Code: Select all
[15:09:38] Writing local files
[15:09:38] Completed 500000 out of 500000 steps (100 percent)
[15:09:38] Writing final coordinates.
[15:09:38] Past main M.D. loop
M E G A - F L O P S A C C O U N T I N G
Parallel run - timing based on wallclock.
RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
NF=No Forces
Computing: M-Number M-Flops % of Flops
-----------------------------------------------------------------------
VdW(T) 1368204.894965 73883064.328110 16.6
RF Coul 547101.468017 18054348.444561 4.1
RF Coul [W3] 2369.684097 232229.041506 0.1
RF Coul + VdW(T) 617184.147334 40116969.576710 9.0
RF Coul + VdW(T) [W3] 286045.280053 37185886.406890 8.4
RF Coul + VdW(T) [W3-W3] 767997.175775 245759096.248000 55.3
Outer nonbonded loop 239835.824247 2398358.242470 0.5
1,4 nonbonded interactions 1059.002118 95310.190620 0.0
NS-Pairs 502289.797695 10548085.751595 2.4
Reset In Box 3883.727673 34953.549057 0.0
Shift-X 77590.155180 465540.931080 0.1
CG-CoM 1770.635412 51348.426948 0.0
Sum Forces 116509.733019 116509.733019 0.0
Bonds 13324.526649 572954.645907 0.1
Angles 15680.031360 2555845.111680 0.6
Propers 5407.510815 1238319.976635 0.3
Impropers 1012.002024 210496.420992 0.0
RB-Dihedrals 14193.528387 3505801.511589 0.8
Virial 38890.577781 700030.400058 0.2
Update 38836.577673 1203933.907863 0.3
Stop-CM 38836.500000 388365.000000 0.1
P-Coupling 38836.577673 233019.466038 0.1
Calc-Ekin 38836.655346 1048589.694342 0.2
Constraint-V 38836.577673 233019.466038 0.1
Constraint-Vir 25212.050424 605089.210176 0.1
Settle 8404.016808 2714497.428984 0.6
-----------------------------------------------------------------------
Total 444151663.110868 100.0
-----------------------------------------------------------------------
NODE (s) Real (s) (%)
Time: 112993.000 112993.000 100.0
1d07h23:13
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 31.762 3.931 0.765 31.387
[15:09:39] Will end MPI now
[15:10:39]
[15:10:39] Finished Work Unit:
[15:10:39] - Reading up to 3728544 from "work/wudata_01.arc": Read 3728544
[15:10:39] - Reading up to 1784984 from "work/wudata_01.xtc": Read 1784984
[15:10:39] goefile size: 0
[15:10:39] logfile size: 16972
[15:10:39] Leaving Run
[15:10:44] - Writing 5534900 bytes of core data to disk...
[15:10:44] ... Done.
[15:10:45] - Shutting down core
[15:10:45]
[15:10:45] Folding@home Core Shutdown: FINISHED_UNIT
[0]0:Return code = 100
[0]1:Return code = 0, signaled with Quit
[0]2:Return code = 0, signaled with Quit
[0]3:Return code = 0, signaled with Quit
[15:10:52] CoreStatus = 64 (100)
[15:10:52] Unit 1 finished with 67 percent of time to deadline remaining.
[15:10:52] Updated performance fraction: 0.651460
[15:10:52] Sending work to server
[15:10:52] + Attempting to send results
[15:10:52] - Reading file work/wuresults_01.dat from core
[15:10:52] (Read 5534900 bytes from disk)
[15:10:52] Connecting to http://171.64.65.56:8080/
[15:12:37] Posted data.
[15:12:37] Initial: 0000; - Uploaded at ~51 kB/s
[15:12:38] - Averaged speed for that direction ~46 kB/s
[15:12:38] + Results successfully sent
[15:12:38] Thank you for your contribution to Folding@Home.
[15:12:38] + Number of Units Completed: 10
[0]0:Return code = 18
[0]1:Return code = 0, signaled with Quit
[0]2:Return code = 0, signaled with Quit
[0]3:Return code = 0, signaled with Quit
[15:16:43] - Warning: Could not delete all work unit files (1): Core returned invalid code
[15:16:43] Trying to send all finished work units
[15:16:43] + No unsent completed units remaining.
[15:16:43] - Preparing to get new work unit...
[15:16:43] + Attempting to get work packet
[15:16:43] - Will indicate memory of 499 MB
[15:16:43] - Connecting to assignment server
[15:16:43] Connecting to http://assign.stanford.edu:8080/
[15:16:43] Posted data.
[15:16:43] Initial: 40AB; - Successful: assigned to (171.64.65.64).
[15:16:43] + News From Folding@Home: Welcome to Folding@Home
[15:16:43] Loaded queue successfully.
[15:16:43] Connecting to http://171.64.65.64:8080/
[15:16:48] Posted data.
[15:16:48] Initial: 0000; - Receiving payload (expected size: 4735567)
[15:17:04] - Downloaded at ~289 kB/s
[15:17:04] - Averaged speed for that direction ~323 kB/s
[15:17:04] + Received work.
[15:17:04] Trying to send all finished work units
[15:17:04] + No unsent completed units remaining.
[15:17:04] + Closed connections
[15:17:04]
[15:17:04] + Processing work unit
[15:17:04] Core required: FahCore_a1.exe
[15:17:04] Core found.
[15:17:04] Working on Unit 02 [August 14 15:17:04]
[15:17:04] + Working ...
[15:17:04] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a1.exe -dir work/ -suffix 02 -checkpoint 15 -forceasm -verbose -lifeline 5474 -version 602'
[15:17:04]
[15:17:04] *------------------------------*
[15:17:04] Folding@Home Gromacs SMP Core
[15:17:04] Version 1.74 (November 27, 2006)
[15:17:04]
[15:17:04] Preparing to commence simulation
[15:17:04] - Ensuring status. Please wait.
[15:17:21] - Assembly optimizations manually forced on.
[15:17:21] - Not checking prior termination.
[15:17:25] - Expanded 4735055 -> 24426905 (decompressed 515.8 percent)
[15:17:26] - Starting from initial work packet
[15:17:26]
[15:17:26] Project: 2665 (Run 0, Clone 479, Gen 20)
[15:17:26]
[15:17:27] Assembly optimizations on if available.
[15:17:27] Entering M.D.
NNODES=4, MYRANK=3, HOSTNAME=nitrodist1-desktop
NNODES=4, MYRANK=1, HOSTNAME=nitrodist1-desktop
NNODES=4, MYRANK=0, HOSTNAME=nitrodist1-desktop
NNODES=4, MYRANK=2, HOSTNAME=nitrodist1-desktop
NODEID=3 argc=15
NODEID=0 argc=15
NODEID=1 argc=15
NODEID=2 argc=15
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.
This inclusion of Gromacs code in the Folding@Home Core is under
a special license (see http://folding.stanford.edu/gromacs.html)
specially granted to Stanford by the copyright holders. If you
are interested in using Gromacs, visit www.gromacs.org where
you can download a free version of Gromacs under
the terms of the GNU General Public License (GPL) as published
by the Free Software Foundation; either version 2 of the License,
or (at your option) any later version.
[15:17:33] Rejecting checkpoint
[15:17:37]
[15:17:37] Writing local files
[15:17:39]
[15:17:39] Writing local files
starting mdrun 'HGG in water'
250000 steps, 500.0 ps.
[15:17:44] Extra SSE boost OK.
[15:17:45] Writing local files
[15:17:47] Completed 0 out of 250000 steps (0 percent)
[15:17:48]
[15:17:48] Folding@home Core Shutdown: INTERRUPTED
[0]0:Return code = 102
[0]1:Return code = 0, signaled with Segmentation fault
[0]2:Return code = 0, signaled with Segmentation fault
[0]3:Return code = 0, signaled with Segmentation fault
[15:17:52] CoreStatus = 66 (102)
[15:17:52] + Shutdown requested by user. Exiting.***** Got a SIGTERM signal (15)
[15:17:52] Killing all core threads
Folding@Home Client Shutdown.
nitrodist1@nitrodist1-desktop:~$ ./startfah
Note: Please read the license agreement (fah6 -license). Further
use of this software requires that you have read and accepted this agreement.
2 cores detected
--- Opening Log file [August 14 19:09:04]
# SMP Client ##################################################################
###############################################################################
Folding@Home Client Version 6.02
http://folding.stanford.edu
###############################################################################
###############################################################################
Launch directory: /home/nitrodist1/folding/FAH
Executable: ./fah6
Arguments: -forceasm -smp -verbosity 9
Warning:
By using the -forceasm flag, you are overriding
safeguards in the program. If you did not intend to
do this, please restart the program without -forceasm.
If work units are not completing fully (and particularly
if your machine is overclocked), then please discontinue
use of the flag.
[19:09:04] - Ask before connecting: No
[19:09:04] - User name: Mark` (Team 2630)
[19:09:04] - User ID: 5E2698AA4E184A22
[19:09:04] - Machine ID: 1
[19:09:04]
[19:09:04] Loaded queue successfully.
[19:09:04] - Autosending finished units...
[19:09:04] Trying to send all finished work units
[19:09:04] + No unsent completed units remaining.
[19:09:04] - Autosend completed
[19:09:04]
[19:09:04] + Processing work unit
[19:09:04] Core required: FahCore_a1.exe
[19:09:04] Core found.
[19:09:04] Working on Unit 02 [August 14 19:09:04]
[19:09:04] + Working ...
[19:09:04] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a1.exe -dir work/ -suffix 02 -checkpoint 15 -forceasm -verbose -lifeline 6478 -version 602'
[19:09:04]
[19:09:04] *------------------------------*
[19:09:04] Folding@Home Gromacs SMP Core
[19:09:04] Version 1.74 (November 27, 2006)
[19:09:04]
[19:09:04] Preparing to commence simulation
[19:09:04] - Ensuring status. Please wait.
[19:09:07]
[19:09:08] Project: 2665 (Run 0, Clone 479, Gen 20)
[19:09:08]
[19:09:09] Assembly optimizations on if available.
[19:09:09] Entering M.D.
[19:09:26] on if available.
[19:09:26] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=nitrodist1-desktop
NNODES=4, MYRANK=1, HOSTNAME=nitrodist1-desktop
NNODES=4, MYRANK=3, HOSTNAME=nitrodist1-desktop
NNODES=4, MYRANK=2, HOSTNAME=nitrodist1-desktop
NODEID=1 argc=15
NODEID=3 argc=15
NODEID=0 argc=15
NODEID=2 argc=15
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.
This inclusion of Gromacs code in the Folding@Home Core is under
a special license (see http://folding.stanford.edu/gromacs.html)
specially granted to Stanford by the copyright holders. If you
are interested in using Gromacs, visit www.gromacs.org where
you can download a free version of Gromacs under
the terms of the GNU General Public License (GPL) as published
by the Free Software Foundation; either version 2 of the License,
or (at your option) any later version.
[19:09:33] Calling FAH init
(single precision)
[19:09:35] Read topology
[19:09:35] (Starting from checkpoint)
[19:09:36] Read checkpoint
starting mdrun 'HGG in water'
250000 steps, 500.0 ps.
[19:09:37] Protein: HGG in water
[19:09:37] Writing local files
[19:09:43] Extra SSE boost OK.
[19:09:45] Writing local files
[19:09:45] Completed 0 out of 250000 steps (0 percent)
[19:09:46]
[19:09:46] Folding@home Core Shutdown: INTERRUPTED
[0]0:Return code = 102
[0]1:Return code = 0, signaled with Segmentation fault
[0]2:Return code = 0, signaled with Segmentation fault
[0]3:Return code = 0, signaled with Segmentation fault
[19:09:50] CoreStatus = 66 (102)
[19:09:50] + Shutdown requested by user. Exiting.***** Got a SIGTERM signal (15)
[19:09:50] Killing all core threads
Folding@Home Client Shutdown.
nitrodist1@nitrodist1-desktop:~$ ./startfah
Note: Please read the license agreement (fah6 -license). Further
use of this software requires that you have read and accepted this agreement.
2 cores detected
--- Opening Log file [August 14 19:12:46]
# SMP Client ##################################################################
###############################################################################
Folding@Home Client Version 6.02
http://folding.stanford.edu
###############################################################################
###############################################################################
Launch directory: /home/nitrodist1/folding/FAH
Executable: ./fah6
Arguments: -forceasm -smp -verbosity 9
Warning:
By using the -forceasm flag, you are overriding
safeguards in the program. If you did not intend to
do this, please restart the program without -forceasm.
If work units are not completing fully (and particularly
if your machine is overclocked), then please discontinue
use of the flag.
[19:12:46] - Ask before connecting: No
[19:12:46] - User name: Mark` (Team 2630)
[19:12:46] - User ID: 5E2698AA4E184A22
[19:12:46] - Machine ID: 1
[19:12:46]
[19:12:46] Loaded queue successfully.
[19:12:46] - Autosending finished units...
[19:12:46] Trying to send all finished work units
[19:12:46] + No unsent completed units remaining.
[19:12:46] - Autosend completed
[19:12:46]
[19:12:46] + Processing work unit
[19:12:46] Core required: FahCore_a1.exe
[19:12:46] Core found.
[19:12:46] Working on Unit 02 [August 14 19:12:46]
[19:12:46] + Working ...
[19:12:46] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a1.exe -dir work/ -suffix 02 -checkpoint 15 -forceasm -verbose -lifeline 6497 -version 602'
[19:12:46]
[19:12:46] *------------------------------*
[19:12:46] Folding@Home Gromacs SMP Core
[19:12:46] Version 1.74 (November 27, 2006)
[19:12:46]
[19:12:46] Preparing to commence simulation
[19:12:46] - Ensuring status. Please wait.
[19:12:48]
[19:12:49] Project: 2665 (Run 0, Clone 479, Gen 20)
[19:12:49]
[19:12:49] Assembly optimizations on if available.
[19:12:49] Entering M.D.
[19:13:06] on if available.
[19:13:06] Entering M.D.
NNODES=4, MYRANK=2, HOSTNAME=nitrodist1-desktop
NNODES=4, MYRANK=0, HOSTNAME=nitrodist1-desktop
NNODES=4, MYRANK=1, HOSTNAME=nitrodist1-desktop
NNODES=4, MYRANK=3, HOSTNAME=nitrodist1-desktop
NODEID=1 argc=15
NODEID=2 argc=15
NODEID=3 argc=15
NODEID=0 argc=15
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.
This inclusion of Gromacs code in the Folding@Home Core is under
a special license (see http://folding.stanford.edu/gromacs.html)
specially granted to Stanford by the copyright holders. If you
are interested in using Gromacs, visit www.gromacs.org where
you can download a free version of Gromacs under
the terms of the GNU General Public License (GPL) as published
by the Free Software Foundation; either version 2 of the License,
or (at your option) any later version.
(single precision)
[19:13:14] Starting from checkpoint)
[19:13:15] ing local files
starting mdrun 'HGG in water'
250000 steps, 500.0 ps.
[19:13:16] Protein: HGG in water
[19:13:16] Writing local files
[19:13:20] Extra SSE boost OK.
[19:13:21] Writing local files
[19:13:21] Completed 0 out of 250000 steps (0 percent)
[19:13:22]
[19:13:22] Folding@home Core Shutdown: INTERRUPTED
[0]0:Return code = 102
[0]1:Return code = 0, signaled with Segmentation fault
[0]2:Return code = 0, signaled with Segmentation fault
[0]3:Return code = 0, signaled with Segmentation fault
[19:13:26] CoreStatus = 66 (102)
[19:13:26] + Shutdown requested by user. Exiting.***** Got a SIGTERM signal (15)
[19:13:26] Killing all core threads
Folding@Home Client Shutdown.
nitrodist1@nitrodist1-desktop:~$
edit: Also, this is under a Q9300 at stock (2.5ghz) and under a guest Ubuntu 64-bit installation in vmware and the host OS is XP Pro 64bit. Memory is at DDR2 800mhz stock and in a 2x2GB configuration.