At least 4 processors must be requested.Core required: FahCore_a2.exe
[02:45:02] Core found.
[02:45:02] - Using generic ./mpiexec
[02:45:02] Working on queue slot 07 [April 1 02:45:02 UTC]
[02:45:02] + Working ...
[02:45:02] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 07 -checkpoint 20 -verbose -lifeline 14271 -version 624'
[02:45:03]
[02:45:03] *------------------------------*
[02:45:03] Folding@Home Gromacs SMP Core
[02:45:03] Version 2.04 (Wed Jan 21 09:16:08 PST 2009)
[02:45:03]
[02:45:03] Preparing to commence simulation
[02:45:03] - Ensuring status. Please wait.
[02:45:03] Working with standard loops on this execution.
[02:45:03] - Files status OK
[02:45:04] - Expanded Called DecompressByteArray: compressed_data_size=Called DecompressByteArray: compressed_data_size=4844371 data_size=23994061, decompressed_data_size=23994061 diff=0
[02:45:04] - Digital signature verAssembly optimizations on if available.
[02:45:04] Entering Entering M.D.
[02:45:14] Project: 2675 (Run 3, Clone 169, Gen 76)
[02:45:14] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=8Core.local
NNODES=4, MYRANK=1, HOSTNAME=8Core.local
NNODES=4, MYRANK=2, HOSTNAME=8Core.local
NNODES=4, MYRANK=3, HOSTNAME=8Core.local
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 4.0.3_pre (-:
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_07.tpr, VERSION 3.3.99_development_20070618 (single precision)
Note: tpx file_version 48, software version 58
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'
19250002 steps, 38500.0 ps (continuing from step 19000002, 38000.0 ps).
t = 38000.020 ps: Water molecule starting at atom 84613 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.020 ps: Water molecule starting at atom 35578 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.020 ps: Water molecule starting at atom 84613 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.027 ps: Water molecule starting at atom 35578 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.031 ps: Water molecule starting at atom 83368 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.035 ps: Water molecule starting at atom 83368 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.035 ps: Water molecule starting at atom 120505 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.039 ps: Water molecule starting at atom 83368 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.043 ps: Water molecule starting at atom 120505 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.043 ps: Water molecule starting at atom 83368 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.043 ps: Water molecule starting at atom 120505 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.043 ps: Water molecule starting at atom 49849 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.043 ps: Water molecule starting at atom 120505 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.047 ps: Water molecule starting at atom 59665 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.047 ps: Water molecule starting at atom 120505 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.051 ps: Water molecule starting at atom 59665 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.051 ps: Water molecule starting at atom 120505 can not be settled.
Check for bad contacts and/or reduce the timestep.
[02:45:27] Folding@home Core Shutdown: INTERRUPTED
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[0]0:Return code = 102
[0]1:Return code = 0, signaled with Quit
[0]2:Return code = 0, signaled with Quit
[0]3:Return code = 0, signaled with Segmentation fault
[02:45:31] CoreStatus = 66 (102)
[02:45:31] + Shutdown requested by user. Exiting.***** Got a SIGTERM signal (15)
[02:45:31] Killing all core threads
Folding@Home Client Shutdown.
Code: Select all
[8Core:~/Applications/Folding@home1] klasseng% /Users/klasseng/Applications/Folding@home1/fah6 -local -smp -verbosity 9
Using local directory for configuration
Note: Please read the license agreement (fah6 -license). Further
use of this software requires that you have read and accepted this agreement.
Using local directory for work files
8 cores detected
--- Opening Log file [April 1 02:45:54 UTC]
# Mac OS X SMP Console Edition ################################################
###############################################################################
Folding@Home Client Version 6.24beta
http://folding.stanford.edu
###############################################################################
###############################################################################
Launch directory: /Users/klasseng/Applications/Folding@home1
Executable: /Users/klasseng/Applications/Folding@home1/fah6
Arguments: -local -smp -verbosity 9
[02:45:54] - Ask before connecting: No
[02:45:54] - User name: klasseng (Team 1971)
[02:45:54] - User ID: 1CC4CEE7245D216E
[02:45:54] - Machine ID: 8
[02:45:54]
[02:45:54] Loaded queue successfully.
[02:45:54]
[02:45:54] - Autosending finished units... [02:45:54]
[02:45:54] + Processing work unit
[02:45:54] Trying to send all finished work units
[02:45:54] + No unsent completed units remaining.
[02:45:54] At least 4 processors must be requested.[02:45:54] - Autosend completed
Core required: FahCore_a2.exe
fah6(14278,0xb0501000) malloc: *** error for object 0xb04ffe0c: Non-aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
[02:45:54] Core found.
[02:45:54] - Using generic ./mpiexec
[02:45:54] Working on queue slot 07 [April 1 02:45:54 UTC]
[02:45:54] + Working ...
[02:45:54] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 07 -checkpoint 20 -verbose -lifeline 14278 -version 624'
[02:45:54]
[02:45:54] *------------------------------*
[02:45:54] Folding@Home Gromacs SMP Core
[02:45:54] Version 2.04 (Wed Jan 21 09:16:08 PST 2009)
[02:45:54]
[02:45:54] Preparing to commence simulation
[02:45:54] - Ensuring status. Please wait.
[02:45:54] Files status OK
[02:45:55] - Expanded 4844371 -> 23994061 (decompressed 495.2 percent)
[02:45:55] Called DecompressByteArray: compressed_data_size=4844371 data_size=23994061, decompressed_data_size=23994061 diff=0
[02:45:56] - Digital signature verified
[02:45:56]
[02:45:56] Project: 2675 (Run 3, Clone 169, Gen 76)
[02:45:56]
[02:45:56] Assembly optimizations on if available.
[02:45:56] Entering M.D.
[02:46:02] Will resume from checkpoint file
[02:46:05] ng M.D.
[02:46:11] Will resume from checkpoint file
NNODES=4, MYRANK=0, HOSTNAME=8Core.local
NNODES=4, MYRANK=1, HOSTNAME=8Core.local
NNODES=4, MYRANK=2, HOSTNAME=8Core.local
NNODES=4, MYRANK=3, HOSTNAME=8Core.local
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 4.0.3_pre (-:
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_07.tpr, VERSION 3.3.99_development_20070618 (single precision)
Note: tpx file_version 48, software version 58
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'
19250002 steps, 38500.0 ps (continuing from step 19000002, 38000.0 ps).
[02:46:14] Resuming from checkpoint
[02:46:14] Verified work/wudata_07.log
[02:46:14] Verified work/wudata_07.trr
[02:46:14] Verified work/wudata_07.xtc
[02:46:14] Verified work/wudata_07.edr
t = 38000.035 ps: Water molecule starting at atom 84613 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.035 ps: Water molecule starting at atom 35578 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.035 ps: Water molecule starting at atom 84613 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.043 ps: Water molecule starting at atom 35578 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.047 ps: Water molecule starting at atom 83368 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.051 ps: Water molecule starting at atom 83368 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.051 ps: Water molecule starting at atom 83368 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.059 ps: Water molecule starting at atom 83368 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.059 ps: Water molecule starting at atom 83368 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.062 ps: Water molecule starting at atom 83368 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.066 ps: Water molecule starting at atom 83368 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.066 ps: Water molecule starting at atom 32365 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.066 ps: Water molecule starting at atom 136810 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.070 ps: Water molecule starting at atom 67171 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 38000.074 ps: Water molecule starting at atom 104245 can not be settled.
Check for bad contacts and/or reduce the timestep.
[0]0:Return code = 0, signaled with Segmentation fault
[0]1:Return code = 0, signaled with Quit
[0]2:Return code = 0, signaled with Quit
[0]3:Return code = 0, signaled with Segmentation fault
[02:46:24] CoreStatus = 0 (0)
[02:46:24] Sending work to server
[02:46:24] Project: 2675 (Run 3, Clone 169, Gen 76)
[02:46:24] - Error: Could not get length of results file work/wuresults_07.dat
[02:46:24] - Error: Could not read unit 07 file. Removing from queue.
[02:46:24] Trying to send all finished work units
[02:46:24] + No unsent completed units remaining.
[02:46:24] - Preparing to get new work unit...
[02:46:24] + Attempting to get work packet
Project: 2675 (Run 2, Clone 264, Gen 21)
