Code: Select all
[01:47:50]
[01:47:50] + Processing work unit
[01:47:50] Core required: FahCore_a2.exe
[01:47:50] Core found.
[01:47:50] Working on queue slot 05 [August 21 01:47:50 UTC]
[01:47:50] + Working ...
[01:47:50] - Calling './mpiexec -np 8 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -nice 19 -suffix 05 -priority 96 -checkpoint 15 -verbose -lifeline 28520 -version 624'
[01:47:50]
[01:47:50] *------------------------------*
[01:47:50] Folding@Home Gromacs SMP Core
[01:47:50] Version 2.08 (Mon May 18 14:47:42 PDT 2009)
[01:47:50]
[01:47:50] Preparing to commence simulation
[01:47:50] - Ensuring status. Please wait.
[01:47:50] Files status OK
[01:47:51] - Expanded 4841420 -> 24004881 (decompressed 495.8 percent)
[01:47:51] Called DecompressByteArray: compressed_data_size=4841420 data_size=24004881, decompressed_data_size=24004881 diff=0
[01:47:51] - Digital signature verified
[01:47:51]
[01:47:51] Project: 2671 (Run 3, Clone 92, Gen 86)
[01:47:51]
[01:47:52] Assembly optimizations on if available.
[01:47:52] Entering M.D.
[01:48:01] (Run 3, Clone 92, Gen 86)
[01:48:01[01:47:50]
[01:47:50] + Processing work unit
[01:47:50] Core required: FahCore_a2.exe
[01:47:50] Core found.
[01:47:50] Working on queue slot 05 [August 21 01:47:50 UTC]
[01:47:50] + Working ...
[01:47:50] - Calling './mpiexec -np 8 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -nice 19 -suffix 05 -priority 96 -checkpoint 15 -verbose -lifeline 28520 -version 624'
[01:47:50]
[01:47:50] *------------------------------*
[01:47:50] Folding@Home Gromacs SMP Core
[01:47:50] Version 2.08 (Mon May 18 14:47:42 PDT 2009)
[01:47:50]
[01:47:50] Preparing to commence simulation
[01:47:50] - Ensuring status. Please wait.
[01:47:50] Files status OK
[01:47:51] - Expanded 4841420 -> 24004881 (decompressed 495.8 percent)
[01:47:51] Called DecompressByteArray: compressed_data_size=4841420 data_size=24004881, decompressed_data_size=24004881 diff=0
[01:47:51] - Digital signature verified
[01:47:51]
[01:47:51] Project: 2671 (Run 3, Clone 92, Gen 86)
[01:47:51]
[01:47:52] Assembly optimizations on if available.
[01:47:52] Entering M.D.
[01:48:01] (Run 3, Clone 92, Gen 86)
[01:48:01]
[01:48:01] Entering M.D.
NNODES=8, MYRANK=1, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=0, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=2, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=4, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=5, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=6, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=7, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=3, HOSTNAME=lab3ia.lab1.com
NODEID=0 argc=22
NODEID=1 argc=22
NODEID=2 argc=22
NODEID=3 argc=22
NODEID=4 argc=22
NODEID=5 argc=22
NODEID=7 argc=22
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.99_development_20090425 (-:
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 (-:
Reading file work/wudata_05.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=6 argc=22
Note: tpx file_version 48, software version 65
NOTE: The tpr file used for this simulation is in an old format, for less memory usage and possibly more performance create a new tpr file with an up to date version of grompp
Making 3D domain decomposition 2 x 2 x 2
starting mdrun '22878 system in water'
21750000 steps, 43500.0 ps (continuing from step 21500000, 43000.0 ps).
[01:52:14] pleted 2500 out of 250000 steps (1%)
[01:56:16] Completed 5000 out of 250000 steps (2%)
[02:00:19] Completed 7500 out of 250000 steps (3%)
[02:04:21] Completed 10000 out of 250000 steps (4%)
[02:08:24] Completed 12500 out of 250000 steps (5%)
[02:12:26] Completed 15000 out of 250000 steps (6%)
[02:16:29] Completed 17500 out of 250000 steps (7%)
[02:20:32] Completed 20000 out of 250000 steps (8%)
[02:24:34] Completed 22500 out of 250000 steps (9%)
[02:28:36] Completed 25000 out of 250000 steps (10%)
[02:32:40] Completed 27500 out of 250000 steps (11%)
[02:36:42] Completed 30000 out of 250000 steps (12%)
[02:40:44] Completed 32500 out of 250000 steps (13%)
[02:44:46] Completed 35000 out of 250000 steps (14%)
[02:48:48] Completed 37500 out of 250000 steps (15%)
[02:52:50] Completed 40000 out of 250000 steps (16%)
[02:56:52] Completed 42500 out of 250000 steps (17%)
[03:00:55] Completed 45000 out of 250000 steps (18%)
[03:04:57] Completed 47500 out of 250000 steps (19%)
[03:08:59] Completed 50000 out of 250000 steps (20%)
[03:13:01] Completed 52500 out of 250000 steps (21%)
[03:17:03] Completed 55000 out of 250000 steps (22%)
[03:21:05] Completed 57500 out of 250000 steps (23%)
[03:25:07] Completed 60000 out of 250000 steps (24%)
[03:29:09] Completed 62500 out of 250000 steps (25%)
[03:33:12] Completed 65000 out of 250000 steps (26%)
[03:37:14] Completed 67500 out of 250000 steps (27%)
[03:41:17] Completed 70000 out of 250000 steps (28%)
[03:45:20] Completed 72500 out of 250000 steps (29%)
[03:49:22] Completed 75000 out of 250000 steps (30%)
[03:53:24] Completed 77500 out of 250000 steps (31%)
[03:57:27] Completed 80000 out of 250000 steps (32%)
[04:01:29] Completed 82500 out of 250000 steps (33%)
[04:05:31] Completed 85000 out of 250000 steps (34%)
[04:09:34] Completed 87500 out of 250000 steps (35%)
[04:13:36] Completed 90000 out of 250000 steps (36%)
[04:17:38] Completed 92500 out of 250000 steps (37%)
[04:21:39] Completed 95000 out of 250000 steps (38%)
[04:25:41] Completed 97500 out of 250000 steps (39%)
[04:29:44] Completed 100000 out of 250000 steps (40%)
[04:33:46] Completed 102500 out of 250000 steps (41%)
[04:37:47] Completed 105000 out of 250000 steps (42%)
[04:41:50] Completed 107500 out of 250000 steps (43%)
[04:45:51] Completed 110000 out of 250000 steps (44%)
[04:49:54] Completed 112500 out of 250000 steps (45%)
[04:53:55] Completed 115000 out of 250000 steps (46%)
[04:57:58] Completed 117500 out of 250000 steps (47%)
[05:02:00] Completed 120000 out of 250000 steps (48%)
Step 21621109, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001319, max 0.058593 (between atoms 22540 and 22543)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 21621115, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.358723, max 12.048203 (between atoms 22540 and 22542)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
22534 22536 90.0 0.1092 0.1353 0.1090
22537 22539 90.0 0.1104 1.2899 0.1090
22540 22542 90.0 0.1010 1.3179 0.1010
Warning: 1-4 interaction between 22539 and 22542 at distance 2.667 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 21621116, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.015050, max 0.567045 (between atoms 22537 and 22538)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
22534 22536 90.0 0.1353 0.1306 0.1090
22537 22538 90.0 0.1035 0.1708 0.1090
Step 21621117, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.372390, max 57.160320 (between atoms 22537 and 22538)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
22534 22536 90.0 0.1306 0.1356 0.1090
22537 22539 90.0 0.1124 2.4521 0.1090
22540 22541 90.0 0.1033 0.1213 0.1010
22540 22543 90.0 0.1322 0.1433 0.1010
t = 43242.236 ps: Water molecule starting at atom 113737 can not be settled.
Check for bad contacts and/or reduce the timestep.
Step 21621118, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 7285966897152.000000 (between atoms 22571 and 22572)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
22534 22535 90.0 0.1094 0.4089 0.1090
22540 22542 90.0 1.1860 3.0812 0.1010
t = 43242.238 ps: Water molecule starting at atom 145072 can not be settled.
Check for bad contacts and/or reduce the timestep.
Warning: 1-4 interaction between 22570 and 22572 at distance 707164614706.821 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
A list of missing interactions:
Bond of 12051 missing -630
Angle of 42162 missing -3746
Ryckaert-Bell. of 53034 missing -6634
LJ-14 of 60858 missing -6664
exclusions of 249876 missing 9543
Molecule type '22878 system in water'
the first 10 missing interactions, except for exclusions:
Ryckaert-Bell. atoms13999140011400314004 global 13999 14001 14003 14004
Ryckaert-Bell. atoms17081170801708217084 global 17081 17080 17082 17084
Ryckaert-Bell. atoms17084170821708017095 global 17084 17082 17080 17095
Ryckaert-Bell. atoms17601176001759817604 global 17601 17600 17598 17604
Ryckaert-Bell. atoms17602176001759817604 global 17602 17600 17598 17604
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090425
Source code file: domdec_top.c, line: 346
Software inconsistency error:
One or more interactions were multiple assigned in the domain decompostion
For more information and tips for trouble shooting please check the GROMACS Wiki at
http://wiki.gromacs.org/index.php/Errors
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 8
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
[cli_2]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_4]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_1]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[07:02:26] - Autosending finished units... [August 21 07:02:26 UTC]
[07:02:26] Trying to send all finished work units
[07:02:26] + No unsent completed units remaining.
[07:02:26] - Autosend completed
[13:02:29] - Autosending finished units... [August 21 13:02:29 UTC]
[13:02:29] Trying to send all finished work units
[13:02:29] + No unsent completed units remaining.
[13:02:29] - Autosend completed
]
[01:48:01] Entering M.D.
NNODES=8,[01:47:50]
[01:47:50] + Processing work unit
[01:47:50] Core required: FahCore_a2.exe
[01:47:50] Core found.
[01:47:50] Working on queue slot 05 [August 21 01:47:50 UTC]
[01:47:50] + Working ...
[01:47:50] - Calling './mpiexec -np 8 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -nice 19 -suffix 05 -priority 96 -checkpoint 15 -verbose -lifeline 28520 -version 624'
[01:47:50]
[01:47:50] *------------------------------*
[01:47:50] Folding@Home Gromacs SMP Core
[01:47:50] Version 2.08 (Mon May 18 14:47:42 PDT 2009)
[01:47:50]
[01:47:50] Preparing to commence simulation
[01:47:50] - Ensuring status. Please wait.
[01:47:50] Files status OK
[01:47:51] - Expanded 4841420 -> 24004881 (decompressed 495.8 percent)
[01:47:51] Called DecompressByteArray: compressed_data_size=4841420 data_size=24004881, decompressed_data_size=24004881 diff=0
[01:47:51] - Digital signature verified
[01:47:51]
[01:47:51] Project: 2671 (Run 3, Clone 92, Gen 86)
[01:47:51]
[01:47:52] Assembly optimizations on if available.
[01:47:52] Entering M.D.
[01:48:01] (Run 3, Clone 92, Gen 86)
[01:48:01]
[01:48:01] Entering M.D.
NNODES=8, MYRANK=1, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=0, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=2, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=4, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=5, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=6, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=7, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=3, HOSTNAME=lab3ia.lab1.com
NODEID=0 argc=22
NODEID=1 argc=22
NODEID=2 argc=22
NODEID=3 argc=22
NODEID=4 argc=22
NODEID=5 argc=22
NODEID=7 argc=22
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.99_development_20090425 (-:
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 (-:
Reading file work/wudata_05.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=6 argc=22
Note: tpx file_version 48, software version 65
NOTE: The tpr file used for this simulation is in an old format, for less memory usage and possibly more performance create a new tpr file with an up to date version of grompp
Making 3D domain decomposition 2 x 2 x 2
starting mdrun '22878 system in water'
21750000 steps, 43500.0 ps (continuing from step 21500000, 43000.0 ps).
[01:52:14] pleted 2500 out of 250000 steps (1%)
[01:56:16] Completed 5000 out of 250000 steps (2%)
[02:00:19] Completed 7500 out of 250000 steps (3%)
[02:04:21] Completed 10000 out of 250000 steps (4%)
[02:08:24] Completed 12500 out of 250000 steps (5%)
[02:12:26] Completed 15000 out of 250000 steps (6%)
[02:16:29] Completed 17500 out of 250000 steps (7%)
[02:20:32] Completed 20000 out of 250000 steps (8%)
[02:24:34] Completed 22500 out of 250000 steps (9%)
[02:28:36] Completed 25000 out of 250000 steps (10%)
[02:32:40] Completed 27500 out of 250000 steps (11%)
[02:36:42] Completed 30000 out of 250000 steps (12%)
[02:40:44] Completed 32500 out of 250000 steps (13%)
[02:44:46] Completed 35000 out of 250000 steps (14%)
[02:48:48] Completed 37500 out of 250000 steps (15%)
[02:52:50] Completed 40000 out of 250000 steps (16%)
[02:56:52] Completed 42500 out of 250000 steps (17%)
[03:00:55] Completed 45000 out of 250000 steps (18%)
[03:04:57] Completed 47500 out of 250000 steps (19%)
[03:08:59] Completed 50000 out of 250000 steps (20%)
[03:13:01] Completed 52500 out of 250000 steps (21%)
[03:17:03] Completed 55000 out of 250000 steps (22%)
[03:21:05] Completed 57500 out of 250000 steps (23%)
[03:25:07] Completed 60000 out of 250000 steps (24%)
[03:29:09] Completed 62500 out of 250000 steps (25%)
[03:33:12] Completed 65000 out of 250000 steps (26%)
[03:37:14] Completed 67500 out of 250000 steps (27%)
[03:41:17] Completed 70000 out of 250000 steps (28%)
[03:45:20] Completed 72500 out of 250000 steps (29%)
[03:49:22] Completed 75000 out of 250000 steps (30%)
[03:53:24] Completed 77500 out of 250000 steps (31%)
[03:57:27] Completed 80000 out of 250000 steps (32%)
[04:01:29] Completed 82500 out of 250000 steps (33%)
[04:05:31] Completed 85000 out of 250000 steps (34%)
[04:09:34] Completed 87500 out of 250000 steps (35%)
[04:13:36] Completed 90000 out of 250000 steps (36%)
[04:17:38] Completed 92500 out of 250000 steps (37%)
[04:21:39] Completed 95000 out of 250000 steps (38%)
[04:25:41] Completed 97500 out of 250000 steps (39%)
[04:29:44] Completed 100000 out of 250000 steps (40%)
[04:33:46] Completed 102500 out of 250000 steps (41%)
[04:37:47] Completed 105000 out of 250000 steps (42%)
[04:41:50] Completed 107500 out of 250000 steps (43%)
[04:45:51] Completed 110000 out of 250000 steps (44%)
[04:49:54] Completed 112500 out of 250000 steps (45%)
[04:53:55] Completed 115000 out of 250000 steps (46%)
[04:57:58] Completed 117500 out of 250000 steps (47%)
[05:02:00] Completed 120000 out of 250000 steps (48%)
Step 21621109, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001319, max 0.058593 (between atoms 22540 and 22543)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 21621115, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.358723, max 12.048203 (between atoms 22540 and 22542)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
22534 22536 90.0 0.1092 0.1353 0.1090
22537 22539 90.0 0.1104 1.2899 0.1090
22540 22542 90.0 0.1010 1.3179 0.1010
Warning: 1-4 interaction between 22539 and 22542 at distance 2.667 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 21621116, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.015050, max 0.567045 (between atoms 22537 and 22538)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
22534 22536 90.0 0.1353 0.1306 0.1090
22537 22538 90.0 0.1035 0.1708 0.1090
Step 21621117, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.372390, max 57.160320 (between atoms 22537 and 22538)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
22534 22536 90.0 0.1306 0.1356 0.1090
22537 22539 90.0 0.1124 2.4521 0.1090
22540 22541 90.0 0.1033 0.1213 0.1010
22540 22543 90.0 0.1322 0.1433 0.1010
t = 43242.236 ps: Water molecule starting at atom 113737 can not be settled.
Check for bad contacts and/or reduce the timestep.
Step 21621118, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 7285966897152.000000 (between atoms 22571 and 22572)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
22534 22535 90.0 0.1094 0.4089 0.1090
22540 22542 90.0 1.1860 3.0812 0.1010
t = 43242.238 ps: Water molecule starting at atom 145072 can not be settled.
Check for bad contacts and/or reduce the timestep.
Warning: 1-4 interaction between 22570 and 22572 at distance 707164614706.821 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
A list of missing interactions:
Bond of 12051 missing -630
Angle of 42162 missing -3746
Ryckaert-Bell. of 53034 missing -6634
LJ-14 of 60858 missing -6664
exclusions of 249876 missing 9543
Molecule type '22878 system in water'
the first 10 missing interactions, except for exclusions:
Ryckaert-Bell. atoms13999140011400314004 global 13999 14001 14003 14004
Ryckaert-Bell. atoms17081170801708217084 global 17081 17080 17082 17084
Ryckaert-Bell. atoms17084170821708017095 global 17084 17082 17080 17095
Ryckaert-Bell. atoms17601176001759817604 global 17601 17600 17598 17604
Ryckaert-Bell. atoms17602176001759817604 global 17602 17600 17598 17604
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090425
Source code file: domdec_top.c, line: 346
Software inconsistency error:
One or more interactions were multiple assigned in the domain decompostion
For more information and tips for trouble shooting please check the GROMACS Wiki at
http://wiki.gromacs.org/index.php/Errors
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 8
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
[cli_2]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_4]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_1]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[07:02:26] - Autosending finished units... [August 21 07:02:26 UTC]
[07:02:26] Trying to send all finished work units
[07:02:26] + No unsent completed units remaining.
[07:02:26] - Autosend completed
[13:02:29] - Autosending finished units... [August 21 13:02:29 UTC]
[13:02:29] Trying to send all finished work units
[13:02:29] + No unsent completed units remaining.
[13:02:29] - Autosend completed
MYRANK=1, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=0, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=2, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=4, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=5, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=6, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=7, HOSTNAME=lab3ia.lab1.com
NNODES=8, MYRANK=3, HOSTNAME=lab3ia.lab1.com
NODEID=0 argc=22
NODEID=1 argc=22
NODEID=2 argc=22
NODEID=3 argc=22
NODEID=4 argc=22
NODEID=5 argc=22
NODEID=7 argc=22
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.99_development_20090425 (-:
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 (-:
Reading file work/wudata_05.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=6 argc=22
Note: tpx file_version 48, software version 65
NOTE: The tpr file used for this simulation is in an old format, for less memory usage and possibly more performance create a new tpr file with an up to date version of grompp
Making 3D domain decomposition 2 x 2 x 2
starting mdrun '22878 system in water'
21750000 steps, 43500.0 ps (continuing from step 21500000, 43000.0 ps).
[01:52:14] pleted 2500 out of 250000 steps (1%)
[01:56:16] Completed 5000 out of 250000 steps (2%)
[02:00:19] Completed 7500 out of 250000 steps (3%)
[02:04:21] Completed 10000 out of 250000 steps (4%)
[02:08:24] Completed 12500 out of 250000 steps (5%)
[02:12:26] Completed 15000 out of 250000 steps (6%)
[02:16:29] Completed 17500 out of 250000 steps (7%)
[02:20:32] Completed 20000 out of 250000 steps (8%)
[02:24:34] Completed 22500 out of 250000 steps (9%)
[02:28:36] Completed 25000 out of 250000 steps (10%)
[02:32:40] Completed 27500 out of 250000 steps (11%)
[02:36:42] Completed 30000 out of 250000 steps (12%)
[02:40:44] Completed 32500 out of 250000 steps (13%)
[02:44:46] Completed 35000 out of 250000 steps (14%)
[02:48:48] Completed 37500 out of 250000 steps (15%)
[02:52:50] Completed 40000 out of 250000 steps (16%)
[02:56:52] Completed 42500 out of 250000 steps (17%)
[03:00:55] Completed 45000 out of 250000 steps (18%)
[03:04:57] Completed 47500 out of 250000 steps (19%)
[03:08:59] Completed 50000 out of 250000 steps (20%)
[03:13:01] Completed 52500 out of 250000 steps (21%)
[03:17:03] Completed 55000 out of 250000 steps (22%)
[03:21:05] Completed 57500 out of 250000 steps (23%)
[03:25:07] Completed 60000 out of 250000 steps (24%)
[03:29:09] Completed 62500 out of 250000 steps (25%)
[03:33:12] Completed 65000 out of 250000 steps (26%)
[03:37:14] Completed 67500 out of 250000 steps (27%)
[03:41:17] Completed 70000 out of 250000 steps (28%)
[03:45:20] Completed 72500 out of 250000 steps (29%)
[03:49:22] Completed 75000 out of 250000 steps (30%)
[03:53:24] Completed 77500 out of 250000 steps (31%)
[03:57:27] Completed 80000 out of 250000 steps (32%)
[04:01:29] Completed 82500 out of 250000 steps (33%)
[04:05:31] Completed 85000 out of 250000 steps (34%)
[04:09:34] Completed 87500 out of 250000 steps (35%)
[04:13:36] Completed 90000 out of 250000 steps (36%)
[04:17:38] Completed 92500 out of 250000 steps (37%)
[04:21:39] Completed 95000 out of 250000 steps (38%)
[04:25:41] Completed 97500 out of 250000 steps (39%)
[04:29:44] Completed 100000 out of 250000 steps (40%)
[04:33:46] Completed 102500 out of 250000 steps (41%)
[04:37:47] Completed 105000 out of 250000 steps (42%)
[04:41:50] Completed 107500 out of 250000 steps (43%)
[04:45:51] Completed 110000 out of 250000 steps (44%)
[04:49:54] Completed 112500 out of 250000 steps (45%)
[04:53:55] Completed 115000 out of 250000 steps (46%)
[04:57:58] Completed 117500 out of 250000 steps (47%)
[05:02:00] Completed 120000 out of 250000 steps (48%)
Step 21621109, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001319, max 0.058593 (between atoms 22540 and 22543)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 21621115, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.358723, max 12.048203 (between atoms 22540 and 22542)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
22534 22536 90.0 0.1092 0.1353 0.1090
22537 22539 90.0 0.1104 1.2899 0.1090
22540 22542 90.0 0.1010 1.3179 0.1010
Warning: 1-4 interaction between 22539 and 22542 at distance 2.667 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 21621116, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.015050, max 0.567045 (between atoms 22537 and 22538)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
22534 22536 90.0 0.1353 0.1306 0.1090
22537 22538 90.0 0.1035 0.1708 0.1090
Step 21621117, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.372390, max 57.160320 (between atoms 22537 and 22538)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
22534 22536 90.0 0.1306 0.1356 0.1090
22537 22539 90.0 0.1124 2.4521 0.1090
22540 22541 90.0 0.1033 0.1213 0.1010
22540 22543 90.0 0.1322 0.1433 0.1010
t = 43242.236 ps: Water molecule starting at atom 113737 can not be settled.
Check for bad contacts and/or reduce the timestep.
Step 21621118, time 43242.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 7285966897152.000000 (between atoms 22571 and 22572)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
22534 22535 90.0 0.1094 0.4089 0.1090
22540 22542 90.0 1.1860 3.0812 0.1010
t = 43242.238 ps: Water molecule starting at atom 145072 can not be settled.
Check for bad contacts and/or reduce the timestep.
Warning: 1-4 interaction between 22570 and 22572 at distance 707164614706.821 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
A list of missing interactions:
Bond of 12051 missing -630
Angle of 42162 missing -3746
Ryckaert-Bell. of 53034 missing -6634
LJ-14 of 60858 missing -6664
exclusions of 249876 missing 9543
Molecule type '22878 system in water'
the first 10 missing interactions, except for exclusions:
Ryckaert-Bell. atoms13999140011400314004 global 13999 14001 14003 14004
Ryckaert-Bell. atoms17081170801708217084 global 17081 17080 17082 17084
Ryckaert-Bell. atoms17084170821708017095 global 17084 17082 17080 17095
Ryckaert-Bell. atoms17601176001759817604 global 17601 17600 17598 17604
Ryckaert-Bell. atoms17602176001759817604 global 17602 17600 17598 17604
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090425
Source code file: domdec_top.c, line: 346
Software inconsistency error:
One or more interactions were multiple assigned in the domain decompostion
For more information and tips for trouble shooting please check the GROMACS Wiki at
http://wiki.gromacs.org/index.php/Errors
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 8
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
[cli_2]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_4]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_1]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[07:02:26] - Autosending finished units... [August 21 07:02:26 UTC]
[07:02:26] Trying to send all finished work units
[07:02:26] + No unsent completed units remaining.
[07:02:26] - Autosend completed
[13:02:29] - Autosending finished units... [August 21 13:02:29 UTC]
[13:02:29] Trying to send all finished work units
[13:02:29] + No unsent completed units remaining.
[13:02:29] - Autosend completed
BW
