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Project: 2683 (Run 0, Clone 12, Gen 15) WMCNBS 100% reprod.

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Project: 2683 (Run 0, Clone 12, Gen 15) WMCNBS 100% reprod.

Posted: Sat Jan 23, 2010 5:58 pm
by tear
Per subject line. Water molecule cannot be settled. 100% reproducible.

Thank you for your kind attention.


tear

Code: Select all

$ ./fah6

Note: Please read the license agreement (fah6 -license). Further
use of this software requires that you have read and accepted this agreement.

32 cores detected


--- Opening Log file [January 23 17:22:18 UTC]


# Linux SMP Console Edition ###################################################
###############################################################################

                       Folding@Home Client Version 6.29

                          http://folding.stanford.edu

###############################################################################
###############################################################################

Launch directory: /fah/clients/fah
Executable: ./fah6
Arguments: -forceasm -verbosity 9 -smp 32

[17:22:18] - Ask before connecting: No
[17:22:18] - Proxy: 127.0.0.1:8880
[17:22:18] - User name: tear (Team 100259)
[17:22:18] - User ID: 2DC41E1609D515E2
[17:22:18] - Machine ID: 1
[17:22:18]
[17:22:18] Loaded queue successfully.
[17:22:18]
[17:22:18] - Autosending finished units... [January 23 17:22:18 UTC]
[17:22:18] + Processing work unit
[17:22:18] Trying to send all finished work units
[17:22:18] Core required: FahCore_a2.exe
[17:22:18] + No unsent completed units remaining.
[17:22:18] - Autosend completed
[17:22:18] Core found.
[17:22:18] Working on queue slot 01 [January 23 17:22:18 UTC]
[17:22:18] + Working ...
[17:22:18] - Calling './mpiexec -np 32 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -nice 19 -suffix 01 -nocpulock -checkpoint 15 -forceasm -verbose -lifeline 22842 -version 629'
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
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Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
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Warning: Ignoring unknown arg
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Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
[17:22:18]
[17:22:18] *------------------------------*
[17:22:18] Folding@Home Gromacs SMP Core
[17:22:18] Version 2.10 (Sun Aug 30 03:43:28 CEST 2009)
[17:22:18]
[17:22:18] Preparing to commence simulation
[17:22:18] - Ensuring status. Please wait.
[17:22:25] Called DecompressByteArray: compressed_data_size=30238980 data_size=159270593, decompressed_data_size=159270593 diff=0
[17:22:27] - Digital signature verified
[17:22:27]
[17:22:27] Project: 2683 (Run 0, Clone 12, Gen 15)
[17:22:27]
[17:22:27] Assembly optimizations on if available.
[17:22:27] Entering M.D.
[17:22:39]  on if available.
[17:22:39] Entering M.D.
NNODES=32, MYRANK=29, HOSTNAME=boo
NNODES=32, MYRANK=3, HOSTNAME=boo
NNODES=32, MYRANK=16, HOSTNAME=boo
NNODES=32, MYRANK=25, HOSTNAME=boo
NNODES=32, MYRANK=30, HOSTNAME=boo
NNODES=32, MYRANK=1, HOSTNAME=boo
NNODES=32, MYRANK=2, HOSTNAME=boo
NNODES=32, MYRANK=4, HOSTNAME=boo
NNODES=32, MYRANK=5, HOSTNAME=boo
NNODES=32, MYRANK=7, HOSTNAME=boo
NNODES=32, MYRANK=8, HOSTNAME=boo
NNODES=32, MYRANK=9, HOSTNAME=boo
NNODES=32, MYRANK=10, HOSTNAME=boo
NNODES=32, MYRANK=11, HOSTNAME=boo
NNODES=32, MYRANK=13, HOSTNAME=boo
NNODES=32, MYRANK=14, HOSTNAME=boo
NNODES=32, MYRANK=15, HOSTNAME=boo
NNODES=32, MYRANK=20, HOSTNAME=boo
NNODES=32, MYRANK=21, HOSTNAME=boo
NNODES=32, MYRANK=24, HOSTNAME=boo
NNODES=32, MYRANK=27, HOSTNAME=boo
NNODES=32, MYRANK=6, HOSTNAME=boo
NNODES=32, MYRANK=17, HOSTNAME=boo
NNODES=32, MYRANK=18, HOSTNAME=boo
NNODES=32, MYRANK=19, HOSTNAME=boo
NNODES=32, MYRANK=22, HOSTNAME=boo
NNODES=32, MYRANK=23, HOSTNAME=boo
NNODES=32, MYRANK=26, HOSTNAME=boo
NNODES=32, MYRANK=28, HOSTNAME=boo
NNODES=32, MYRANK=31, HOSTNAME=boo
NNODES=32, MYRANK=12, HOSTNAME=boo
NNODES=32, MYRANK=0, HOSTNAME=boo
NODEID=0 argc=20
NODEID=1 argc=20
NODEID=2 argc=20
NODEID=3 argc=20
NODEID=4 argc=20
NODEID=5 argc=20
NODEID=8 argc=20
NODEID=16 argc=20
NODEID=6 argc=20
NODEID=7 argc=20
NODEID=9 argc=20
NODEID=10 argc=20
NODEID=11 argc=20
NODEID=17 argc=20
NODEID=18 argc=20
NODEID=19 argc=20
NODEID=20 argc=20
NODEID=21 argc=20
NODEID=22 argc=20
NODEID=23 argc=20
NODEID=24 argc=20
NODEID=25 argc=20
NODEID=26 argc=20
NODEID=27 argc=20
NODEID=28 argc=20
NODEID=29 argc=20
NODEID=30 argc=20
NODEID=31 argc=20
NODEID=12 argc=20
NODEID=13 argc=20
NODEID=14 argc=20
NODEID=15 argc=20
Reading file work/wudata_01.tpr, VERSION 3.3.99_development_20070618 (single precision)
Note: tpx file_version 48, software version 68

Will use 24 particle-particle and 8 PME only nodes
This is a guess, check the performance at the end of the log file

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 2D domain decomposition 8 x 1 x 3
starting mdrun 'SINGLE VESICLE in water'
4000000 steps,  16000.0 ps (continuing from step 3750000,  15000.0 ps).
[17:23:10] Completed 0 out of 250000 steps  (0%)

t = 15000.001 ps: Water molecule starting at atom 909891 can not be settled.
Check for bad contacts and/or reduce the timestep.

-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090605
Source code file: pme.c, line: 561

Fatal error:
2 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group in dimension x
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 31, will try to stop all the nodes
Halting parallel program mdrun on CPU 31 out of 32

gcq#0: Thanx for Using GROMACS - Have a Nice Day

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 31
[17:23:13]
[17:23:13] Folding@home Core Shutdown: INTERRUPTED
[17:23:30] ***** Got an Activate signal (2)
[17:23:30] Killing all core threads

Folding@Home Client Shutdown.

Re: Project: 2683 (Run 0, Clone 12, Gen 15) WMCNBS 100% reprod.

Posted: Sat Jan 23, 2010 9:39 pm
by Tigerbiten
I've just had two attempts to fold this protien fail ..... :(

Code: Select all

--- Opening Log file [January 23 21:16:04 UTC] 


# Linux SMP Console Edition ###################################################
###############################################################################

                       Folding@Home Client Version 6.24R3

                          http://folding.stanford.edu

###############################################################################
###############################################################################

Launch directory: /home/Nigel/foldingathome/CPU1
Executable: /home/Nigel/foldingathome/CPU1/fah6
Arguments: -verbosity 9 -smp 8 -smp 8 -bigadv -verbosity 9 

[21:16:04] - Ask before connecting: No
[21:16:04] - User name: Tigerbiten (Team 33)
[21:16:04] - User ID: 246014491DD9236B
[21:16:04] - Machine ID: 1
[21:16:04] 
[21:16:04] Work directory not found. Creating...
[21:16:04] Could not open work queue, generating new queue...
[21:16:04] - Preparing to get new work unit...
[21:16:04] Cleaning up work directory
[21:16:04] + Attempting to get work packet
[21:16:04] - Will indicate memory of 4999 MB
[21:16:04] - Connecting to assignment server
[21:16:04] Connecting to http://assign.stanford.edu:8080/
[21:16:04] - Autosending finished units... [January 23 21:16:04 UTC]
[21:16:04] Trying to send all finished work units
[21:16:04] + No unsent completed units remaining.
[21:16:04] - Autosend completed
[21:16:07] Posted data.
[21:16:07] Initial: 43AB; - Successful: assigned to (171.67.108.22).
[21:16:07] + News From Folding@Home: Welcome to Folding@Home
[21:16:07] Loaded queue successfully.
[21:16:07] Connecting to http://171.67.108.22:8080/
[21:16:47] Posted data.
[21:16:47] Initial: 0000; - Receiving payload (expected size: 30239492)
[21:23:16] - Downloaded at ~75 kB/s
[21:23:16] - Averaged speed for that direction ~75 kB/s
[21:23:16] + Received work.
[21:23:16] + Closed connections
[21:23:16] 
[21:23:16] + Processing work unit
[21:23:16] Core required: FahCore_a2.exe
[21:23:16] Core found.
[21:23:16] Working on queue slot 01 [January 23 21:23:16 UTC]
[21:23:16] + Working ...
[21:23:16] - Calling './mpiexec -np 8 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -nice 19 -suffix 01 -checkpoint 30 -verbose -lifeline 14794 -version 624'

[21:23:17] 
[21:23:17] *------------------------------*
[21:23:17] Folding@Home Gromacs SMP Core
[21:23:17] Version 2.10 (Sun Aug 30 03:43:28 CEST 2009)
[21:23:17] 
[21:23:17] Preparing to commence simulation
[21:23:17] - Ensuring status. Please wait.
[21:23:21] 238980 -> 159270593 (decompressed 100.6 percent)
[21:23:23] Called DecompressByteArray: compressed_data_size=30238980 data_size=159270593, decompressed_data_size=159270593 diff=0
[21:23:24] - Digital signature verified
[21:23:24] 
[21:23:24] Project: 2683 (Run 0, Clone 12, Gen 15)
[21:23:24] 
[21:23:25] Entering M.D.
[21:23:39] lone 12, Gen 15)
[21:23:39] 
[21:23:39] Entering M.D.
[21:24:04] lding@home Core Shutdown: INTERRUPTED
That how far it got both times.
I'll delete it again and hope to get a new protien.

Re: Project: 2683 (Run 0, Clone 12, Gen 15) WMCNBS 100% reprod.

Posted: Sun Jan 24, 2010 4:35 am
by bruce
This WU has been reported as "bad"
All times are UTC
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