Code: Select all
[00:32:02] Completed 250000 out of 250000 steps (100%)
[00:32:47] DynamicWrapper: Finished Work Unit: sleep=10000
[00:32:57]
[00:32:57] Finished Work Unit:
[00:32:57] - Reading up to 64407792 from "work/wudata_07.trr": Read 64407792
[00:33:16] trr file hash check passed.
[00:33:16] - Reading up to 31749260 from "work/wudata_07.xtc": Read 31749260
[00:33:17] xtc file hash check passed.
[00:33:17] edr file hash check passed.
[00:33:17] logfile size: 190159
[00:33:17] Leaving Run
[00:33:20] - Writing 96508087 bytes of core data to disk...
[00:33:43] Done: 96507575 -> 91747659 (compressed to 6.0 percent)
[00:33:44] ... Done.
[00:33:54] - Shutting down core
[00:33:54]
[00:33:54] Folding@home Core Shutdown: FINISHED_UNIT
[00:33:56] CoreStatus = 64 (100)
[00:33:56] Unit 7 finished with 86 percent of time to deadline remaining.
[00:33:56] Updated performance fraction: 0.828753
[00:33:56] Sending work to server
[00:33:56] Project: 8102 (Run 0, Clone 18, Gen 65)
[00:33:56] + Attempting to send results [September 30 00:33:56 UTC]
[00:33:56] - Reading file work/wuresults_07.dat from core
[00:33:56] (Read 91748171 bytes from disk)
[00:33:56] Connecting to http://128.143.231.201:8080/
[00:39:31] Posted data.
[00:39:31] Initial: 0000; - Uploaded at ~267 kB/s
[00:39:31] - Averaged speed for that direction ~260 kB/s
[00:39:31] - Server reports problem with unit.
[00:39:31] Trying to send all finished work units
[00:39:31] + No unsent completed units remaining.
[00:39:31] - Preparing to get new work unit...
[00:39:31] Cleaning up work directory
[00:39:31] + Attempting to get work packet
[00:39:31] Passkey found
[00:39:31] - Will indicate memory of 32234 MB
[00:39:31] - Connecting to assignment server
[00:39:31] Connecting to http://assign.stanford.edu:8080/
[00:39:31] Posted data.
[00:39:31] Initial: 8F80; - Successful: assigned to (128.143.231.201).
[00:39:31] + News From Folding@Home: Welcome to Folding@Home
[00:39:32] Loaded queue successfully.
[00:39:32] Sent data
[00:39:32] Connecting to http://128.143.231.201:8080/
[00:39:39] Posted data.
[00:39:39] Initial: 0000; - Receiving payload (expected size: 30336617)
[00:39:58] - Downloaded at ~1559 kB/s
[00:39:58] - Averaged speed for that direction ~1661 kB/s
[00:39:58] + Received work.
[00:39:58] Trying to send all finished work units
[00:39:58] + No unsent completed units remaining.
[00:39:58] + Closed connections
[00:39:58]
[00:39:58] + Processing work unit
[00:39:58] Core required: FahCore_a5.exe
[00:39:58] Core found.
[00:39:58] Working on queue slot 08 [September 30 00:39:58 UTC]
[00:39:58] + Working ...
[00:39:58] - Calling './FahCore_a5.exe -dir work/ -nice 19 -suffix 08 -np 48 -checkpoint 15 -verbose -lifeline 4080 -version 634'
[00:39:58]
[00:39:58] *------------------------------*
[00:39:58] Folding@Home Gromacs SMP Core
[00:39:58] Version 2.27 (Thu Feb 10 09:46:40 PST 2011)
[00:39:58]
[00:39:58] Preparing to commence simulation
[00:39:58] - Looking at optimizations...
[00:39:58] - Created dyn
[00:39:58] - Files status OK
[00:40:01] - Expanded 30336105 -> 33163648 (decompressed 109.3 percent)
[00:40:01] Called DecompressByteArray: compressed_data_size=30336105 data_size=33163648, decompressed_data_size=33163648 diff=0
[00:40:01] - Digital signature verified
[00:40:01]
[00:40:01] Project: 8102 (Run 0, Clone 18, Gen 65)
[00:40:01]
[00:40:01] Assembly optimizations on if available.
[00:40:01] Entering M.D.
[00:40:09] Mapping NT from 48 to 48
[00:40:11] Completed 0 out of 250000 steps (0%)
Code: Select all
[05:40:42] Completed 250000 out of 250000 steps (100%)
Writing final coordinates.
Average load imbalance: 0.6 %
Part of the total run time spent waiting due to load imbalance: 0.2 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 %
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 49548.447 49548.447 100.0
13h45:48
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 2199.300 113.900 1.744 13.763
Thanx for Using GROMACS - Have a Nice Day
[05:42:26] DynamicWrapper: Finished Work Unit: sleep=10000
[05:42:36]
[05:42:36] Finished Work Unit:
[05:42:37] - Reading up to 64407792 from "work/wudata_02.trr": Read 64407792
[05:43:53] trr file hash check passed.
[05:44:56] - Reading up to 31749936 from "work/wudata_02.xtc": Read 31749936
[05:44:56] xtc file hash check passed.
[05:44:56] edr file hash check passed.
[05:44:56] logfile size: 190273
[05:44:56] Leaving Run
[05:45:01] - Writing 96508877 bytes of core data to disk...
[05:45:23] Done: 96508365 -> 91766720 (compressed to 6.0 percent)
[05:45:24] ... Done.
[05:45:36] - Shutting down core
[05:45:36]
[05:45:36] Folding@home Core Shutdown: FINISHED_UNIT
[05:45:38] CoreStatus = 64 (100)
[05:45:38] Sending work to server
[05:45:38] Project: 8102 (Run 0, Clone 21, Gen 87)
[05:45:38] + Attempting to send results [September 30 05:45:38 UTC]
[05:51:15] - Server reports problem with unit.
[05:51:15] - Preparing to get new work unit...
[05:51:15] Cleaning up work directory
[05:51:17] + Attempting to get work packet
[05:51:17] Passkey found
[05:51:17] - Connecting to assignment server
[05:51:17] - Successful: assigned to (128.143.231.201).
[05:51:17] + News From Folding@Home: Welcome to Folding@Home
[05:51:17] Loaded queue successfully.
[05:51:44] + Closed connections
[05:51:44]
[05:51:44] + Processing work unit
[05:51:44] Core required: FahCore_a5.exe
[05:51:44] Core found.
[05:51:44] Working on queue slot 03 [September 30 05:51:44 UTC]
[05:51:44] + Working ...
thekraken: The Kraken 0.7-pre15 (compiled Sat Jun 16 11:22:13 PDT 2012 by rick@rick-H8QG6)
thekraken: Processor affinity wrapper for Folding@Home
thekraken: The Kraken comes with ABSOLUTELY NO WARRANTY; licensed under GPLv2
thekraken: PID: 9843
thekraken: Logging to thekraken.log
[05:51:44]
[05:51:44] *------------------------------*
[05:51:44] Folding@Home Gromacs SMP Core
[05:51:44] Version 2.27 (Thu Feb 10 09:46:40 PST 2011)
[05:51:44]
[05:51:44] Preparing to commence simulation
[05:51:44] - Looking at optimizations...
[05:51:44] - Created dyn
[05:51:44] - Files status OK
[05:51:47] - Expanded 30337264 -> 33163648 (decompressed 109.3 percent)
[05:51:47] Called DecompressByteArray: compressed_data_size=30337264 data_size=33163648, decompressed_data_size=33163648 diff=0
[05:51:47] - Digital signature verified
[05:51:47]
[05:51:47] Project: 8102 (Run 0, Clone 21, Gen 87)
[05:51:47]
[05:51:47] Assembly optimizations on if available.
[05:51:47] Entering M.D.
:-) 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 (-:
Reading file work/wudata_03.tpr, VERSION 4.5.5-dev-20120903-d64b9e3 (single precision)
[05:51:54] Mapping NT from 48 to 48
Starting 48 threads
Making 2D domain decomposition 12 x 4 x 1
starting mdrun 'FP_membrane in water'
22000000 steps, 88000.0 ps (continuing from step 21750000, 87000.0 ps).
[05:51:59] Completed 0 out of 250000 steps (0%)
NOTE: Turning on dynamic load balancing
Code: Select all
07:00:24] Completed 247500 out of 250000 steps (99%)
[07:08:04] Completed 250000 out of 250000 steps (100%)
Writing final coordinates.
Average load imbalance: 0.4 %
Part of the total run time spent waiting due to load imbalance: 0.1 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 %
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 42402.010 42402.010 100.0
11h46:42
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 2368.943 122.680 1.878 12.779
Thanx for Using GROMACS - Have a Nice Day
[07:09:09] DynamicWrapper: Finished Work Unit: sleep=10000
[07:09:19]
[07:09:19] Finished Work Unit:
[07:09:19] - Reading up to 64407792 from "work/wudata_03.trr": Read 64407792
[07:09:20] trr file hash check passed.
[07:09:20] - Reading up to 31748100 from "work/wudata_03.xtc": Read 31748100
[07:09:20] xtc file hash check passed.
[07:09:20] edr file hash check passed.
[07:09:20] logfile size: 190846
[07:09:20] Leaving Run
[07:09:23] - Writing 96507614 bytes of core data to disk...
[07:09:45] Done: 96507102 -> 91777511 (compressed to 6.0 percent)
[07:09:45] ... Done.
[07:09:57] - Shutting down core
[07:09:57]
[07:09:57] Folding@home Core Shutdown: FINISHED_UNIT
[07:09:59] CoreStatus = 64 (100)
[07:09:59] Unit 3 finished with 86 percent of time to deadline remaining.
[07:09:59] Updated performance fraction: 0.842553
[07:09:59] Sending work to server
[07:09:59] Project: 8102 (Run 0, Clone 27, Gen 82)
[07:09:59] + Attempting to send results [September 30 07:09:59 UTC]
[07:09:59] - Reading file work/wuresults_03.dat from core
[07:09:59] (Read 91778023 bytes from disk)
[07:09:59] Connecting to http://128.143.231.201:8080/
[07:15:35] Posted data.
[07:15:35] Initial: 0000; - Uploaded at ~266 kB/s
[07:15:35] - Averaged speed for that direction ~259 kB/s
[07:15:35] - Server reports problem with unit.
[07:15:35] Trying to send all finished work units
[07:15:35] + No unsent completed units remaining.
[07:15:35] - Preparing to get new work unit...
[07:15:35] Cleaning up work directory
[07:15:36] + Attempting to get work packet
[07:15:36] Passkey found
[07:15:36] - Will indicate memory of 32234 MB
[07:15:36] - Connecting to assignment server
[07:15:36] Connecting to http://assign.stanford.edu:8080/
[07:15:36] Posted data.
[07:15:36] Initial: 8F80; - Successful: assigned to (128.143.231.201).
[07:15:36] + News From Folding@Home: Welcome to Folding@Home
[07:15:37] Loaded queue successfully.
[07:15:37] Sent data
[07:15:37] Connecting to http://128.143.231.201:8080/
[07:15:43] Posted data.
[07:15:43] Initial: 0000; - Receiving payload (expected size: 30348695)
[07:16:05] - Downloaded at ~1347 kB/s
[07:16:05] - Averaged speed for that direction ~1583 kB/s
[07:16:05] + Received work.
[07:16:05] Trying to send all finished work units
[07:16:05] + No unsent completed units remaining.
[07:16:05] + Closed connections
[07:16:05]
[07:16:05] + Processing work unit
[07:16:05] Core required: FahCore_a5.exe
[07:16:05] Core found.
[07:16:05] Working on queue slot 04 [September 30 07:16:05 UTC]
[07:16:05] + Working ...
[07:16:05] - Calling './FahCore_a5.exe -dir work/ -nice 19 -suffix 04 -np 48 -checkpoint 15 -verbose -lifeline 5440 -version 634'
thekraken: The Kraken 0.7-pre15 (compiled Sun Jun 17 18:12:50 PDT 2012 by rick1@rick1-H8QG6)
thekraken: Processor affinity wrapper for Folding@Home
thekraken: The Kraken comes with ABSOLUTELY NO WARRANTY; licensed under GPLv2
thekraken: PID: 6161
thekraken: Logging to thekraken.log
[07:16:05]
[07:16:05] *------------------------------*
[07:16:05] Folding@Home Gromacs SMP Core
[07:16:05] Version 2.27 (Thu Feb 10 09:46:40 PST 2011)
[07:16:05]
[07:16:05] Preparing to commence simulation
[07:16:05] - Looking at optimizations...
[07:16:05] - Created dyn
[07:16:05] - Files status OK
[07:16:08] - Expanded 30348183 -> 33163648 (decompressed 109.2 percent)
[07:16:08] Called DecompressByteArray: compressed_data_size=30348183 data_size=33163648, decompressed_data_size=33163648 diff=0
[07:16:08] - Digital signature verified
[07:16:08]
[07:16:08] Project: 8102 (Run 0, Clone 27, Gen 82)
[07:16:08]
[07:16:08] Assembly optimizations on if available.
[07:16:08] Entering M.D.
:-) 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 (-:
Reading file work/wudata_04.tpr, VERSION 4.5.5-dev-20120903-d64b9e3 (single precision)
[07:16:15] Mapping NT from 48 to 48
Starting 48 threads
Making 2D domain decomposition 12 x 4 x 1
starting mdrun 'FP_membrane in water'
20750000 steps, 83000.0 ps (continuing from step 20500000, 82000.0 ps).
[07:16:18] Completed 0 out of 250000 steps (0%)