Project: 8046 (Run 222, Clone 35, Gen 8)

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bollix47
Posts: 2941
Joined: Sun Dec 02, 2007 5:04 am
Location: Canada

Project: 8046 (Run 222, Clone 35, Gen 8)

Post by bollix47 »

Never really gets started. Had to delete work/00 a couple times, turn off advanced and reboot computer before the client could get another WU. Sorry, but I didn't think to try the --dump 00. :e?:

Code: Select all

22:36:26:WU01:FS00:0xa4:Completed 250000 out of 250000 steps  (100%)
22:36:26:WU01:FS00:0xa4:DynamicWrapper: Finished Work Unit: sleep=10000
22:36:27:WU00:FS00:Connecting to assign3.stanford.edu:8080
22:36:27:WU00:FS00:News: Welcome to Folding@Home
22:36:27:WU00:FS00:Assigned to work server 171.67.108.60
22:36:27:WU00:FS00:Requesting new work unit for slot 00: RUNNING smp:16 from 171.67.108.60
22:36:27:WU00:FS00:Connecting to 171.67.108.60:8080
[91m22:36:28:ERROR:WU00:FS00:Exception: Have already seen this work unit 0x000000196652edcc4fd93e5ce12c0045 aborting download[0m
22:36:28:WU00:FS00:Connecting to assign3.stanford.edu:8080
22:36:28:WU00:FS00:News: Welcome to Folding@Home
22:36:28:WU00:FS00:Assigned to work server 171.67.108.60
22:36:28:WU00:FS00:Requesting new work unit for slot 00: RUNNING smp:16 from 171.67.108.60
22:36:28:WU00:FS00:Connecting to 171.67.108.60:8080
[91m22:36:29:ERROR:WU00:FS00:Exception: Have already seen this work unit 0x000000196652edcc4fd93e5ce12c0045 aborting download[0m
22:36:36:WU01:FS00:0xa4:
22:36:36:WU01:FS00:0xa4:Finished Work Unit:
22:36:36:WU01:FS00:0xa4:- Reading up to 594996 from "01/wudata_01.trr": Read 594996
22:36:36:WU01:FS00:0xa4:trr file hash check passed.
22:36:36:WU01:FS00:0xa4:- Reading up to 352332 from "01/wudata_01.xtc": Read 352332
22:36:36:WU01:FS00:0xa4:xtc file hash check passed.
22:36:36:WU01:FS00:0xa4:edr file hash check passed.
22:36:36:WU01:FS00:0xa4:logfile size: 23038
22:36:36:WU01:FS00:0xa4:Leaving Run
22:36:37:WU01:FS00:0xa4:- Writing 975954 bytes of core data to disk...
22:36:37:WU01:FS00:0xa4:Done: 975442 -> 928208 (compressed to 95.1 percent)
22:36:37:WU01:FS00:0xa4:  ... Done.
22:36:38:WU01:FS00:0xa4:- Shutting down core
22:36:38:WU01:FS00:0xa4:
22:36:38:WU01:FS00:0xa4:Folding@home Core Shutdown: FINISHED_UNIT
22:36:38:WU01:FS00:FahCore returned: FINISHED_UNIT (100 = 0x64)
22:36:38:WU01:FS00:Sending unit results: id:01 state:SEND error:OK project:8046 run:170 clone:22 gen:25 core:0xa4 unit:0x000000196652edcc4fd93e5ce12c0045
22:36:38:WU01:FS00:Uploading 906.95KiB to 171.67.108.60
22:36:38:WU01:FS00:Connecting to 171.67.108.60:8080
22:36:44:WU01:FS00:Upload 98.79%
22:36:46:WU01:FS00:Upload complete
22:36:46:WU01:FS00:Server responded WORK_ACK (400)
22:36:46:WU01:FS00:Final credit estimate, 874.00 points
22:36:46:WU01:FS00:Cleaning up
22:37:28:WU00:FS00:Connecting to assign3.stanford.edu:8080
22:37:28:WU00:FS00:News: Welcome to Folding@Home
22:37:28:WU00:FS00:Assigned to work server 171.67.108.60
22:37:28:WU00:FS00:Requesting new work unit for slot 00: READY smp:16 from 171.67.108.60
22:37:28:WU00:FS00:Connecting to 171.67.108.60:8080
22:37:29:WU00:FS00:Downloading 468.63KiB
22:37:30:WU00:FS00:Download complete
22:37:30:WU00:FS00:Received Unit: id:00 state:DOWNLOAD error:OK project:8046 run:222 clone:35 gen:8 core:0xa4 unit:0x000000126652edcc4fd9418f0fe5ba9d
22:37:30:WU00:FS00:Starting
22:37:30:WU00:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /home/bollix/fah/cores/www.stanford.edu/~pande/Linux/AMD64/Core_a4.fah/FahCore_a4 -dir 00 -suffix 01 -version 701 -lifeline 1694 -checkpoint 30 -np 16
22:37:30:WU00:FS00:Started FahCore on PID 5472
22:37:30:WU00:FS00:Core PID:5476
22:37:30:WU00:FS00:FahCore 0xa4 started
22:37:31:WU00:FS00:0xa4:
22:37:31:WU00:FS00:0xa4:*------------------------------*
22:37:31:WU00:FS00:0xa4:Folding@Home Gromacs GB Core
22:37:31:WU00:FS00:0xa4:Version 2.27 (Dec. 15, 2010)
22:37:31:WU00:FS00:0xa4:
22:37:31:WU00:FS00:0xa4:Preparing to commence simulation
22:37:31:WU00:FS00:0xa4:- Looking at optimizations...
22:37:31:WU00:FS00:0xa4:- Created dyn
22:37:31:WU00:FS00:0xa4:- Files status OK
22:37:31:WU00:FS00:0xa4:- Expanded 479368 -> 1078076 (decompressed 224.8 percent)
22:37:31:WU00:FS00:0xa4:Called DecompressByteArray: compressed_data_size=479368 data_size=1078076, decompressed_data_size=1078076 diff=0
22:37:31:WU00:FS00:0xa4:- Digital signature verified
22:37:31:WU00:FS00:0xa4:
22:37:31:WU00:FS00:0xa4:Project: 8046 (Run 222, Clone 35, Gen 8)
22:37:31:WU00:FS00:0xa4:
22:37:31:WU00:FS00:0xa4:Assembly optimizations on if available.
22:37:31:WU00:FS00:0xa4:Entering M.D.
22:37:37:WU00:FS00:0xa4:Completed 0 out of 250000 steps  (0%)
22:37:37:WU00:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
22:37:37:WU00:FS00:Starting
22:37:37:WU00:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /home/bollix/fah/cores/www.stanford.edu/~pande/Linux/AMD64/Core_a4.fah/FahCore_a4 -dir 00 -suffix 01 -version 701 -lifeline 1694 -checkpoint 30 -np 16
22:37:37:WU00:FS00:Started FahCore on PID 5495
22:37:37:WU00:FS00:Core PID:5499
22:37:37:WU00:FS00:FahCore 0xa4 started
22:37:38:WU00:FS00:0xa4:
22:37:38:WU00:FS00:0xa4:*------------------------------*
22:37:38:WU00:FS00:0xa4:Folding@Home Gromacs GB Core
22:37:38:WU00:FS00:0xa4:Version 2.27 (Dec. 15, 2010)
22:37:38:WU00:FS00:0xa4:
22:37:38:WU00:FS00:0xa4:Preparing to commence simulation
22:37:38:WU00:FS00:0xa4:- Ensuring status. Please wait.
22:37:47:WU00:FS00:0xa4:- Looking at optimizations...
22:37:47:WU00:FS00:0xa4:- Working with standard loops on this execution.
22:37:47:WU00:FS00:0xa4:- Previous termination of core was improper.
22:37:47:WU00:FS00:0xa4:- Files status OK
22:37:47:WU00:FS00:0xa4:- Expanded 479368 -> 1078076 (decompressed 224.8 percent)
22:37:47:WU00:FS00:0xa4:Called DecompressByteArray: compressed_data_size=479368 data_size=1078076, decompressed_data_size=1078076 diff=0
22:37:47:WU00:FS00:0xa4:- Digital signature verified
22:37:47:WU00:FS00:0xa4:
22:37:47:WU00:FS00:0xa4:Project: 8046 (Run 222, Clone 35, Gen 8)
22:37:47:WU00:FS00:0xa4:
22:37:47:WU00:FS00:0xa4:Entering M.D.
22:37:53:WU00:FS00:0xa4:Completed 0 out of 250000 steps  (0%)
22:37:54:WU00:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
22:38:37:WU00:FS00:Starting
22:38:37:WU00:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /home/bollix/fah/cores/www.stanford.edu/~pande/Linux/AMD64/Core_a4.fah/FahCore_a4 -dir 00 -suffix 01 -version 701 -lifeline 1694 -checkpoint 30 -np 16
22:38:37:WU00:FS00:Started FahCore on PID 5518
22:38:37:WU00

Code: Select all

*********************** Log Started 2012-06-21T23:56:23Z ***********************
23:56:23:************************* Folding@home Client *************************
23:56:23:    Website: http://folding.stanford.edu/
23:56:23:  Copyright: (c) 2009-2012 Stanford University
23:56:23:     Author: Joseph Coffland <joseph@cauldrondevelopment.com>
23:56:23:       Args: 
23:56:23:     Config: /home/bollix/fah/config.xml
23:56:23:******************************** Build ********************************
23:56:23:    Version: 7.1.52
23:56:23:       Date: Mar 20 2012
23:56:23:       Time: 13:19:11
23:56:23:    SVN Rev: 3515
23:56:23:     Branch: fah/trunk/client
23:56:23:   Compiler: GNU 4.6.2
23:56:23:    Options: -std=gnu++98 -O3 -funroll-loops -mfpmath=sse -ffast-math
23:56:23:             -fno-unsafe-math-optimizations -msse2
23:56:23:   Platform: linux2 3.2.0-1-amd64
23:56:23:       Bits: 64
23:56:23:       Mode: Release
23:56:23:******************************* System ********************************
23:56:23:        CPU: Intel(R) Xeon(R) CPU E5540 @ 2.53GHz
23:56:23:     CPU ID: GenuineIntel Family 6 Model 26 Stepping 5
23:56:23:       CPUs: 16
23:56:23:     Memory: 11.75GiB
23:56:23:Free Memory: 10.52GiB
23:56:23:    Threads: POSIX_THREADS
23:56:23: On Battery: false
23:56:23: UTC offset: -4
23:56:23:        PID: 5971
23:56:23:        CWD: /home/bollix/fah
23:56:23:         OS: Linux 3.0.0-21-generic x86_64
23:56:23:    OS Arch: AMD64
23:56:23:       GPUs: 3
23:56:23:      GPU 0: UNSUPPORTED: Rage XL (Intel Corporation)
23:56:23:      GPU 1: UNSUPPORTED: Rage XL (Intel Corporation)
23:56:23:      GPU 2: ATI:3 RV770 [Radeon HD 4870]
23:56:23:       CUDA: Not detected
23:56:23:***********************************************************************
23:56:23:<config>
23:56:23:  <!-- FahCore Control -->
23:56:23:  <checkpoint v='30'/>
23:56:23:  <core-priority v='low'/>
23:56:23:
23:56:23:  <!-- Network -->
23:56:23:  <proxy v=':8080'/>
23:56:23:
23:56:23:  <!-- Remote Command Server -->
23:56:23:  <command-allow v='127.0.0.1,192.168.2.100-192.168.2.149'/>
23:56:23:  <command-allow-no-pass v='127.0.0.1,192.168.2.100-192.168.2.149'/>
23:56:23:
23:56:23:  <!-- User Information -->
23:56:23:  <passkey v='********************************'/>
23:56:23:  <team v='39340'/>
23:56:23:  <user v='bollix47'/>
23:56:23:
23:56:23:  <!-- Folding Slots -->
23:56:23:  <slot id='0' type='SMP'>
23:56:23:    <cpus v='-1'/>
23:56:23:    <max-packet-size v='big'/>
23:56:23:    <next-unit-percentage v='100'/>
23:56:23:  </slot>
23:56:23:</config>
23:56:23:Trying to access database...
23:56:23:Successfully acquired database lock
23:56:23:Enabled folding slot 00: READY smp:16
23:56:23:WU00:FS00:Starting
23:56:23:WU00:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /home/bollix/fah/cores/www.stanford.edu/~pande/Linux/AMD64/Core_a4.fah/FahCore_a4 -dir 00 -suffix 01 -version 701 -lifeline 5971 -checkpoint 30 -np 16
23:56:23:WU00:FS00:Started FahCore on PID 5979
23:56:23:WU00:FS00:Core PID:5983
23:56:23:WU00:FS00:FahCore 0xa4 started
23:56:23:WU00:FS00:0xa4:
23:56:23:WU00:FS00:0xa4:*------------------------------*
23:56:23:WU00:FS00:0xa4:Folding@Home Gromacs GB Core
23:56:23:WU00:FS00:0xa4:Version 2.27 (Dec. 15, 2010)
23:56:23:WU00:FS00:0xa4:
23:56:23:WU00:FS00:0xa4:Preparing to commence simulation
23:56:23:WU00:FS00:0xa4:- Ensuring status. Please wait.
23:56:26:Server connection id=1 on 0.0.0.0:36330 from 192.168.2.103
23:56:33:WU00:FS00:0xa4:- Looking at optimizations...
23:56:33:WU00:FS00:0xa4:- Working with standard loops on this execution.
23:56:33:WU00:FS00:0xa4:- Previous termination of core was improper.
23:56:33:WU00:FS00:0xa4:- Going to use standard loops.
23:56:33:WU00:FS00:0xa4:- Files status OK
23:56:33:WU00:FS00:0xa4:- Expanded 479368 -> 1078076 (decompressed 224.8 percent)
23:56:33:WU00:FS00:0xa4:Called DecompressByteArray: compressed_data_size=479368 data_size=1078076, decompressed_data_size=1078076 diff=0
23:56:33:WU00:FS00:0xa4:- Digital signature verified
23:56:33:WU00:FS00:0xa4:
23:56:33:WU00:FS00:0xa4:Project: 8046 (Run 222, Clone 35, Gen 8)
23:56:33:WU00:FS00:0xa4:
23:56:33:WU00:FS00:0xa4:Entering M.D.
23:56:39:WU00:FS00:0xa4:Completed 0 out of 250000 steps  (0%)
23:56:39:WU00:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
23:56:39:WU00:FS00:Starting
23:56:39:WU00:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /home/bollix/fah/cores/www.stanford.edu/~pande/Linux/AMD64/Core_a4.fah/FahCore_a4 -dir 00 -suffix 01 -version 701 -lifeline 5971 -checkpoint 30 -np 16
23:56:39:WU00:FS00:Started FahCore on PID 6003
23:56:39:WU00:FS00:Core PID:6007
23:56:39:WU00:FS00:FahCore 0xa4 started
23:56:40:WU00:FS00:0xa4:
23:56:40:WU00:FS00:0xa4:*------------------------------*
23:56:40:WU00:FS00:0xa4:Folding@Home Gromacs GB Core
23:56:40:WU00:FS00:0xa4:Version 2.27 (Dec. 15, 2010)
23:56:40:WU00:FS00:0xa4:
23:56:40:WU00:FS00:0xa4:Preparing to commence simulation
23:56:40:WU00:FS00:0xa4:- Ensuring status. Please wait.
23:56:49:WU00:FS00:0xa4:- Looking at optimizations...
23:56:49:WU00:FS00:0xa4:- Working with standard loops on this execution.
23:56:49:WU00:FS00:0xa4:- Previous termination of core was improper.
23:56:49:WU00:FS00:0xa4:- Going to use standard loops.
23:56:49:WU00:FS00:0xa4:- Files status OK
23:56:49:WU00:FS00:0xa4:- Expanded 479368 -> 1078076 (decompressed 224.8 percent)
23:56:49:WU00:FS00:0xa4:Called DecompressByteArray: compressed_data_size=479368 data_size=1078076, decompressed_data_size=1078076 diff=0
23:56:49:WU00:FS00:0xa4:- Digital signature verified
23:56:49:WU00:FS00:0xa4:
23:56:49:WU00:FS00:0xa4:Project: 8046 (Run 222, Clone 35, Gen 8)
23:56:49:WU00:FS00:0xa4:
23:56:49:WU00:FS00:0xa4:Entering M.D.
23:56:55:WU00:FS00:0xa4:Completed 0 out of 250000 steps  (0%)
23:56:55:WU00:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
23:57:39:WU00:FS00:Starting
23:57:39:WU00:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /home/bollix/fah/cores/www.stanford.edu/~pande/Linux/AMD64/Core_a4.fah/FahCore_a4 -dir 00 -suffix 01 -version 701 -lifeline 5971 -checkpoint 30 -np 16
23:57:39:WU00:FS00:Started FahCore on PID 6026
23:57:39:WU00:FS00:Core PID:6030
23:57:39:WU00:FS00:FahCore 0xa4 started
23:57:40:WU00:FS00:0xa4:
23:57:40:WU00:FS00:0xa4:*------------------------------*
23:57:40:WU00:FS00:0xa4:Folding@Home Gromacs GB Core
23:57:40:WU00:FS00:0xa4:Version 2.27 (Dec. 15, 2010)
23:57:40:WU00:FS00:0xa4:
23:57:40:WU00:FS00:0xa4:Preparing to commence simulation
23:57:40:WU00:FS00:0xa4:- Ensuring status. Please wait.
23:57:49:WU00:FS00:0xa4:- Looking at optimizations...
23:57:49:WU00:FS00:0xa4:- Working with standard loops on this execution.
23:57:49:WU00:FS00:0xa4:- Previous termination of core was improper.
23:57:49:WU00:FS00:0xa4:- Going to use standard loops.
23:57:49:WU00:FS00:0xa4:- Files status OK
23:57:49:WU00:FS00:0xa4:- Expanded 479368 -> 1078076 (decompressed 224.8 percent)
23:57:49:WU00:FS00:0xa4:Called DecompressByteArray: compressed_data_size=479368 data_size=1078076, decompressed_data_size=1078076 diff=0
23:57:49:WU00:FS00:0xa4:- Digital signature verified
23:57:49:WU00:FS00:0xa4:
23:57:49:WU00:FS00:0xa4:Project: 8046 (Run 222, Clone 35, Gen 8)
23:57:49:WU00:FS00:0xa4:
23:57:49:WU00:FS00:0xa4:Entering M.D.
23:57:55:WU00:FS00:0xa4:Completed 0 out of 250000 steps  (0%)
23:57:55:WU00:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
23:58:04:FS00:Paused
23:58:59:Server connection id=2 on 0.0.0.0:36330 from 192.168.2.103
23:59:31:FS00:Unpaused
23:59:32:WU00:FS00:Starting
23:59:32:WU00:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /home/bollix/fah/cores/www.stanford.edu/~pande/Linux/AMD64/Core_a4.fah/FahCore_a4 -dir 00 -suffix 01 -version 701 -lifeline 5971 -checkpoint 30 -np 16
23:59:32:WU00:FS00:Started FahCore on PID 6052
23:59:32:WU00:FS00:Core PID:6056
23:59:32:WU00:FS00:FahCore 0xa4 started
23:59:32:WU00:FS00:0xa4:
23:59:32:WU00:FS00:0xa4:*------------------------------*
23:59:32:WU00:FS00:0xa4:Folding@Home Gromacs GB Core
23:59:32:WU00:FS00:0xa4:Version 2.27 (Dec. 15, 2010)
23:59:32:WU00:FS00:0xa4:
23:59:32:WU00:FS00:0xa4:Preparing to commence simulation
23:59:32:WU00:FS00:0xa4:- Ensuring status. Please wait.
23:59:41:WU00:FS00:0xa4:- Looking at optimizations...
23:59:41:WU00:FS00:0xa4:- Working with standard loops on this execution.
23:59:41:WU00:FS00:0xa4:- Previous termination of core was improper.
23:59:41:WU00:FS00:0xa4:- Going to use standard loops.
23:59:41:WU00:FS00:0xa4:- Files status OK
23:59:41:WU00:FS00:0xa4:- Expanded 479368 -> 1078076 (decompressed 224.8 percent)
23:59:41:WU00:FS00:0xa4:Called DecompressByteArray: compressed_data_size=479368 data_size=1078076, decompressed_data_size=1078076 diff=0
23:59:41:WU00:FS00:0xa4:- Digital signature verified
23:59:41:WU00:FS00:0xa4:
23:59:41:WU00:FS00:0xa4:Project: 8046 (Run 222, Clone 35, Gen 8)
23:59:41:WU00:FS00:0xa4:
23:59:41:WU00:FS00:0xa4:Entering M.D.
23:59:48:WU00:FS00:0xa4:Completed 0 out of 250000 steps  (0%)
23:59:48:WU00:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
00:01:09:WU00:FS00:Starting
00:01:09:WU00:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /home/bollix/fah/cores/www.stanford.edu/~pande/Linux/AMD64/Core_a4.fah/FahCore_a4 -dir 00 -suffix 01 -version 701 -lifeline 5971 -checkpoint 30 -np 16
00:01:09:WU00:FS00:Started FahCore on PID 6082
00:01:09:WU00:FS00:Core PID:6086
00:01:09:WU00:FS00:FahCore 0xa4 started
00:01:09:WU00:FS00:0xa4:
00:01:09:WU00:FS00:0xa4:*------------------------------*
00:01:09:WU00:FS00:0xa4:Folding@Home Gromacs GB Core
00:01:09:WU00:FS00:0xa4:Version 2.27 (Dec. 15, 2010)
00:01:09:WU00:FS00:0xa4:
00:01:09:WU00:FS00:0xa4:Preparing to commence simulation
00:01:09:WU00:FS00:0xa4:- Ensuring status. Please wait.
00:01:19:WU00:FS00:0xa4:- Looking at optimizations...
00:01:19:WU00:FS00:0xa4:- Working with standard loops on this execution.
00:01:19:WU00:FS00:0xa4:- Previous termination of core was improper.
00:01:19:WU00:FS00:0xa4:- Going to use standard loops.
00:01:19:WU00:FS00:0xa4:- Files status OK
00:01:19:WU00:FS00:0xa4:- Expanded 479368 -> 1078076 (decompressed 224.8 percent)
00:01:19:WU00:FS00:0xa4:Called DecompressByteArray: compressed_data_size=479368 data_size=1078076, decompressed_data_size=1078076 diff=0
00:01:19:WU00:FS00:0xa4:- Digital signature verified
00:01:19:WU00:FS00:0xa4:
00:01:19:WU00:FS00:0xa4:Project: 8046 (Run 222, Clone 35, Gen 8)
00:01:19:WU00:FS00:0xa4:
00:01:19:WU00:FS00:0xa4:Entering M.D.
00:01:25:WU00:FS00:0xa4:Completed 0 out of 250000 steps  (0%)
00:01:25:WU00:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
00:02:24:FS00:Paused
[93m00:02:50:WARNING:Caught signal SIGINT(2) on PID 5971[0m
00:02:50:Exiting, please wait. . .
00:02:51:Clean exit
bruce
Posts: 20910
Joined: Thu Nov 29, 2007 10:13 pm
Location: So. Cal.

Re: Project: 8046 (Run 222, Clone 35, Gen 8)

Post by bruce »

The error message INTERRUPTED (102 = 66) is listed in the Wiki as "unknown" http://fahwiki.net/index.php/CoreStatus_codes so nobody on the forum has discovered it's meaning. Nevertheless, I checked on Project: 8046 (Run 222, Clone 35, Gen 8) and the WU has failed and been reissued several times. I think it's what we commonly call a "bad WU" As you know, that happens with a small percentage of WUs.

Although it's an unusual error that didn't show up in V7 testing I'm going to add it to a ticket. FAHClient should really know how to deal with the error without forcing you to manually delete it. Did you happen to save a backup copy of the files in WORK?
bollix47
Posts: 2941
Joined: Sun Dec 02, 2007 5:04 am
Location: Canada

Re: Project: 8046 (Run 222, Clone 35, Gen 8)

Post by bollix47 »

All the files are in the Trash. I should be able to restore them after backing up the current WU if you need them. I'll need some fairly explicit instructions on how to tar them and where to send the file.
bollix47
Posts: 2941
Joined: Sun Dec 02, 2007 5:04 am
Location: Canada

Re: Project: 8046 (Run 222, Clone 35, Gen 8)

Post by bollix47 »

Here's the .log from the trash:

Code: Select all

Log file opened on Thu Jun 21 20:01:24 2012
Host: Discovery  pid: 6086  nodeid: 0  nnodes:  1
The Gromacs distribution was built @TMP_TIME@ by
kyleb@kyleb-desktop [CMAKE] (@TMP_MACHINE@)


                         :-)  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  (-:


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------

Input Parameters:
   integrator           = md
   nsteps               = 250000
   init_step            = 2000000
   ns_type              = Grid
   nstlist              = 10
   ndelta               = 2
   nstcomm              = 10
   comm_mode            = Linear
   nstlog               = 50000
   nstxout              = 250000
   nstvout              = 0
   nstfout              = 0
   nstcalcenergy        = 10
   nstenergy            = 50000
   nstxtcout            = 50000
   init_t               = 0
   delta_t              = 0.002
   xtcprec              = 1000
   nkx                  = 56
   nky                  = 56
   nkz                  = 56
   pme_order            = 4
   ewald_rtol           = 1e-05
   ewald_geometry       = 0
   epsilon_surface      = 0
   optimize_fft         = TRUE
   ePBC                 = xyz
   bPeriodicMols        = FALSE
   bContinuation        = TRUE
   bShakeSOR            = FALSE
   etc                  = V-rescale
   nsttcouple           = 10
   epc                  = Parrinello-Rahman
   epctype              = Isotropic
   nstpcouple           = 10
   tau_p                = 1
   ref_p (3x3):
      ref_p[    0]={ 1.01325e+00,  0.00000e+00,  0.00000e+00}
      ref_p[    1]={ 0.00000e+00,  1.01325e+00,  0.00000e+00}
      ref_p[    2]={ 0.00000e+00,  0.00000e+00,  1.01325e+00}
   compress (3x3):
      compress[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
      compress[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
      compress[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
   refcoord_scaling     = No
   posres_com (3):
      posres_com[0]= 0.00000e+00
      posres_com[1]= 0.00000e+00
      posres_com[2]= 0.00000e+00
   posres_comB (3):
      posres_comB[0]= 0.00000e+00
      posres_comB[1]= 0.00000e+00
      posres_comB[2]= 0.00000e+00
   andersen_seed        = 815131
   rlist                = 1.2
   rlistlong            = 1.2
   rtpi                 = 0.05
   coulombtype          = PME
   rcoulomb_switch      = 0
   rcoulomb             = 1.2
   vdwtype              = Switch
   rvdw_switch          = 0.9
   rvdw                 = 1.2
   epsilon_r            = 1
   epsilon_rf           = 1
   tabext               = 1
   implicit_solvent     = No
   gb_algorithm         = Still
   gb_epsilon_solvent   = 80
   nstgbradii           = 1
   rgbradii             = 1
   gb_saltconc          = 0
   gb_obc_alpha         = 1
   gb_obc_beta          = 0.8
   gb_obc_gamma         = 4.85
   gb_dielectric_offset = 0.009
   sa_algorithm         = Ace-approximation
   sa_surface_tension   = 2.05016
   DispCorr             = EnerPres
   free_energy          = no
   init_lambda          = 0
   delta_lambda         = 0
   n_foreign_lambda     = 0
   sc_alpha             = 0
   sc_power             = 0
   sc_sigma             = 0.3
   sc_sigma_min         = 0.3
   nstdhdl              = 10
   separate_dhdl_file   = yes
   dhdl_derivatives     = yes
   dh_hist_size         = 0
   dh_hist_spacing      = 0.1
   nwall                = 0
   wall_type            = 9-3
   wall_atomtype[0]     = -1
   wall_atomtype[1]     = -1
   wall_density[0]      = 0
   wall_density[1]      = 0
   wall_ewald_zfac      = 3
   pull                 = no
   disre                = No
   disre_weighting      = Conservative
   disre_mixed          = FALSE
   dr_fc                = 1000
   dr_tau               = 0
   nstdisreout          = 100
   orires_fc            = 0
   orires_tau           = 0
   nstorireout          = 100
   dihre-fc             = 1000
   em_stepsize          = 0.01
   em_tol               = 1e-06
   niter                = 20
   fc_stepsize          = 0
   nstcgsteep           = 1000
   nbfgscorr            = 10
   ConstAlg             = Lincs
   shake_tol            = 0.0001
   lincs_order          = 4
   lincs_warnangle      = 30
   lincs_iter           = 1
   bd_fric              = 0
   ld_seed              = 1993
   cos_accel            = 0
   deform (3x3):
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   userint1             = 0
   userint2             = 0
   userint3             = 0
   userint4             = 0
   userreal1            = 0
   userreal2            = 0
   userreal3            = 0
   userreal4            = 0
grpopts:
   nrdf:       33339
   ref_t:         298
   tau_t:         0.2
anneal:          No
ann_npoints:           0
   acc:	           0           0           0
   nfreeze:           N           N           N
   energygrp_flags[  0]: 0
   efield-x:
      n = 0
   efield-xt:
      n = 0
   efield-y:
      n = 0
   efield-yt:
      n = 0
   efield-z:
      n = 0
   efield-zt:
      n = 0
   bQMMM                = FALSE
   QMconstraints        = 0
   QMMMscheme           = 0
   scalefactor          = 1
qm_opts:
   ngQM                 = 0

Initializing Domain Decomposition on 16 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
    two-body bonded interactions: 0.399 nm, LJ-14, atoms 51 62
  multi-body bonded interactions: 0.486 nm, CMAP Dih., atoms 320 329
Minimum cell size due to bonded interactions: 0.535 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.222 nm
Estimated maximum distance required for P-LINCS: 0.222 nm
Using 0 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 16 cells with a minimum initial size of 0.668 nm
The maximum allowed number of cells is: X 8 Y 8 Z 8
Domain decomposition grid 4 x 4 x 1, separate PME nodes 0
PME domain decomposition: 4 x 4 x 1
Domain decomposition nodeid 0, coordinates 0 0 0

Table routines are used for coulomb: TRUE
Table routines are used for vdw:     TRUE
Will do PME sum in reciprocal space.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Will do ordinary reciprocal space Ewald sum.
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
Long Range LJ corr.: <C6> 2.8742e-04
System total charge: 0.000
Generated table with 1100 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ6Switch.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ12Switch.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ12.
Tabscale = 500 points/nm

Enabling SPC-like water optimization for 5365 molecules.

Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing x86_64 SSE2 support... present.



Initializing Parallel LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 116-122
-------- -------- --- Thank You --- -------- --------

The number of constraints is 252
There are inter charge-group constraints,
will communicate selected coordinates each lincs iteration

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------


Linking all bonded interactions to atoms
There are 2472 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME

The initial number of communication pulses is: X 1 Y 1
The initial domain decomposition cell size is: X 1.37 nm Y 1.37 nm

The maximum allowed distance for charge groups involved in interactions is:
                 non-bonded interactions           1.200 nm
(the following are initial values, they could change due to box deformation)
            two-body bonded interactions  (-rdd)   1.200 nm
          multi-body bonded interactions  (-rdd)   1.200 nm
  atoms separated by up to 5 constraints  (-rcon)  1.374 nm

When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 2 Y 2
The minimum size for domain decomposition cells is 0.930 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.68 Y 0.68
The maximum allowed distance for charge groups involved in interactions is:
                 non-bonded interactions           1.200 nm
            two-body bonded interactions  (-rdd)   1.200 nm
          multi-body bonded interactions  (-rdd)   0.930 nm
  atoms separated by up to 5 constraints  (-rcon)  0.930 nm


Making 2D domain decomposition grid 4 x 4 x 1, home cell index 0 0 0

Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------

There are: 16563 Atoms
Charge group distribution at step 2000000: 338 330 364 334 346 404 455 341 340 399 416 347 342 361 361 355
Grid: 4 x 4 x 8 cells
Initial temperature: 298.793 K

Started mdrun on node 0 Thu Jun 21 20:01:25 2012

           Step           Time         Lambda
        2000000     4000.00000        0.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    2.80100e+02    9.82700e+02    4.83177e+02    8.29358e+01   -1.12157e+02
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    1.32909e+02    1.13001e+04    4.40546e+04   -8.75301e+02   -2.41729e+05
   Coul. recip. Position Rest.      Potential    Kinetic En.   Total Energy
   -2.07338e+04    1.16766e+02   -2.06017e+05    6.72981e+04   -1.38719e+05
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    4.85560e+02   -8.76230e+01    6.39274e+03    5.65040e-04
bruce
Posts: 20910
Joined: Thu Nov 29, 2007 10:13 pm
Location: So. Cal.

Re: Project: 8046 (Run 222, Clone 35, Gen 8)

Post by bruce »

I'm interested in the files from which the WU can be started plus the logs. I'm not certain which one(s) are needed but the idea is to capture what was downloaded so they can reproduce the error. I'll PM you my email unless you'd rather host it somewhere.
bollix47
Posts: 2941
Joined: Sun Dec 02, 2007 5:04 am
Location: Canada

Re: Project: 8046 (Run 222, Clone 35, Gen 8)

Post by bollix47 »

I currently don't have a hosting service.

If you could PM me your e-mail address I can send the files.
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