Did something go wrong?

freeloader1969 · Jul 1, 2012

Can anyone tell me what went wrong with this unit. It took almost three days to complete and it looks like I didn't get any points for it. I have the wuresults_02.dat file in my work folder and it's 222 MB in size but it hasn't been uploaded for some reason. Is there anyway to force the client to upload that result?

Code:

[00:55:48] Completed 247500 out of 250000 steps  (99%)
[01:44:18] Completed 250000 out of 250000 steps  (100%)
[01:44:44] DynamicWrapper: Finished Work Unit: sleep=10000
[01:44:54] 
[01:44:54] Finished Work Unit:
[01:44:54] - Reading up to 121622496 from "work/wudata_02.trr": Read 121622496
[01:44:55] trr file hash check passed.
[01:44:55] - Reading up to 108851792 from "work/wudata_02.xtc": Read 108851792
[01:44:56] xtc file hash check passed.
[01:44:56] edr file hash check passed.
[01:44:56] logfile size: 227075
[01:44:56] Leaving Run
[01:44:57] - Writing 230874355 bytes of core data to disk...
[01:46:18] Done: 230873843 -> 222501081 (compressed to 3.3 percent)
[01:46:18]   ... Done.
[04:07:29] - Shutting down core
[04:07:29] 
[04:07:29] Folding@home Core Shutdown: FINISHED_UNIT


--- Opening Log file [July 1 10:19:20 UTC] 


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

                       Folding@Home Client Version 6.34

                          http://folding.stanford.edu

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

Launch directory: /home/mike/fah
Executable: ./fah6
Arguments: -smp 16 -bigbeta -verbosity 9 

[10:19:20] - Ask before connecting: No
[10:19:20] - User name: freeloader (Team 33)
[10:19:20] - User ID: 499F34AC40272FCC
[10:19:20] - Machine ID: 1
[10:19:20] 
[10:19:20] Loaded queue successfully.
[10:19:20] 
[10:19:20] + Processing work unit
[10:19:20] Core required: FahCore_a5.exe
[10:19:20] - Autosending finished units... [July 1 10:19:20 UTC]
[10:19:20] Core found.
[10:19:20] Trying to send all finished work units
[10:19:20] + No unsent completed units remaining.
[10:19:20] - Autosend completed

orion · Jul 1, 2012

What WU was it and how big was the down load size?

Sounds like one of those bad WU's http://foldingforum.org/viewtopic.php?f=19&t=20692&start=60#p210196

tear · Jul 1, 2012

It looks like log lacks continuity --

Code:

[04:07:29] 
[04:07:29] Folding@home Core Shutdown: FINISHED_UNIT

What happened after that?

There's a chance that qfix may help things but we'll need to see full log
first...

Also, the 2h+ pause, here:

Code:

[01:46:18]   ... Done.
[04:07:29] - Shutting down core

suggests that you're running into FAH's disk thrashing bug.

What OS are you running? Have you run any system updates? What does 'uname -r' return?

freeloader1969 · Jul 1, 2012

I'm using Ubuntu 12.04 (64 bit). The unit was a 6903 (Run 9, Clone 12, Gen 99). Here's the full logs. Uname -r returns "3.2.0-26-generic" The initial download size of the work unit was 57 MB.

Code:

[14:27:34] Verifying core Core_a5.fah...
[14:27:34] Signature is VALID
[14:27:34] 
[14:27:34] Trying to unzip core FahCore_a5.exe
[14:27:34] Decompressed FahCore_a5.exe (6272504 bytes) successfully
[14:27:34] + Core successfully engaged
[14:28:23] 
[14:28:23] + Processing work unit
[14:28:23] Core required: FahCore_a5.exe
[14:28:23] Core found.
[14:28:23] Working on queue slot 02 [June 27 14:28:23 UTC]
[14:28:23] + Working ...
[14:28:23] - Calling './FahCore_a5.exe -dir work/ -nice 19 -suffix 02 -np 16 -checkpoint 15 -verbose -lifeline 2667 -version 634'

[14:28:24] 
[14:28:24] *------------------------------*
[14:28:24] Folding@Home Gromacs SMP Core
[14:28:24] Version 2.27 (Thu Feb 10 09:46:40 PST 2011)
[14:28:24] 
[14:28:24] Preparing to commence simulation
[14:28:24] - Looking at optimizations...
[14:28:24] - Created dyn
[14:28:24] - Files status OK
[14:28:32] - Expanded 57242250 -> 71846524 (decompressed 50.4 percent)
[14:28:32] Called DecompressByteArray: compressed_data_size=57242250 data_size=71846524, decompressed_data_size=71846524 diff=0
[14:28:32] - Digital signature verified
[14:28:32] 
[14:28:32] Project: 6903 (Run 9, Clone 12, Gen 99)
[14:28:32] 
[14:28:32] Assembly optimizations on if available.
[14:28:32] Entering M.D.
[14:28:42] Mapping NT from 16 to 16 
[14:28:48] Completed 0 out of 250000 steps  (0%)
[14:32:03] ***** Got an Activate signal (2)
[14:32:03] Killing all core threads

Folding@Home Client Shutdown.


--- Opening Log file [June 27 14:37:43 UTC] 


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

                       Folding@Home Client Version 6.34

                          http://folding.stanford.edu

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

Launch directory: /home/mike/fah
Executable: ./fah6
Arguments: -smp 16 -bigbeta -verbosity 9 

[14:37:43] - Ask before connecting: No
[14:37:43] - User name: freeloader (Team 33)
[14:37:43] - User ID: 499F34AC40272FCC
[14:37:43] - Machine ID: 1
[14:37:43] 
[14:37:43] Loaded queue successfully.
[14:37:43] 
[14:37:43] + Processing work unit
[14:37:43] Core required: FahCore_a5.exe
[14:37:43] - Autosending finished units... [June 27 14:37:43 UTC]
[14:37:43] Core found.
[14:37:43] Trying to send all finished work units
[14:37:43] + No unsent completed units remaining.
[14:37:43] - Autosend completed
[14:37:43] Working on queue slot 02 [June 27 14:37:43 UTC]
[14:37:43] + Working ...
[14:37:43] - Calling './FahCore_a5.exe -dir work/ -nice 19 -suffix 02 -np 16 -checkpoint 15 -verbose -lifeline 2793 -version 634'

[14:37:43] 
[14:37:43] *------------------------------*
[14:37:43] Folding@Home Gromacs SMP Core
[14:37:43] Version 2.27 (Thu Feb 10 09:46:40 PST 2011)
[14:37:43] 
[14:37:43] Preparing to commence simulation
[14:37:43] - Looking at optimizations...
[14:37:43] - Files status OK
[14:37:51] - Expanded 57242250 -> 71846524 (decompressed 50.4 percent)
[14:37:51] Called DecompressByteArray: compressed_data_size=57242250 data_size=71846524, decompressed_data_size=71846524 diff=0
[14:37:52] - Digital signature verified
[14:37:52] 
[14:37:52] Project: 6903 (Run 9, Clone 12, Gen 99)
[14:37:52] 
[14:37:52] Assembly optimizations on if available.
[14:37:52] Entering M.D.
[14:38:01] Mapping NT from 16 to 16 
[14:38:07] Completed 0 out of 250000 steps  (0%)
[14:39:07] ***** Got an Activate signal (2)
[14:39:07] Killing all core threads

Folding@Home Client Shutdown.


--- Opening Log file [June 27 14:39:31 UTC] 


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

                       Folding@Home Client Version 6.34

                          http://folding.stanford.edu

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

Launch directory: /home/mike/fah
Executable: ./fah6
Arguments: -smp 16 -bigbeta -verbosity 9 

[14:39:31] - Ask before connecting: No
[14:39:31] - User name: freeloader (Team 33)
[14:39:31] - User ID: 499F34AC40272FCC
[14:39:31] - Machine ID: 1
[14:39:31] 
[14:39:31] Loaded queue successfully.
[14:39:31] 
[14:39:31] - Autosending finished units... [June 27 14:39:31 UTC]
[14:39:31] + Processing work unit
[14:39:31] Trying to send all finished work units
[14:39:31] Core required: FahCore_a5.exe
[14:39:31] + No unsent completed units remaining.
[14:39:31] Core found.
[14:39:31] - Autosend completed
[14:39:31] Working on queue slot 02 [June 27 14:39:31 UTC]
[14:39:31] + Working ...
[14:39:31] - Calling './FahCore_a5.exe -dir work/ -nice 19 -suffix 02 -np 16 -checkpoint 15 -verbose -lifeline 2917 -version 634'

[14:39:32] 
[14:39:32] *------------------------------*
[14:39:32] Folding@Home Gromacs SMP Core
[14:39:32] Version 2.27 (Thu Feb 10 09:46:40 PST 2011)
[14:39:32] 
[14:39:32] Preparing to commence simulation
[14:39:32] - Looking at optimizations...
[14:39:32] - Files status OK
[14:39:40] - Expanded 57242250 -> 71846524 (decompressed 50.4 percent)
[14:39:40] Called DecompressByteArray: compressed_data_size=57242250 data_size=71846524, decompressed_data_size=71846524 diff=0
[14:39:40] - Digital signature verified
[14:39:40] 
[14:39:40] Project: 6903 (Run 9, Clone 12, Gen 99)
[14:39:40] 
[14:39:40] Assembly optimizations on if available.
[14:39:40] Entering M.D.
[14:39:50] Mapping NT from 16 to 16 
[14:39:56] Completed 0 out of 250000 steps  (0%)
[15:31:34] Completed 2500 out of 250000 steps  (1%)
[16:36:36] Completed 5000 out of 250000 steps  (2%)
[16:48:28] ***** Got an Activate signal (2)
[16:48:28] Killing all core threads

Folding@Home Client Shutdown.


--- Opening Log file [June 27 16:57:24 UTC] 


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

                       Folding@Home Client Version 6.34

                          http://folding.stanford.edu

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

Launch directory: /home/mike/fah
Executable: ./fah6
Arguments: -smp 16 -bigbeta -verbosity 9 

[16:57:24] - Ask before connecting: No
[16:57:24] - User name: freeloader (Team 33)
[16:57:24] - User ID: 499F34AC40272FCC
[16:57:24] - Machine ID: 1
[16:57:24] 
[16:57:24] Loaded queue successfully.
[16:57:24] 
[16:57:24] + Processing work unit
[16:57:24] Core required: FahCore_a5.exe
[16:57:24] - Autosending finished units... [June 27 16:57:24 UTC]
[16:57:24] Core found.
[16:57:24] Trying to send all finished work units
[16:57:24] + No unsent completed units remaining.
[16:57:24] - Autosend completed
[16:57:25] Working on queue slot 02 [June 27 16:57:25 UTC]
[16:57:25] + Working ...
[16:57:25] - Calling './FahCore_a5.exe -dir work/ -nice 19 -suffix 02 -np 16 -checkpoint 15 -verbose -lifeline 2162 -version 634'

[16:57:25] 
[16:57:25] *------------------------------*
[16:57:25] Folding@Home Gromacs SMP Core
[16:57:25] Version 2.27 (Thu Feb 10 09:46:40 PST 2011)
[16:57:25] 
[16:57:25] Preparing to commence simulation
[16:57:25] - Looking at optimizations...
[16:57:25] - Files status OK
[16:57:34] - Expanded 57242250 -> 71846524 (decompressed 50.4 percent)
[16:57:34] Called DecompressByteArray: compressed_data_size=57242250 data_size=71846524, decompressed_data_size=71846524 diff=0
[16:57:34] - Digital signature verified
[16:57:34] 
[16:57:34] Project: 6903 (Run 9, Clone 12, Gen 99)
[16:57:34] 
[16:57:35] Assembly optimizations on if available.
[16:57:35] Entering M.D.
[16:57:41] Using Gromacs checkpoints
[16:57:55] Mapping NT from 16 to 16 
[16:58:49] Resuming from checkpoint
[16:58:52] Verified work/wudata_02.log
[16:58:53] Verified work/wudata_02.trr
[16:58:53] Verified work/wudata_02.xtc
[16:58:53] Verified work/wudata_02.edr
[16:58:55] Completed 5110 out of 250000 steps  (2%)
[17:49:04] Completed 7500 out of 250000 steps  (3%)
[17:54:27] ***** Got an Activate signal (2)
[17:54:27] Killing all core threads

Folding@Home Client Shutdown.


--- Opening Log file [June 27 18:01:11 UTC] 


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

                       Folding@Home Client Version 6.34

                          http://folding.stanford.edu

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

Launch directory: /home/mike/fah
Executable: ./fah6
Arguments: -smp 16 -bigbeta -verbosity 9 

[18:01:11] - Ask before connecting: No
[18:01:11] - User name: freeloader (Team 33)
[18:01:11] - User ID: 499F34AC40272FCC
[18:01:11] - Machine ID: 1
[18:01:11] 
[18:01:12] Loaded queue successfully.
[18:01:12] 
[18:01:12] - Autosending finished units... [June 27 18:01:12 UTC]
[18:01:12] + Processing work unit
[18:01:12] Trying to send all finished work units
[18:01:12] Core required: FahCore_a5.exe
[18:01:12] + No unsent completed units remaining.
[18:01:12] - Autosend completed
[18:01:12] Core found.
[18:01:12] Working on queue slot 02 [June 27 18:01:12 UTC]
[18:01:12] + Working ...
[18:01:12] - Calling './FahCore_a5.exe -dir work/ -nice 19 -suffix 02 -np 16 -checkpoint 15 -verbose -lifeline 2241 -version 634'

[18:01:12] 
[18:01:12] *------------------------------*
[18:01:12] Folding@Home Gromacs SMP Core
[18:01:12] Version 2.27 (Thu Feb 10 09:46:40 PST 2011)
[18:01:12] 
[18:01:12] Preparing to commence simulation
[18:01:12] - Looking at optimizations...
[18:01:12] - Files status OK
[18:01:21] - Expanded 57242250 -> 71846524 (decompressed 50.4 percent)
[18:01:21] Called DecompressByteArray: compressed_data_size=57242250 data_size=71846524, decompressed_data_size=71846524 diff=0
[18:01:21] - Digital signature verified
[18:01:21] 
[18:01:21] Project: 6903 (Run 9, Clone 12, Gen 99)
[18:01:21] 
[18:01:22] Assembly optimizations on if available.
[18:01:22] Entering M.D.
[18:01:28] Using Gromacs checkpoints
[18:01:39] Mapping NT from 16 to 16 
[18:02:23] Resuming from checkpoint
[18:02:32] Verified work/wudata_02.log
[18:02:33] Verified work/wudata_02.trr
[18:02:33] Verified work/wudata_02.xtc
[18:02:33] Verified work/wudata_02.edr
[18:02:34] Completed 7200 out of 250000 steps  (2%)
[18:09:44] Completed 7500 out of 250000 steps  (3%)
[18:53:39] Completed 10000 out of 250000 steps  (4%)
[19:37:26] Completed 12500 out of 250000 steps  (5%)
[20:21:12] Completed 15000 out of 250000 steps  (6%)
[21:05:33] Completed 17500 out of 250000 steps  (7%)
[21:55:10] Completed 20000 out of 250000 steps  (8%)
[22:40:49] Completed 22500 out of 250000 steps  (9%)
[23:29:52] Completed 25000 out of 250000 steps  (10%)
[00:01:12] - Autosending finished units... [June 28 00:01:12 UTC]
[00:01:12] Trying to send all finished work units
[00:01:12] + No unsent completed units remaining.
[00:01:12] - Autosend completed
[00:14:10] Completed 27500 out of 250000 steps  (11%)
[00:57:59] Completed 30000 out of 250000 steps  (12%)
[01:45:48] Completed 32500 out of 250000 steps  (13%)
[02:32:38] Completed 35000 out of 250000 steps  (14%)
[03:17:50] Completed 37500 out of 250000 steps  (15%)
[04:01:40] Completed 40000 out of 250000 steps  (16%)
[04:47:20] Completed 42500 out of 250000 steps  (17%)
[05:31:06] Completed 45000 out of 250000 steps  (18%)
[06:01:12] - Autosending finished units... [June 28 06:01:12 UTC]
[06:01:12] Trying to send all finished work units
[06:01:12] + No unsent completed units remaining.
[06:01:12] - Autosend completed
[06:15:25] Completed 47500 out of 250000 steps  (19%)
[06:59:19] Completed 50000 out of 250000 steps  (20%)
[07:43:17] Completed 52500 out of 250000 steps  (21%)
[08:27:13] Completed 55000 out of 250000 steps  (22%)
[09:11:09] Completed 57500 out of 250000 steps  (23%)
[09:55:04] Completed 60000 out of 250000 steps  (24%)
[10:38:59] Completed 62500 out of 250000 steps  (25%)
[11:22:55] Completed 65000 out of 250000 steps  (26%)
[12:01:12] - Autosending finished units... [June 28 12:01:12 UTC]
[12:01:12] Trying to send all finished work units
[12:01:12] + No unsent completed units remaining.
[12:01:12] - Autosend completed
[12:06:51] Completed 67500 out of 250000 steps  (27%)
[12:50:47] Completed 70000 out of 250000 steps  (28%)
[13:38:28] Completed 72500 out of 250000 steps  (29%)
[14:39:03] Completed 75000 out of 250000 steps  (30%)
[15:35:02] Completed 77500 out of 250000 steps  (31%)
[16:18:52] Completed 80000 out of 250000 steps  (32%)
[17:02:42] Completed 82500 out of 250000 steps  (33%)
[17:46:25] Completed 85000 out of 250000 steps  (34%)
[18:01:11] - Autosending finished units... [June 28 18:01:11 UTC]
[18:01:11] Trying to send all finished work units
[18:01:11] + No unsent completed units remaining.
[18:01:11] - Autosend completed
[18:14:21] ***** Got an Activate signal (2)
[18:14:21] Killing all core threads

Folding@Home Client Shutdown.
[18:24:59] Completed 227500 out of 250000 steps  (91%)
[19:13:12] Completed 230000 out of 250000 steps  (92%)
[20:00:30] Completed 232500 out of 250000 steps  (93%)
[20:47:58] Completed 235000 out of 250000 steps  (94%)
[21:41:59] Completed 237500 out of 250000 steps  (95%)
[22:29:33] Completed 240000 out of 250000 steps  (96%)
[23:17:51] Completed 242500 out of 250000 steps  (97%)
[00:07:17] Completed 245000 out of 250000 steps  (98%)
[00:24:07] - Autosending finished units... [July 1 00:24:07 UTC]
[00:24:07] Trying to send all finished work units
[00:24:07] + No unsent completed units remaining.
[00:24:07] - Autosend completed
[00:55:48] Completed 247500 out of 250000 steps  (99%)
[01:44:18] Completed 250000 out of 250000 steps  (100%)
[01:44:44] DynamicWrapper: Finished Work Unit: sleep=10000
[01:44:54] 
[01:44:54] Finished Work Unit:
[01:44:54] - Reading up to 121622496 from "work/wudata_02.trr": Read 121622496
[01:44:55] trr file hash check passed.
[01:44:55] - Reading up to 108851792 from "work/wudata_02.xtc": Read 108851792
[01:44:56] xtc file hash check passed.
[01:44:56] edr file hash check passed.
[01:44:56] logfile size: 227075
[01:44:56] Leaving Run
[01:44:57] - Writing 230874355 bytes of core data to disk...
[01:46:18] Done: 230873843 -> 222501081 (compressed to 3.3 percent)
[01:46:18]   ... Done.
[04:07:29] - Shutting down core
[04:07:29] 
[04:07:29] Folding@home Core Shutdown: FINISHED_UNIT


--- Opening Log file [July 1 10:19:20 UTC] 


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

                       Folding@Home Client Version 6.34

                          http://folding.stanford.edu

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

Launch directory: /home/mike/fah
Executable: ./fah6
Arguments: -smp 16 -bigbeta -verbosity 9 

[10:19:20] - Ask before connecting: No
[10:19:20] - User name: freeloader (Team 33)
[10:19:20] - User ID: 499F34AC40272FCC
[10:19:20] - Machine ID: 1
[10:19:20] 
[10:19:20] Loaded queue successfully.
[10:19:20] 
[10:19:20] + Processing work unit
[10:19:20] Core required: FahCore_a5.exe
[10:19:20] - Autosending finished units... [July 1 10:19:20 UTC]
[10:19:20] Core found.
[10:19:20] Trying to send all finished work units
[10:19:20] + No unsent completed units remaining.
[10:19:20] - Autosend completed
[10:19:20] Working on queue slot 02 [July 1 10:19:20 UTC]
[10:19:20] + Working ...
[10:19:20] - Calling './FahCore_a5.exe -dir work/ -nice 19 -suffix 02 -np 16 -checkpoint 15 -verbose -lifeline 2430 -version 634'

[10:19:20] 
[10:19:20] *------------------------------*
[10:19:20] Folding@Home Gromacs SMP Core
[10:19:20] Version 2.27 (Thu Feb 10 09:46:40 PST 2011)
[10:19:20] 
[10:19:20] Preparing to commence simulation
[10:19:20] - Ensuring status. Please wait.
[10:19:30] - Looking at optimizations...
[10:19:30] - Working with standard loops on this execution.
[10:19:30] - Created dyn
[10:19:30] - Files status OK
[10:19:30] Bad core type 0 expted=165
[10:19:30] Error: Work unit read from disk is invalid
[10:19:30] 
[10:19:30] Folding@home Core Shutdown: BAD_FILE_FORMAT
[10:19:30] CoreStatus = 6F (111)
[10:19:30] + The core could not recognize the format of the provided work file.
[10:19:30] Deleting current work unit & continuing...
[10:23:20] ***** Got an Activate signal (2)
[10:23:20] - Warning: Could not delete all work unit files (2): Core file absent
[10:23:20] Trying to send all finished work units
[10:23:20] + No unsent completed units remaining.
[10:23:20] - Preparing to get new work unit...
[10:23:20] Cleaning up work directory
[10:23:20] + Attempting to get work packet
[10:23:20] Passkey found
[10:23:20] - Will indicate memory of 16048 MB
[10:23:20] - Connecting to assignment server
[10:23:20] Connecting to http://assign.stanford.edu:8080/
[10:23:20] Killing all core threads

Folding@Home Client Shutdown.


--- Opening Log file [July 1 10:23:34 UTC] 


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

                       Folding@Home Client Version 6.34

                          http://folding.stanford.edu

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

Launch directory: /home/mike/fah
Executable: ./fah6
Arguments: -smp 16 -bigbeta -verbosity 9 

[10:23:34] - Ask before connecting: No
[10:23:34] - User name: freeloader (Team 33)
[10:23:34] - User ID: 499F34AC40272FCC
[10:23:34] - Machine ID: 1
[10:23:34] 
[10:23:35] Loaded queue successfully.
[10:23:35] - Preparing to get new work unit...
[10:23:35] - Autosending finished units... [July 1 10:23:35 UTC]
[10:23:35] Cleaning up work directory
[10:23:35] Trying to send all finished work units
[10:23:35] + No unsent completed units remaining.
[10:23:35] - Autosend completed
[10:23:35] + Attempting to get work packet
[10:23:35] Passkey found
[10:23:35] - Will indicate memory of 16048 MB
[10:23:35] - Connecting to assignment server
[10:23:35] Connecting to http://assign.stanford.edu:8080/
[10:23:35] Posted data.
[10:23:35] Initial: ED82; - Successful: assigned to (130.237.232.237).
[10:23:35] + News From Folding@Home: Welcome to Folding@Home
[10:23:35] Loaded queue successfully.
[10:23:35] Sent data
[10:23:35] Connecting to http://130.237.232.237:8080/
[10:23:48] Posted data.
[10:23:48] Initial: 0000; - Receiving payload (expected size: 57242762)
[10:26:03] - Downloaded at ~414 kB/s
[10:26:03] - Averaged speed for that direction ~315 kB/s
[10:26:03] + Received work.
[10:26:03] + Closed connections
[10:26:03] 
[10:26:03] + Processing work unit
[10:26:03] Core required: FahCore_a5.exe
[10:26:03] Core found.
[10:26:03] Working on queue slot 03 [July 1 10:26:03 UTC]
[10:26:03] + Working ...
[10:26:03] - Calling './FahCore_a5.exe -dir work/ -nice 19 -suffix 03 -np 16 -checkpoint 15 -verbose -lifeline 2806 -version 634'

[10:26:04] 
[10:26:04] *------------------------------*
[10:26:04] Folding@Home Gromacs SMP Core
[10:26:04] Version 2.27 (Thu Feb 10 09:46:40 PST 2011)
[10:26:04] 
[10:26:04] Preparing to commence simulation
[10:26:04] - Looking at optimizations...
[10:26:04] - Created dyn
[10:26:04] - Files status OK
[10:26:12] - Expanded 57242250 -> 71846524 (decompressed 50.4 percent)
[10:26:12] Called DecompressByteArray: compressed_data_size=57242250 data_size=71846524, decompressed_data_size=71846524 diff=0
[10:26:12] - Digital signature verified
[10:26:12] 
[10:26:12] Project: 6903 (Run 9, Clone 12, Gen 99)
[10:26:12] 
[10:26:12] Assembly optimizations on if available.
[10:26:12] Entering M.D.
[10:26:22] Mapping NT from 16 to 16 
[10:26:28] Completed 0 out of 250000 steps  (0%)
[11:12:57] Completed 2500 out of 250000 steps  (1%)
[11:56:50] Completed 5000 out of 250000 steps  (2%)
[12:40:38] Completed 7500 out of 250000 steps  (3%)
[13:24:32] Completed 10000 out of 250000 steps  (4%)
[14:08:27] Completed 12500 out of 250000 steps  (5%)

tear · Jul 1, 2012

For 12.04 see musky's great writeup at: http://hardforum.com/showthread.php?t=1695762

In a nutshell -- do this:

Code:

sudo sed -ri '/barrier=/ {p;d}; /ext[34]/ {s/([ \t]ext[34][ \t]+)([^ \t]+)([ \t])/\1\2,barrier=0\3/}' /etc/fstab

then reboot your machine.

qfix may be able to help w/your lost unit -- stop your client, then go to your fah directory and run
these:

Code:

wget http://linuxminded.xs4all.nl/software/qd-tools/source/qfix/qfix.c
gcc -o qfix qfix.c
./qfix

Hopefully qfix will be able to restore slot no 2 to "finished" state.

freeloader1969 · Jul 1, 2012

Results from running Qfix.

Code:

entry 4, status 0, address 0.0.0.0
entry 5, status 0, address 0.0.0.0
entry 6, status 0, address 0.0.0.0
entry 7, status 0, address 0.0.0.0
entry 8, status 0, address 0.0.0.0
entry 9, status 0, address 0.0.0.0
entry 0, status 0, address 0.0.0.0
entry 1, status 0, address 171.67.108.52:8080
entry 2, status 0, address 130.237.232.237:8080
  Found results <work/wuresults_02.dat>: proj 28532, run 63412, clone 10506, gen 19945
   -- queue entry: proj 6903, run 9, clone 12, gen 99
   -- doesn't match queue entry
entry 3, status 1, address 130.237.232.237:8080
File is OK

tear · Jul 1, 2012

Oww, that doesn't look good.

I wonder whether it's due to file corruption or perhaps qfix not being
able to parse it (A5 is a fairly new core given last qfix update
was in 2008).

For now it looks like there's not too much we can do about your lost
unit. I'm pretty confident that disk thrashing bug is (indirectly) responsible
for this so once you work around it (vide: sed line) you should be good
to go.

In the mean time, I'll check if qfix can parse newer wuresults files....

freeloader1969 · Jul 1, 2012

I fixed the barrier issue now. I'm figuring I lost the unit.

Code:

# /etc/fstab: static file system information.
#
# Use 'blkid' to print the universally unique identifier for a
# device; this may be used with UUID= as a more robust way to name devices
# that works even if disks are added and removed. See fstab(5).
#
# <file system> <mount point>   <type>  <options>       <dump>  <pass>
proc            /proc           proc    nodev,noexec,nosuid 0       0
# / was on /dev/sda1 during installation
UUID=591cbedf-b91a-4011-adc9-ea26b0dcac02 /               ext4    errors=remount-ro,barrier=0 0       1
# swap was on /dev/sda5 during installation
UUID=8fe31b43-eea6-4cfc-b144-5db56264befd none            swap    sw              0       0

tear · Jul 1, 2012

I think I'm onto something. Looks like qfix needs to be updated for newer wuresults file format.
It looks tricky but don't lose your hope just yet

freeloader1969 · Jul 1, 2012

tear said:
I think I'm onto something. Looks like qfix needs to be updated for newer wuresults file format.
It looks tricky but don't lost your hope just yet

Awesome Tear. I have not deleted anything in the work folder so maybe there's still hope.

I am on another unit though, so hopefully that won't interfere with anything.

tear · Jul 1, 2012

Sure, leaving previous results is safe.

Ok, I've got something here -- try this (just like the last time):

Code:

wget http://darkswarm.org/qfix-tear1.c
gcc -o qfix-tear1 qfix-tear1.c
./qfix-tear1

freeloader1969 · Jul 1, 2012

Looks promising Tear...

Code:

mike@MilkyWayG34:~/fah$ gcc -o qfix-tear1 qfix-tear1.c
mike@MilkyWayG34:~/fah$ ./qfix-tear1
entry 4, status 0, address 0.0.0.0
entry 5, status 0, address 0.0.0.0
entry 6, status 0, address 0.0.0.0
entry 7, status 0, address 0.0.0.0
entry 8, status 0, address 0.0.0.0
entry 9, status 0, address 0.0.0.0
entry 0, status 0, address 0.0.0.0
entry 1, status 0, address 171.67.108.52:8080
entry 2, status 0, address 130.237.232.237:8080
  Found results <work/wuresults_02.dat>: proj 6903, run 9, clone 12, gen 99
   -- queue entry: proj 6903, run 9, clone 12, gen 99
   -- requeued for upload
entry 3, status 1, address 130.237.232.237:8080
File needed repair.  Errors fixed: 1.
mike@MilkyWayG34:~/fah$



--- Opening Log file [July 1 16:25:05 UTC] 


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

                       Folding@Home Client Version 6.34

                          http://folding.stanford.edu

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

Launch directory: /home/mike/fah
Executable: ./fah6
Arguments: -smp 16 -bigbeta -verbosity 9 

[16:25:05] - Ask before connecting: No
[16:25:05] - User name: freeloader (Team 33)
[16:25:05] - User ID: 499F34AC40272FCC
[16:25:05] - Machine ID: 1
[16:25:05] 
[16:25:05] Loaded queue successfully.
[16:25:05] 
[16:25:05] - Autosending finished units... [July 1 16:25:05 UTC]
[16:25:05] + Processing work unit
[16:25:05] Trying to send all finished work units
[16:25:05] Core required: FahCore_a5.exe
[16:25:05] Project: 6903 (Run 9, Clone 12, Gen 99)
[16:25:05] Core found.


[16:25:05] + Attempting to send results [July 1 16:25:05 UTC]
[16:25:05] - Reading file work/wuresults_02.dat from core
[16:25:05] Working on queue slot 03 [July 1 16:25:05 UTC]
[16:25:09] + Working ...
[16:25:09] - Calling './FahCore_a5.exe -dir work/ -nice 19 -suffix 03 -np 16 -checkpoint 15 -verbose -lifeline 4624 -version 634'

[16:25:09]   (Read 222501593 bytes from disk)
[16:25:09] Connecting to http://130.237.232.237:8080/
thekraken: The Kraken 0.7-pre15 (compiled Wed Jun 27 09:49:59 EDT 2012 by mike@MilkyWayG34)
thekraken: Processor affinity wrapper for Folding@Home
thekraken: The Kraken comes with ABSOLUTELY NO WARRANTY; licensed under GPLv2
thekraken: PID: 4629
thekraken: Logging to thekraken.log
[16:25:09] 
[16:25:09] *------------------------------*
[16:25:09] Folding@Home Gromacs SMP Core
[16:25:09] Version 2.27 (Thu Feb 10 09:46:40 PST 2011)
[16:25:09] 
[16:25:09] Preparing to commence simulation
[16:25:09] - Looking at optimizations...
[16:25:09] - Files status OK
[16:25:17] - Expanded 57242250 -> 71846524 (decompressed 50.4 percent)
[16:25:17] Called DecompressByteArray: compressed_data_size=57242250 data_size=71846524, decompressed_data_size=71846524 diff=0
[16:25:18] - Digital signature verified
[16:25:18] 
[16:25:18] Project: 6903 (Run 9, Clone 12, Gen 99)
[16:25:18] 
[16:25:18] Assembly optimizations on if available.
[16:25:18] Entering M.D.
[16:25:24] Using Gromacs checkpoints
                         :-)  G  R  O  M  A  C  S  (-:

                   Groningen Machine for Chemical Simulation

                            :-)  VERSION 4.5.3  (-:

        Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
      Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, 
        Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, 
           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, 
                Michael Shirts, Alfons Sijbers, Peter Tieleman,

               Berk Hess, David van der Spoel, and Erik Lindahl.

       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
            Copyright (c) 2001-2010, The GROMACS development team at
        Uppsala University & The Royal Institute of Technology, Sweden.
            check out http://www.gromacs.org for more information.


                               :-)  Gromacs  (-:

[16:25:34] Mapping NT from 16 to 16 
Reading file work/wudata_03.tpr, VERSION 4.5.4-dev-20110530-cc815 (single precision)
Starting 16 threads

Reading checkpoint file work/wudata_03.cpt generated: Sun Jul  1 12:19:14 2012


Making 1D domain decomposition 16 x 1 x 1
starting mdrun 'Overlay'
25000000 steps, 100000.0 ps (continuing from step 24767920,  99071.7 ps).
[16:26:26] Resuming from checkpoint
[16:26:29] Verified work/wudata_03.log
[16:26:30] Verified work/wudata_03.trr
[16:26:30] Verified work/wudata_03.xtc
[16:26:30] Verified work/wudata_03.edr
[16:26:31] Completed 17920 out of 250000 steps  (7%)

tear · Jul 1, 2012

RAWR!

I understand you did that with client turned off? (it may otherwise overwrite qfix mods)

EDIT: ok, your edit answers my question

let's wait and see what happens!

freeloader1969 · Jul 1, 2012

Thanks so much Tear, the unit was sent.

Code:

[17:07:16] Completed 20000 out of 250000 steps  (8%)
[17:30:06] Posted data.
[17:30:06] Initial: 0000; - Uploaded at ~55 kB/s
[17:30:06] - Averaged speed for that direction ~55 kB/s
[17:30:06] + Results successfully sent
[17:30:06] Thank you for your contribution to Folding@Home.
[17:30:06] + Starting local stats count at 1
[17:30:15] + Sent 1 of 1 completed units to the server
[17:30:15] - Autosend completed

tear · Jul 1, 2012

Excellent, I'll share the mod with current maintainer of qfix.

freeloader1969 · Jul 1, 2012

Picked up 238,000 points for that. Wow, glad I didn't loose it.

Edward2 · Jul 1, 2012

tear, the things that you can do are amazing. I'm definitely impressed.

Nathan_P · Jul 1, 2012

As always, Tear's talent never ceases to amaze

Pity you can't be nominated for HDCOTY again

ChelseaOilman · Jul 1, 2012

Hi freeloader (team 33),
Your WU (P6903 R9 C12 G99) was added to the stats database on 2012-07-01 11:08:30 for 238731 points of credit.

Did something go wrong?

freeloader1969

2[H]4U

orion

Weaksauce

tear

[H]ard|DCer of the Year 2011

freeloader1969

2[H]4U

tear

[H]ard|DCer of the Year 2011

freeloader1969

2[H]4U

tear

[H]ard|DCer of the Year 2011

freeloader1969

2[H]4U

tear

[H]ard|DCer of the Year 2011

freeloader1969

2[H]4U

tear

[H]ard|DCer of the Year 2011

freeloader1969

2[H]4U

tear

[H]ard|DCer of the Year 2011

freeloader1969

2[H]4U

tear

[H]ard|DCer of the Year 2011

freeloader1969

2[H]4U

Edward2

n00b

Nathan_P

[H]ard DCOTM x3

ChelseaOilman

[H]ard|Gawd