Project: 6316 (Run 156, Clone 0, Gen 8) GROMACS error

[swashburnsr]

I keep getting this error, and I have not been able to find a reason why.

[12:53:28] Loaded queue successfully.
[12:53:28]
[12:53:28] + Processing work unit
[12:53:28] Core required: FahCore_78.exe
[12:53:28] Core found.
[12:53:29] Working on queue slot 05 [June 21 12:53:29 UTC]
[12:53:29] + Working ...
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
[12:53:29]
[12:53:29] *------------------------------*
[12:53:29] Folding@Home Gromacs Core
[12:53:29] Version 1.90 (March 8, 2006)
[12:53:29]
[12:53:29] Preparing to commence simulation
[12:53:29] - Ensuring status. Please wait.
[12:53:46] - Looking at optimizations...
[12:53:46] - Working with standard loops on this execution.
[12:53:46] - Created dyn
[12:53:46] - Files status OK
[12:53:46] - Expanded 445502 -> 1512269 (decompressed 339.4 percent)
[12:53:46] - Starting from initial work packet
[12:53:46]
[12:53:46] Project: 6316 (Run 156, Clone 0, Gen 8)
[12:53:46]
[12:53:46] Entering M.D.

Gromacs is Copyright (c) 1991-2003, University of Groningen, The Netherlands
...

[12:53:52] Gromacs error.
[12:53:52]
[12:53:52] Folding@home Core Shutdown: UNKNOWN_ERROR
[12:53:52] CoreStatus = 79 (121)
[12:53:52] Client-core communications error: ERROR 0x79
[12:53:52] This is a sign of more serious problems, shutting down.

[PantherX]

Welcome to the Forum swashburnsr,

We would also need a brief description of your hardware like; CPU Model, RAM, OS, Have you Overclocked your CPU, etc. Also you have this:
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Could you please post the entire FAHLog here. Do make sure that you use the Code Button so that the FAHLog appears like this:

Code: Select all

FAHLog here.

[swashburnsr]

Code: Select all

CPU: Quad Core 6600
RAM: 6 gig
OS: CentOS - Linux version 2.6.18-164.11.1.el5 ([email protected]) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-46)) #1 SMP Wed Jan 20 07:32:21 EST 2010


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

                       Folding@Home Client Version 6.29

                          http://folding.stanford.edu

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

Launch directory: /home/swashbur/folding
Executable: ./fah6


[12:53:28] - Ask before connecting: No
[12:53:28] - User name: swashburnsr (Team 11108)
[12:53:28] - User ID: 411AD2244C12B283
[12:53:28] - Machine ID: 1
[12:53:28] 
[12:53:28] Loaded queue successfully.
[12:53:28] 
[12:53:28] + Processing work unit
[12:53:28] Core required: FahCore_78.exe
[12:53:28] Core found.
[12:53:29] Working on queue slot 05 [June 21 12:53:29 UTC]
[12:53:29] + Working ...
[12:53:29] 
[12:53:29] *------------------------------*
[12:53:29] Folding@Home Gromacs Core
[12:53:29] Version 1.90 (March 8, 2006)
[12:53:29] 
[12:53:29] Preparing to commence simulation
[12:53:29] - Ensuring status. Please wait.
[12:53:46] - Looking at optimizations...
[12:53:46] - Working with standard loops on this execution.
[12:53:46] - Created dyn
[12:53:46] - Files status OK
[12:53:46] - Expanded 445502 -> 1512269 (decompressed 339.4 percent)
[12:53:46] - Starting from initial work packet
[12:53:46] 
[12:53:46] Project: 6316 (Run 156, Clone 0, Gen 8)
[12:53:46] 
[12:53:46] Entering M.D.
[12:53:52] Gromacs error.
[12:53:52] 
[12:53:52] Folding@home Core Shutdown: UNKNOWN_ERROR
[12:53:52] CoreStatus = 79 (121)
[12:53:52] Client-core communications error: ERROR 0x79
[12:53:52] This is a sign of more serious problems, shutting down.

[herbak]

Any update on this?
I'm seeing the same problem right now. Linux Xubuntu 10.04, 32-bit, PIII CPU, Linux Client v6.02.

Here's a reasonable chunk of my FAHlog.txt showing that I had just completed a WU and it was trying to get another one, but it just wouldn't run: (btw - this machine has been running quite literally for years with no FAH issues to date)

Code: Select all

[05:11:20] Timered checkpoint triggered.
[05:11:26] Writing local files
[05:11:26] Completed 250000 out of 250000 steps  (100%)
[05:11:27] Writing final coordinates.
[05:11:31] Past main M.D. loop
[05:12:31] 
[05:12:31] Finished Work Unit:
[05:12:31] - Reading up to 316872 from "work/wudata_09.arc": Read 316872
[05:12:31] - Reading up to 234560 from "work/wudata_09.xtc": Read 234560
[05:12:31] goefile size: 0
[05:12:31] logfile size: 97719
[05:12:32] Leaving Run
[05:12:32] - Writing 717971 bytes of core data to disk...
[05:12:37] Done: 717459 -> 590543 (compressed to 82.3 percent)
[05:12:37]   ... Done.
[05:13:14] - Shutting down core
[05:13:14] 
[05:13:14] Folding@home Core Shutdown: FINISHED_UNIT
[05:14:38] CoreStatus = 64 (100)
[05:14:38] Unit 9 finished with 10 percent of time to deadline remaining.
[05:14:38] Updated performance fraction: 0.431304
[05:14:38] Sending work to server
[05:14:38] - Read packet limit of 540015616... Set to 524286976.


[05:14:38] + Attempting to send results
[05:14:38] - Reading file work/wuresults_09.dat from core
[05:14:38]   (Read 591055 bytes from disk)
[05:14:38] Connecting to http://171.64.65.62:8080/
[05:14:49] Posted data.
[05:14:49] Initial: 0000; - Uploaded at ~52 kB/s
[05:14:49] - Averaged speed for that direction ~45 kB/s
[05:14:49] + Results successfully sent
[05:14:49] Thank you for your contribution to Folding@Home.
[05:14:49] + Number of Units Completed: 5

[05:15:01] Trying to send all finished work units
[05:15:01] + No unsent completed units remaining.
[05:15:01] - Preparing to get new work unit...
[05:15:01] + Attempting to get work packet
[05:15:01] - Will indicate memory of 150 MB
[05:15:01] - Detect CPU. Vendor: GenuineIntel, Family: 6, Model: 8, Stepping: 1
[05:15:01] - Connecting to assignment server
[05:15:01] Connecting to http://assign.stanford.edu:8080/
[05:15:02] Posted data.
[05:15:02] Initial: 40AB; - Successful: assigned to (171.64.65.111).
[05:15:02] + News From Folding@Home: Welcome to Folding@Home
[05:15:03] Loaded queue successfully.
[05:15:03] Connecting to http://171.64.65.111:8080/
[05:15:04] Posted data.
[05:15:04] Initial: 0000; - Receiving payload (expected size: 446014)
[05:15:06] - Downloaded at ~217 kB/s
[05:15:06] - Averaged speed for that direction ~179 kB/s
[05:15:06] + Received work.
[05:15:06] Trying to send all finished work units
[05:15:06] + No unsent completed units remaining.
[05:15:06] + Closed connections
[05:15:06] 
[05:15:06] + Processing work unit
[05:15:06] Core required: FahCore_78.exe
[05:15:06] Core found.
[05:15:06] Working on Unit 00 [July 17 05:15:06]
[05:15:06] + Working ...
[05:15:06] - Calling './FahCore_78.exe -dir work/ -suffix 00 -checkpoint 15 -verbose -lifeline 1040 -version 602'

[05:15:06] 
[05:15:06] *------------------------------*
[05:15:06] Folding@Home Gromacs Core
[05:15:06] Version 1.90 (March 8, 2006)
[05:15:06] 
[05:15:06] Preparing to commence simulation
[05:15:06] - Looking at optimizations...
[05:15:06] - Created dyn
[05:15:06] - Files status OK
[05:15:08] - Expanded 445502 -> 1512269 (decompressed 339.4 percent)
[05:15:09] - Starting from initial work packet
[05:15:09] 
[05:15:09] Project: 6316 (Run 156, Clone 0, Gen 8)
[05:15:09] 
[05:15:09] Assembly optimizations on if available.
[05:15:09] Entering M.D.
[05:15:16] Gromacs error.
[05:15:16] 
[05:15:16] Folding@home Core Shutdown: UNKNOWN_ERROR
[05:15:51] CoreStatus = 79 (121)
[05:15:51] Client-core communications error: ERROR 0x79
[05:15:51] Deleting current work unit & continuing...
[05:16:17] Trying to send all finished work units
[05:16:17] + No unsent completed units remaining.
[05:16:17] - Preparing to get new work unit...
[05:16:17] + Attempting to get work packet
[05:16:17] - Will indicate memory of 150 MB
[05:16:17] - Connecting to assignment server
[05:16:17] Connecting to http://assign.stanford.edu:8080/
[05:16:18] Posted data.
[05:16:18] Initial: 40AB; - Successful: assigned to (171.64.65.111).
[05:16:18] + News From Folding@Home: Welcome to Folding@Home
[05:16:18] Loaded queue successfully.
[05:16:18] Connecting to http://171.64.65.111:8080/
[05:16:19] Posted data.
[05:16:19] Initial: 0000; - Receiving payload (expected size: 446014)
[05:16:21] - Downloaded at ~217 kB/s
[05:16:21] - Averaged speed for that direction ~187 kB/s
[05:16:21] + Received work.
[05:16:21] + Closed connections
[05:16:26] 
[05:16:26] + Processing work unit
[05:16:26] Core required: FahCore_78.exe
[05:16:26] Core found.
[05:16:26] Working on Unit 01 [July 17 05:16:26]
[05:16:26] + Working ...
[05:16:26] - Calling './FahCore_78.exe -dir work/ -suffix 01 -checkpoint 15 -verbose -lifeline 1040 -version 602'

[05:16:27] 
[05:16:27] *------------------------------*
[05:16:27] Folding@Home Gromacs Core
[05:16:27] Version 1.90 (March 8, 2006)
[05:16:27] 
[05:16:27] Preparing to commence simulation
[05:16:27] - Looking at optimizations...
[05:16:27] - Created dyn
[05:16:27] - Files status OK
[05:16:28] - Expanded 445502 -> 1512269 (decompressed 339.4 percent)
[05:16:29] - Starting from initial work packet
[05:16:29] 
[05:16:29] Project: 6316 (Run 156, Clone 0, Gen 8)
[05:16:29] 
[05:16:29] Assembly optimizations on if available.
[05:16:29] Entering M.D.
[05:16:36] Gromacs error.
[05:16:36] 
[05:16:36] Folding@home Core Shutdown: UNKNOWN_ERROR
[05:17:20] CoreStatus = 79 (121)
[05:17:20] Client-core communications error: ERROR 0x79
[05:17:20] Deleting current work unit & continuing...
[05:17:47] Trying to send all finished work units
[05:17:47] + No unsent completed units remaining.
[05:17:47] - Preparing to get new work unit...
[05:17:47] + Attempting to get work packet
[05:17:47] - Will indicate memory of 150 MB
[05:17:47] - Connecting to assignment server
[05:17:47] Connecting to http://assign.stanford.edu:8080/
[05:17:48] Posted data.
[05:17:48] Initial: 40AB; - Successful: assigned to (171.64.65.111).
[05:17:48] + News From Folding@Home: Welcome to Folding@Home
[05:17:48] Loaded queue successfully.
[05:17:48] Connecting to http://171.64.65.111:8080/
[05:17:49] Posted data.
[05:17:49] Initial: 0000; - Receiving payload (expected size: 446014)
[05:17:51] - Downloaded at ~217 kB/s
[05:17:51] - Averaged speed for that direction ~193 kB/s
[05:17:51] + Received work.
[05:17:51] + Closed connections
[05:17:56] 
[05:17:56] + Processing work unit
[05:17:56] Core required: FahCore_78.exe
[05:17:56] Core found.
[05:17:56] Working on Unit 02 [July 17 05:17:56]
[05:17:56] + Working ...
[05:17:56] - Calling './FahCore_78.exe -dir work/ -suffix 02 -checkpoint 15 -verbose -lifeline 1040 -version 602'

[05:17:56] 
[05:17:56] *------------------------------*
[05:17:56] Folding@Home Gromacs Core
[05:17:56] Version 1.90 (March 8, 2006)
[05:17:56] 
[05:17:56] Preparing to commence simulation
[05:17:56] - Looking at optimizations...
[05:17:56] - Created dyn
[05:17:56] - Files status OK
[05:17:59] - Expanded 445502 -> 1512269 (decompressed 339.4 percent)
[05:17:59] - Starting from initial work packet
[05:17:59] 
[05:17:59] Project: 6316 (Run 156, Clone 0, Gen 8)
[05:17:59] 
[05:17:59] Assembly optimizations on if available.
[05:17:59] Entering M.D.
[05:18:06] Gromacs error.
[05:18:06] 
[05:18:06] Folding@home Core Shutdown: UNKNOWN_ERROR
[05:18:13] ***** Got a SIGTERM signal (15)
[05:18:13] Killing all core threads

Folding@Home Client Shutdown.


--- Opening Log file [July 17 08:05:52] 


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

                       Folding@Home Client Version 6.02

                          http://folding.stanford.edu

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

Launch directory: /home/paw/FAH
Executable: ./fah6
Arguments: -verbosity 9 

[08:05:52] - Ask before connecting: No
[08:05:52] - User name: simbel (Team 0)
[08:05:52] - User ID: EA256656DBF25E9
[08:05:52] - Machine ID: 1
[08:05:52] 
[08:05:53] Loaded queue successfully.
[08:05:53] 
[08:05:53] + Processing work unit
[08:05:53] Core required: FahCore_78.exe
[08:05:53] Core found.
[08:05:53] - Autosending finished units...
[08:05:53] Trying to send all finished work units
[08:05:53] + No unsent completed units remaining.
[08:05:53] - Autosend completed
[08:05:53] Working on Unit 02 [July 17 08:05:53]
[08:05:53] + Working ...
[08:05:53] - Calling './FahCore_78.exe -dir work/ -suffix 02 -checkpoint 15 -verbose -lifeline 25970 -version 602'

[08:05:53] 
[08:05:53] *------------------------------*
[08:05:53] Folding@Home Gromacs Core
[08:05:53] Version 1.90 (March 8, 2006)
[08:05:53] 
[08:05:53] Preparing to commence simulation
[08:05:53] - Ensuring status. Please wait.
[08:06:10] - Looking at optimizations...
[08:06:10] - Working with standard loops on this execution.
[08:06:11] - Created dyn
[08:06:11] - Files status OK
[08:06:11] - Expanded 445502 -> 1512269 (decompressed 339.4 percent)
[08:06:11] - Starting from initial work packet
[08:06:11] 
[08:06:11] Project: 6316 (Run 156, Clone 0, Gen 8)
[08:06:11] 
[08:06:11] Entering M.D.
[08:06:18] Gromacs error.
[08:06:18] 
[08:06:18] Folding@home Core Shutdown: UNKNOWN_ERROR
[08:06:43] ***** Got an Activate signal (2)
[08:06:43] Killing all core threads

Folding@Home Client Shutdown.

[herbak]

Back up and running... A combination of
- deleting the "work" directory
- deleting FahCore_78 (to get a new one downloaded, just in case),
- deleting items in the queue via the "fah6 -queuinfo" and "fah6 -delete x" cmdline options
seemed to help

A couple of tries to re-start and it's all running again. I don't know exactly *which* of the above fixed the issue.
Symptoms would seem to indicate maybe "just" a bad WU that got stuck in the local queue...

Edit by Mod:
The WU (P6316,R156,C0,G8) has been reported as a bad WU.