Project: 2684 (Run 2, Clone 3, Gen 2)

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ei57
Posts: 64
Joined: Thu Jun 12, 2008 10:23 am

Project: 2684 (Run 2, Clone 3, Gen 2)

Post by ei57 »

Here is another one - multiple EUE's.

Code: Select all

[04:25:25] Project: 2684 (Run 2, Clone 3, Gen 2)
[04:25:25] 
[04:25:25] Assembly optimizations on if available.
[04:25:25] Entering M.D.
Starting 8 threads
NNODES=8, MYRANK=3, HOSTNAME=thread #3
NNODES=8, MYRANK=2, HOSTNAME=thread #2
NNODES=8, MYRANK=1, HOSTNAME=thread #1
NNODES=8, MYRANK=0, HOSTNAME=thread #0
NNODES=8, MYRANK=5, HOSTNAME=thread #5
NNODES=8, MYRANK=6, HOSTNAME=thread #6
NNODES=8, MYRANK=7, HOSTNAME=thread #7
NNODES=8, MYRANK=4, HOSTNAME=thread #4
Reading file work/wudata_05.tpr, VERSION 4.0.99_development_20090605 (single precision)
Making 1D domain decomposition 8 x 1 x 1
starting mdrun 'SINGLE VESICLE in water'
750000 steps,   3000.0 ps (continuing from step 500000,   2000.0 ps).
[04:25:37] Completed 0 out of 250000 steps  (0%)
[05:17:01] Completed 2500 out of 250000 steps  (1%)
[06:07:53] - Autosending finished units... [June 8 06:07:53 UTC]
[06:07:53] Trying to send all finished work units
[06:07:53] + No unsent completed units remaining.
[06:07:53] - Autosend completed
[06:08:07] Completed 5000 out of 250000 steps  (2%)
[06:59:25] Completed 7500 out of 250000 steps  (3%)
[07:50:29] Completed 10000 out of 250000 steps  (4%)
[08:41:31] Completed 12500 out of 250000 steps  (5%)
[09:32:34] Completed 15000 out of 250000 steps  (6%)
[10:23:36] Completed 17500 out of 250000 steps  (7%)
[11:14:49] Completed 20000 out of 250000 steps  (8%)
[12:06:09] Completed 22500 out of 250000 steps  (9%)
[12:07:53] - Autosending finished units... [June 8 12:07:53 UTC]
[12:07:53] Trying to send all finished work units
[12:07:53] + No unsent completed units remaining.
[12:07:53] - Autosend completed
[12:57:13] Completed 25000 out of 250000 steps  (10%)
[13:48:25] Completed 27500 out of 250000 steps  (11%)
[14:39:38] Completed 30000 out of 250000 steps  (12%)
[15:31:17] Completed 32500 out of 250000 steps  (13%)
[16:21:44] Completed 35000 out of 250000 steps  (14%)
[17:12:15] Completed 37500 out of 250000 steps  (15%)
[18:03:23] Completed 40000 out of 250000 steps  (16%)
[18:07:53] - Autosending finished units... [June 8 18:07:53 UTC]
[18:07:53] Trying to send all finished work units
[18:07:53] + No unsent completed units remaining.
[18:07:53] - Autosend completed
Segmentation fault
[18:39:43] CoreStatus = 8B (139)
[18:39:43] Client-core communications error: ERROR 0x8b
[18:39:43] Deleting current work unit & continuing...
[18:39:57] Trying to send all finished work units
[18:39:57] + No unsent completed units remaining.
[18:39:57] - Preparing to get new work unit...
[18:39:57] Cleaning up work directory
[18:39:57] + Attempting to get work packet
[18:39:57] Passkey found
[18:39:57] - Will indicate memory of 5975 MB
[18:39:57] - Connecting to assignment server
[18:39:57] Connecting to http://assign.stanford.edu:8080/
[18:39:58] Posted data.
[18:39:58] Initial: 43AB; - Successful: assigned to (171.67.108.22).
[18:39:58] + News From Folding@Home: Welcome to Folding@Home
[18:39:58] Loaded queue successfully.
[18:39:58] Connecting to http://171.67.108.22:8080/
[18:40:11] Posted data.
[18:40:11] Initial: 0000; - Receiving payload (expected size: 24838183)
[18:41:13] - Downloaded at ~391 kB/s
[18:41:13] - Averaged speed for that direction ~357 kB/s
[18:41:13] + Received work.
[18:41:13] + Closed connections
[18:41:18] 
[18:41:18] + Processing work unit
[18:41:18] Core required: FahCore_a3.exe
[18:41:18] Core found.
[18:41:18] Working on queue slot 06 [June 8 18:41:18 UTC]
[18:41:18] + Working ...
[18:41:18] - Calling './FahCore_a3.exe -dir work/ -nice 19 -suffix 06 -np 8 -checkpoint 15 -verbose -lifeline 1688 -version 629'

[18:41:18] 
[18:41:18] *------------------------------*
[18:41:18] Folding@Home Gromacs SMP Core
[18:41:18] Version 2.21 (May 10, 2010)
[18:41:18] 
[18:41:18] Preparing to commence simulation
[18:41:18] - Looking at optimizations...
[18:41:18] - Created dyn
[18:41:18] - Files status OK
[18:41:20] - Expanded 24837671 -> 30791309 (decompressed 123.9 percent)
[18:41:20] Called DecompressByteArray: compressed_data_size=24837671 data_size=30791309, decompressed_data_size=30791309 diff=0
[18:41:20] - Digital signature verified
[18:41:20] 
[18:41:20] Project: 2684 (Run 2, Clone 3, Gen 2)
[18:41:20] 
[18:41:20] Assembly optimizations on if available.
[18:41:20] Entering M.D.
Starting 8 threads
NNODES=8, MYRANK=0, HOSTNAME=thread #0
NNODES=8, MYRANK=3, HOSTNAME=thread #3
NNODES=8, MYRANK=5, HOSTNAME=thread #5
NNODES=8, MYRANK=2, HOSTNAME=thread #2
NNODES=8, MYRANK=1, HOSTNAME=thread #1
NNODES=8, MYRANK=6, HOSTNAME=thread #6
NNODES=8, MYRANK=7, HOSTNAME=thread #7
NNODES=8, MYRANK=4, HOSTNAME=thread #4
Reading file work/wudata_06.tpr, VERSION 4.0.99_development_20090605 (single precision)
Making 1D domain decomposition 8 x 1 x 1
starting mdrun 'SINGLE VESICLE in water'
750000 steps,   3000.0 ps (continuing from step 500000,   2000.0 ps).

t = 2000.000 ps: Water molecule starting at atom 172479 can not be settled.
Check for bad contacts and/or reduce the timestep.
[18:41:32] Completed 0 out of 250000 steps  (0%)

-------------------------------------------------------
Program mdrun, VERSION 4.0.99-dev-20100510-f91fd
Source code file: /data0/FAHdev/a3_development/gromacs/src/mdlib/pme.c, line: 529

Fatal error:
6 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension xThis usually means that your system is not well equilibrated
For more information and tips for trouble shooting please check the GROMACS website at
http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Thanx for Using GROMACS - Have a Nice Day

[18:41:34] mdrun returned 255
[18:41:34] Going to send back what have done -- stepsTotalG=250000
[18:41:34] Work fraction=8589934592.0000 steps=250000.
[18:41:38] logfile size=12551 infoLength=12551 edr=25 trr=1
[18:41:38] logfile size: 12551 info=12551 bed=25 hdr=1
[18:41:38] - Writing 13089 bytes of core data to disk...
[18:41:39]   ... Done.
[18:41:43] 
[18:41:43] Folding@home Core Shutdown: UNSTABLE_MACHINE
[18:41:43] CoreStatus = 7A (122)
[18:41:43] Sending work to server
[18:41:43] Project: 2684 (Run 2, Clone 3, Gen 2)


[18:41:43] + Attempting to send results [June 8 18:41:43 UTC]
[18:41:43] - Reading file work/wuresults_06.dat from core
[18:41:43]   (Read 13089 bytes from disk)
[18:41:43] Connecting to http://171.67.108.22:8080/
[18:41:45] Posted data.
[18:41:45] Initial: 0000; - Uploaded at ~4 kB/s
[18:41:46] - Averaged speed for that direction ~74 kB/s
[18:41:46] + Results successfully sent
[18:41:46] Thank you for your contribution to Folding@Home.
[18:41:46] Trying to send all finished work units
[18:41:46] + No unsent completed units remaining.
[18:41:46] - Preparing to get new work unit...
[18:41:46] Cleaning up work directory
[18:41:46] + Attempting to get work packet
[18:41:46] Passkey found
[18:41:46] - Will indicate memory of 5975 MB
[18:41:46] - Connecting to assignment server
[18:41:46] Connecting to http://assign.stanford.edu:8080/
[18:41:47] Posted data.
[18:41:47] Initial: 43AB; - Successful: assigned to (171.67.108.22).
[18:41:47] + News From Folding@Home: Welcome to Folding@Home
[18:41:47] Loaded queue successfully.
[18:41:47] Connecting to http://171.67.108.22:8080/
[18:41:57] Posted data.
[18:41:57] Initial: 0000; - Receiving payload (expected size: 24838183)
[18:42:58] - Downloaded at ~397 kB/s
[18:42:58] - Averaged speed for that direction ~365 kB/s
[18:42:58] + Received work.
[18:42:58] Trying to send all finished work units
[18:42:58] + No unsent completed units remaining.
[18:42:58] + Closed connections
[18:43:03] 
[18:43:03] + Processing work unit
[18:43:03] Core required: FahCore_a3.exe
[18:43:03] Core found.
[18:43:03] Working on queue slot 07 [June 8 18:43:03 UTC]
[18:43:03] + Working ...
[18:43:03] - Calling './FahCore_a3.exe -dir work/ -nice 19 -suffix 07 -np 8 -checkpoint 15 -verbose -lifeline 1688 -version 629'

[18:43:03] 
[18:43:03] *------------------------------*
[18:43:03] Folding@Home Gromacs SMP Core
[18:43:03] Version 2.21 (May 10, 2010)
[18:43:03] 
[18:43:03] Preparing to commence simulation
[18:43:03] - Looking at optimizations...
[18:43:03] - Created dyn
[18:43:03] - Files status OK
[18:43:05] - Expanded 24837671 -> 30791309 (decompressed 123.9 percent)
[18:43:05] Called DecompressByteArray: compressed_data_size=24837671 data_size=30791309, decompressed_data_size=30791309 diff=0
[18:43:05] - Digital signature verified
[18:43:05] 
[18:43:05] Project: 2684 (Run 2, Clone 3, Gen 2)
[18:43:05] 
[18:43:05] Assembly optimizations on if available.
[18:43:05] Entering M.D.
Starting 8 threads
NNODES=8, MYRANK=0, HOSTNAME=thread #0
NNODES=8, MYRANK=3, HOSTNAME=thread #3
NNODES=8, MYRANK=2, HOSTNAME=thread #2
NNODES=8, MYRANK=4, HOSTNAME=thread #4
NNODES=8, MYRANK=5, HOSTNAME=thread #5
Reading file work/wudata_07.tpr, VERSION 4.0.99_development_20090605 (single precision)
NNODES=8, MYRANK=6, HOSTNAME=thread #6
NNODES=8, MYRANK=1, HOSTNAME=thread #1
NNODES=8, MYRANK=7, HOSTNAME=thread #7
Making 1D domain decomposition 8 x 1 x 1
starting mdrun 'SINGLE VESICLE in water'
750000 steps,   3000.0 ps (continuing from step 500000,   2000.0 ps).
[18:43:17] Completed 0 out of 250000 steps  (0%)
Segmentation fault
[18:43:19] CoreStatus = 8B (139)
[18:43:19] Client-core communications error: ERROR 0x8b
[18:43:19] Deleting current work unit & continuing...
[18:43:33] Trying to send all finished work units
[18:43:33] + No unsent completed units remaining.
[18:43:33] - Preparing to get new work unit...
[18:43:33] Cleaning up work directory
[18:43:33] + Attempting to get work packet
[18:43:33] Passkey found
[18:43:33] - Will indicate memory of 5975 MB
[18:43:33] - Connecting to assignment server
[18:43:33] Connecting to http://assign.stanford.edu:8080/
[18:43:34] Posted data.
[18:43:34] Initial: 43AB; - Successful: assigned to (171.67.108.22).
[18:43:34] + News From Folding@Home: Welcome to Folding@Home
[18:43:34] Loaded queue successfully.
[18:43:34] Connecting to http://171.67.108.22:8080/
[18:43:45] Posted data.
[18:43:45] Initial: 0000; - Receiving payload (expected size: 24838183)
[18:45:12] - Downloaded at ~278 kB/s
[18:45:12] - Averaged speed for that direction ~347 kB/s
[18:45:12] + Received work.
[18:45:12] + Closed connections
[18:45:17] 
[18:45:17] + Processing work unit
[18:45:17] Core required: FahCore_a3.exe
[18:45:17] Core found.
[18:45:17] Working on queue slot 08 [June 8 18:45:17 UTC]
[18:45:17] + Working ...
[18:45:17] - Calling './FahCore_a3.exe -dir work/ -nice 19 -suffix 08 -np 8 -checkpoint 15 -verbose -lifeline 1688 -version 629'

[18:45:18] 
[18:45:18] *------------------------------*
[18:45:18] Folding@Home Gromacs SMP Core
[18:45:18] Version 2.21 (May 10, 2010)
[18:45:18] 
[18:45:18] Preparing to commence simulation
[18:45:18] - Looking at optimizations...
[18:45:18] - Created dyn
[18:45:18] - Files status OK
[18:45:20] - Expanded 24837671 -> 30791309 (decompressed 123.9 percent)
[18:45:20] Called DecompressByteArray: compressed_data_size=24837671 data_size=30791309, decompressed_data_size=30791309 diff=0
[18:45:20] - Digital signature verified
[18:45:20] 
[18:45:20] Project: 2684 (Run 2, Clone 3, Gen 2)
[18:45:20] 
[18:45:20] Assembly optimizations on if available.
[18:45:20] Entering M.D.
Starting 8 threads
NNODES=8, MYRANK=0, HOSTNAME=thread #0
NNODES=8, MYRANK=4, HOSTNAME=thread #4
NNODES=8, MYRANK=3, HOSTNAME=thread #3
NNODES=8, MYRANK=6, HOSTNAME=thread #6
NNODES=8, MYRANK=7, HOSTNAME=thread #7
NNODES=8, MYRANK=1, HOSTNAME=thread #1
NNODES=8, MYRANK=2, HOSTNAME=thread #2
NNODES=8, MYRANK=5, HOSTNAME=thread #5
Reading file work/wudata_08.tpr, VERSION 4.0.99_development_20090605 (single precision)
Making 1D domain decomposition 8 x 1 x 1
starting mdrun 'SINGLE VESICLE in water'
750000 steps,   3000.0 ps (continuing from step 500000,   2000.0 ps).
[18:45:31] Completed 0 out of 250000 steps  (0%)
[19:36:36] Completed 2500 out of 250000 steps  (1%)
[20:26:49] Completed 5000 out of 250000 steps  (2%)
[21:17:35] Completed 7500 out of 250000 steps  (3%)
[22:08:48] Completed 10000 out of 250000 steps  (4%)
[22:59:57] Completed 12500 out of 250000 steps  (5%)
[23:50:52] Completed 15000 out of 250000 steps  (6%)
[00:07:26] - Autosending finished units... [June 9 00:07:26 UTC]
[00:07:26] Trying to send all finished work units
[00:07:26] + No unsent completed units remaining.
[00:07:26] - Autosend completed
[00:41:28] Completed 17500 out of 250000 steps  (7%)
[01:32:28] Completed 20000 out of 250000 steps  (8%)
[02:22:58] Completed 22500 out of 250000 steps  (9%)
[03:13:33] Completed 25000 out of 250000 steps  (10%)
[04:04:14] Completed 27500 out of 250000 steps  (11%)
[04:55:07] Completed 30000 out of 250000 steps  (12%)
[05:46:08] Completed 32500 out of 250000 steps  (13%)
[06:07:26] - Autosending finished units... [June 9 06:07:26 UTC]
[06:07:26] Trying to send all finished work units
[06:07:26] + No unsent completed units remaining.
[06:07:26] - Autosend completed
[06:37:08] Completed 35000 out of 250000 steps  (14%)
[07:27:53] Completed 37500 out of 250000 steps  (15%)
[08:18:41] Completed 40000 out of 250000 steps  (16%)
[09:09:23] Completed 42500 out of 250000 steps  (17%)
[10:00:27] Completed 45000 out of 250000 steps  (18%)
[10:51:35] Completed 47500 out of 250000 steps  (19%)
[11:42:41] Completed 50000 out of 250000 steps  (20%)
Segmentation fault
[11:54:10] CoreStatus = 8B (139)
[11:54:10] Client-core communications error: ERROR 0x8b
[11:54:10] Deleting current work unit & continuing...
HW:
i7 930@3.5GHz, 6 GB ram
OS
Ubuntu 9.10
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