Project: 2675 (Run 3, Clone 13, Gen 159) WMCNBS 100% reprod.

[tear]

Per subject. Water molecule can not be settled, 100% reproducible.

Code: Select all

[21:07:39]
[21:07:39] *------------------------------*
[21:07:39] Folding@Home Gromacs SMP Core
[21:07:39] Version 2.10 (Sun Aug 30 03:43:28 CEST 2009)
[21:07:39]
[21:07:39] Preparing to commence simulation
[21:07:39] - Ensuring status. Please wait.
[21:07:40] Called DecompressByteArray: compressed_data_size=4842739 data_size=23994061, decompressed_data_size=23994061 diff=0
[21:07:40] - Digital signature verified
[21:07:40]
[21:07:40] Project: 2675 (Run 3, Clone 13, Gen 159)
[21:07:40]
[21:07:40] Assembly optimizations on if available.
[21:07:40] Entering M.D.
[21:07:49]  on if available.
[21:07:49] Entering M.D.
NNODES=11, MYRANK=6, HOSTNAME=tentacle
NNODES=11, MYRANK=0, HOSTNAME=tentacle
NODEID=0 argc=20
NNODES=11, MYRANK=1, HOSTNAME=tentacle
NODEID=1 argc=20
NNODES=11, MYRANK=3, HOSTNAME=tentacle
NNODES=11, MYRANK=4, HOSTNAME=tentacle
NODEID=4 argc=20
NNODES=11, MYRANK=5, HOSTNAME=tentacle
NODEID=5 argc=20
NNODES=11, MYRANK=7, HOSTNAME=tentacle
NODEID=7 argc=20
NNODES=11, MYRANK=8, HOSTNAME=tentacle
NODEID=8 argc=20
NNODES=11, MYRANK=9, HOSTNAME=tentacle
NODEID=9 argc=20
NNODES=11, MYRANK=10, HOSTNAME=tentacle
NODEID=10 argc=20
NODEID=6 argc=20
NNODES=11, MYRANK=2, HOSTNAME=tentacle
NODEID=2 argc=20
NODEID=3 argc=20
Reading file work/wudata_02.tpr, VERSION 3.3.99_development_20070618 (single precision)
Note: tpx file_version 48, software version 68

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 1D domain decomposition 1 x 1 x 11
starting mdrun '22878 system in water'
40000004 steps,  80000.0 ps (continuing from step 39750004,  79500.0 ps).

t = 79500.012 ps: Water molecule starting at atom 132199 can not be settled.
Check for bad contacts and/or reduce the timestep.
[21:07:58]  (0%)

t = 79500.012 ps: Water molecule starting at atom 60856 can not be settled.
Check for bad contacts and/or reduce the timestep.
[21:07:58]
[21:07:58] Folding@home Core Shutdown: INTERRUPTED
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[0]0:Return code = 102
[0]1:Return code = 0, signaled with Quit
[0]2:Return code = 0, signaled with Segmentation fault
[0]3:Return code = 0, signaled with Segmentation fault
[0]4:Return code = 0, signaled with Quit
[0]5:Return code = 0, signaled with Segmentation fault
[0]6:Return code = 0, signaled with Segmentation fault
[0]7:Return code = 0, signaled with Quit
[0]8:Return code = 0, signaled with Quit
[0]9:Return code = 0, signaled with Quit
[0]10:Return code = 0, signaled with Quit
[21:08:09] CoreStatus = 66 (102)
[21:08:09] + Shutdown requested by user. Exiting.***** Got a SIGTERM signal (15)
[21:08:09] Killing all core threads

tear

[andrey.d]

I've got exactly the same WU with exactly the same errors. Here is the screen output.

Code: Select all

[09:07:42] Folding@Home Gromacs SMP Core
[09:07:42] Version 2.10 (Sun Aug 30 03:43:28 CEST 2009)
[09:07:42] 
[09:07:42] Preparing to commence simulation
[09:07:42] - Ensuring status. Please wait.
[09:07:45] Called DecompressByteArray: compressed_data_size=4842739 data_size=23994061, decompressed_data_size=23994061 diff=0
[09:07:45] - Digital signature verified
[09:07:45] 
[09:07:45] Project: 2675 (Run 3, Clone 13, Gen 159)
[09:07:45] 
[09:07:45] Assembly optimizations on if available.
[09:07:45] Entering M.D.
[09:07:56]  on if available.
[09:07:56] Entering M.D.
NNODES=4, MYRANK=1, HOSTNAME=***
NNODES=4, MYRANK=3, HOSTNAME=***
NNODES=4, MYRANK=0, HOSTNAME=***
NODEID=0 argc=20
NODEID=1 argc=20
NNODES=4, MYRANK=2, HOSTNAME=***
NODEID=2 argc=20
NODEID=3 argc=20
Reading file work/wudata_05.tpr, VERSION 3.3.99_development_20070618 (single precision)
Note: tpx file_version 48, software version 68

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 1D domain decomposition 1 x 1 x 4
starting mdrun '22878 system in water'
40000004 steps,  80000.0 ps (continuing from step 39750004,  79500.0 ps).

t = 79500.012 ps: Water molecule starting at atom 132199 can not be settled.
Check for bad contacts and/or reduce the timestep.

t = 79500.012 ps: Water molecule starting at atom 60856 can not be settled.
Check for bad contacts and/or reduce the timestep.
[09:08:13]  (0%)
[09:08:13] 
[09:08:13] Folding@home Core Shutdown: INTERRUPTED
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0

This unit have been assigned to me several times. Can't get another one. Please, someone, fix this.

[kasson]

deleted.