console output:
Code: Select all
[13:31:34] - Preparing to get new work unit...
[13:31:34] + Attempting to get work packet
[13:31:34] - Connecting to assignment server
[13:32:04] + Could not connect to Assignment Server
[13:32:09] - Successful: assigned to (171.64.65.56).
[13:32:09] + News From Folding@Home: Welcome to Folding@Home
[13:32:10] Loaded queue successfully.
[13:32:32] + Closed connections
[13:32:32]
[13:32:32] + Processing work unit
[13:32:32] Core required: FahCore_a2.exe
[13:32:32] Core found.
[13:32:32] Working on queue slot 03 [February 2 13:32:32 UTC]
[13:32:32] + Working ...
[13:32:32]
[13:32:32] *------------------------------*
[13:32:32] Folding@Home Gromacs SMP Core
[13:32:32] Version 2.01 (Wed Aug 13 13:11:25 PDT 2008)
[13:32:32]
[13:32:32] Preparing to commence simulation
[13:32:32] - Ensuring status. Please wait.
[13:32:33] Called DecompressByteArray: compressed_data_size=4843187 data_size=23
991465, decompressed_data_size=23991465 diff=0
[13:32:33] - Digital signature verified
[13:32:33]
[13:32:33] Project: 2669 (Run 4, Clone 130, Gen 93)
[13:32:33]
[13:32:34] Assembly optimizations on if available.
[13:32:34] Entering M.D.
[13:32:43] Run 4, Clone 130, Gen 93)
[13:32:43]
[13:32:43] Entering M.D.
NNODES=4, MYRANK=1, HOSTNAME=computenode
NNODES=4, MYRANK=3, HOSTNAME=computenode
NNODES=4, MYRANK=0, HOSTNAME=computenode
NNODES=4, MYRANK=2, HOSTNAME=computenode
NODEID=0 argc=19
NODEID=1 argc=19
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 3.3.99_development_200800503 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
:-) mdrun (-:
NODEID=2 argc=19
Reading file work/wudata_03.tpr, VERSION 3.3.99_development_20070618 (single pre
cision)
NODEID=3 argc=19
Note: tpx file_version 48, software version 56
Making 1D domain decomposition 1 x 1 x 4
starting mdrun '22908 system'
250000 steps, 500.0 ps.
Writing checkpoint, step 23254310 at Mon Feb 2 08:47:53 2009
[13:50:17] Completed 5000 out of 250000 steps (2%)
Warning: 1-4 interaction between 4304 and 4307 at distance 4.253 which is larger
than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step 23255150, time 46510.3 (ps) LINCS WARNING
relative constraint deviation after LINCS:rms 119.100666, max 1250.533325 (between atoms 1784 and 1786)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
4284 4285 90.0 0.1090 0.2877 0.1090
1048 1049 90.0 0.4149 43.0812 0.1090
1839 1841 90.0 0.4356 39.8000 0.1090
4326 4327 90.0 4.0366 4.6309 0.1090
Step 23255150, time 46510.3 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 11.641771, max 741.092529 (between atoms 648 and 649)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
3796 3797 109.7 0.1496 37.6851 0.1090
748 749 90.0 0.5155 1.2280 0.1090
759 761 90.0 0.2801 4.5306 0.1090
1722 1723 90.0 0.7101 16.9347 0.1080
2747 2749 90.0 0.2495 54.1120 0.1090
2747 2750 90.0 0.1090 0.6444 0.1090
11028 11031 90.0 0.6327 0.6224 0.1090
648 649 90.0 4.8884 80.8881 0.1090
648 650 90.0 0.1090 0.8178 0.1090
1714 1715 90.0 4.5846 4.0031 0.1010
2703 2704 90.0 0.1514 0.1961 0.1090
1136 1138 100.8 0.3025 38.8230 0.1090
4288 4289 90.0 4.2014 13.4680 0.1080
4290 4291 90.0 4.4915 0.7988 0.1080
4295 4296 90.0 0.1332 1.8362 0.1080
4308 4309 90.0 0.1466 1.2763 0.1010
4317 4319 90.0 0.2096 0.1839 0.1010
4322 4323 90.0 0.4110 0.2573 0.1010
748 749 90.0 0.5155 1.2280 0.1090
755 757 90.0 0.0957 0.2070 0.1090
755 758 90.0 4.4688 17.6286 0.1090
759 761 90.0 0.2801 4.5306 0.1090
1105 1106 90.0 0.2139 0.6048 0.1090
1105 1107 90.0 0.3077 0.7556 0.1090
1105 1108 90.0 0.2780 17.3693 0.1090
1109 1111 90.0 0.1786 1.3798 0.1090
1109 1112 90.0 0.2535 45.5130 0.1090
1722 1723 90.0 0.7101 16.9347 0.1080
1751 1752 90.0 0.5871 1.4279 0.1090
1753 1754 90.0 0.2095 0.5934 0.1090
4004 4005 90.0 0.5697 4.5967 0.1080
4006 4007 90.0 0.5475 20.8929 0.1080
4013 4014 90.0 0.2475 30.2776 0.1080
1759 1761 90.0 0.1010 3.4092 0.1090
1762 1763 90.0 0.2171 6.3100 0.1090
1771 1772 90.0 0.1514 0.2821 0.1010
1781 1782 90.0 0.1316 0.8647 0.1090
3988 3989 90.0 0.1356 3.6785 0.1090
3996 3997 90.0 0.3458 2.1064 0.1010
1773 1774 90.0 0.0957 0.1213 0.1090
3967 3968 90.0 0.5545 31.0942 0.1090
3969 3971 98.3 0.2804 5.2844 0.1090
3980 3981 90.0 0.2871 0.3412 0.1080
1811 1812 90.0 0.0957 0.5598 0.1090
1813 1814 90.0 3.8905 0.7083 0.1090
1813 1816 90.0 3.9632 18.7577 0.1090
1817 1818 90.0 0.1679 5.2708 0.1090
1820 1821 90.0 0.1090 1.3929 0.1090
1820 1822 90.0 0.1090 1.3820 0.1090
1820 1823 90.0 0.1565 34.9529 0.1090
2589 2590 90.0 0.9175 7.8300 0.1080
2596 2597 90.0 0.1429 0.1758 0.1080
2712 2713 90.0 2.9174 1.4521 0.1090
2743 2744 90.0 0.7324 8.1218 0.1090
2743 2745 107.9 0.1090 28.8564 0.1090
2747 2749 90.0 0.2495 54.1120 0.1090
2747 2750 90.0 0.1090 0.6444 0.1090
3695 3696 90.0 0.1758 5.4562 0.1090
3695 3697 90.0 0.2697 5.2099 0.1090
1809 1810 90.0 0.2273 0.5567 0.1090
1846 1848 90.0 0.2644 1.3768 0.1090
1849 1850 90.0 0.9625 3.8481 0.1090
1849 1851 90.0 1.0533 3.8508 0.1090
2568 2569 90.0 0.0957 0.1832 0.1010
2570 2571 90.0 4.3239 0.7156 0.1090
2572 2573 90.0 0.2134 0.2034 0.1090
2572 2574 90.0 0.2981 0.1973 0.1090
2583 2584 130.3 0.2043 17.0944 0.1090
3765 3766 90.0 0.2262 0.6822 0.1090
3767 3768 90.0 0.5670 9.9597 0.1090
3773 3774 90.0 0.2085 3.5425 0.1010
3779 3781 90.0 0.1473 0.9097 0.1090
3796 3797 109.7 0.1496 37.6851 0.1090
2538 2539 90.0 0.1514 0.9233 0.1010
2538 2541 90.0 3.9077 2.1298 0.1010
11028 11031 90.0 0.6327 0.6224 0.1090
648 649 90.0 4.8884 80.8881 0.1090
648 650 90.0 0.1090 0.8178 0.1090
689 690 90.0 0.1236 3.0329 0.1090
712 713 90.0 0.4285 0.4445 0.1090
714 716 90.0 0.2052 0.5545 0.1090
717 719 90.0 4.6208 4.4334 0.1090
720 721 90.0 0.1090 20.9946 0.1090
720 722 90.0 0.1552 22.2096 0.1090
723 724 90.0 0.1090 0.2717 0.1090
1116 1118 90.0 0.5591 0.5412 0.1090
1136 1138 100.8 0.3025 38.8230 0.1090
1714 1715 90.0 4.5846 4.0031 0.1010
1738 1739 90.0 0.2121 0.3723 0.1090
1777 1778 90.0 0.7630 113.2012 0.1090
1777 1779 90.0 0.8289 112.4427 0.1090
4017 4018 90.0 0.0957 0.2896 0.1010
4021 4022 90.0 0.1514 5.8779 0.1090
4021 4023 90.0 0.5614 12.9137 0.1090
4027 4028 90.0 0.1514 4.2149 0.1090
2592 2593 90.0 0.0957 0.1759 0.0960
2703 2704 90.0 0.1514 0.1961 0.1090
2633 2634 90.0 0.0957 0.3069 0.1090
2602 2603 90.0 0.0957 0.2395 0.1090
2609 2610 90.0 0.1514 1.1208 0.1010
7592 7593 90.0 1.2159 98.9983 0.1092
7629 7630 90.0 1.0133 63.1244 0.1010
t = 46510.301 ps: Water molecule starting at atom 82915 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
A list of missing interactions:
Settle of 41097 missing -8
exclusions of 249888 missing 615
-------------------------------------------------------
Program mdrun, VERSION 3.3.99_development_200800503
Source code file: domdec_top.c, line: 87
Software inconsistency error:
Some interactions seem to be assigned multiple times
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 3, will try to stop all the nodes
Halting parallel program mdrun on CPU 3 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
A list of missing interactions:
Settle of 41097 missing -8
exclusions of 249888 missing 615
-------------------------------------------------------
Program mdrun, VERSION 3.3.99_development_200800503
Source code file: domdec_top.c, line: 87
Software inconsistency error:
Some interactions seem to be assigned multiple times
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 3, will try to stop all the nodes
Halting parallel program mdrun on CPU 3 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_3]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
[13:50:50]
[13:50:50] Folding@home Core Shutdown: INTERRUPTED
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
Code: Select all
--- Opening Log file [February 2 21:34:40 UTC]
# Linux SMP Console Edition ###################################################
###############################################################################
Folding@Home Client Version 6.24beta
http://folding.stanford.edu
###############################################################################
###############################################################################
Launch directory: /share/fah1
Executable: ./fah6
Arguments: -smp 4
[21:34:40] - Ask before connecting: No
[21:34:40] - User name: alpha754293 (Team 596)
[21:34:40] - User ID: 47FBD1D4056DB49E
[21:34:40] - Machine ID: 1
[21:34:40]
[21:34:41] Loaded queue successfully.
[21:34:41]
[21:34:41] + Processing work unit
[21:34:41] Core required: FahCore_a2.exe
[21:34:41] Core found.
[21:34:41] Working on queue slot 03 [February 2 21:34:41 UTC]
[21:34:41] + Working ...
[21:34:41]
[21:34:41] *------------------------------*
[21:34:41] Folding@Home Gromacs SMP Core
[21:34:41] Version 2.01 (Wed Aug 13 13:11:25 PDT 2008)
[21:34:41]
[21:34:41] Preparing to commence simulation
[21:34:41] - Ensuring status. Please wait.
[21:34:42] Called DecompressByteArray: compressed_data_size=4843187 data_size=23991465, decompressed_data_size=23991465 diff=0
[21:34:42] - Digital signature verified
[21:34:42]
[21:34:42] Project: 2669 (Run 4, Clone 130, Gen 93)
[21:34:42]
[21:34:42] Assembly optimizations on if available.
[21:34:42] Entering M.D.
[21:34:48] Will resume from checkpoint file
[21:34:52] ng M.D.
[21:34:58] Will resume from checkpoint file
[21:34:59] Resuming from checkpoint
[21:34:59] Verified work/wudata_03.log
[21:34:59] Verified work/wudata_03.trr
[21:34:59] Verified work/wudata_03.xtc
[21:34:59] Verified work/wudata_03.edr
[21:34:59] Completed 5010 out of 250000 steps (2%)
[21:43:52] Completed 7500 out of 250000 steps (3%)
Restarted the client, and seems to be running ok for the time being.