Code: Select all
[05:01:32] Initial: 43AB; - Successful: assigned to (171.67.108.24).
[05:01:32] + News From Folding@Home: Welcome to Folding@Home
[05:01:32] Loaded queue successfully.
[05:01:32] Connecting to http://171.67.108.24:8080/
[05:01:40] Posted data.
[05:01:40] Initial: 0000; - Receiving payload (expected size: 1507339)
[05:01:43] - Downloaded at ~490 kB/s
[05:01:43] - Averaged speed for that direction ~457 kB/s
[05:01:43] + Received work.
[05:01:43] Trying to send all finished work units
[05:01:43] + No unsent completed units remaining.
[05:01:43] + Closed connections
[05:01:43]
[05:01:43] + Processing work unit
[05:01:43] Core required: FahCore_a2.exe
[05:01:43] Core found.
[05:01:43] Working on Unit 00 [September 11 05:01:43]
[05:01:43] + Working ...
[05:01:43] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 00 -checkpoint 15 -verbose -lifeline 2780 -version 602'
[05:01:43]
[05:01:43] *------------------------------*
[05:01:43] Folding@Home Gromacs SMP Core
[05:01:43] Version 2.10 (Sun Aug 30 03:43:28 CEST 2009)
[05:01:43]
[05:01:43] Preparing to commence simulation
[05:01:43] - Ensuring status. Please wait.
[05:01:43] Files status OK
[05:01:43] - Expanded 1506827 -> 24012993 (decompressed 1593.6 percent)
[05:01:43] Called DecompressByteArray: compressed_data_size=1506827 data_size=24012993, decompressed_data_size=24012993 diff=0
[05:01:44] - Digital signature verified
[05:01:44]
[05:01:44] Project: 2671 (Run 12, Clone 40, Gen 89)
[05:01:44]
[05:01:44] Assembly optimizations on if available.
[05:01:44] Entering M.D.
[05:01:53] Run 12, Clone 40, Gen 89)
[05:01:53]
[05:01:53] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=tinalinux
NNODES=4, MYRANK=1, HOSTNAME=tinalinux
NNODES=4, MYRANK=3, HOSTNAME=tinalinux
NODEID=0 argc=20
NODEID=1 argc=20
Reading file work/wudata_00.tpr, VERSION 3.3.99_development_20070618 (single precision)
NNODES=4, MYRANK=2, HOSTNAME=tinalinux
NODEID=2 argc=20
NODEID=3 argc=20
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 '22884 system in water'
22500000 steps, 45000.0 ps (continuing from step 22250000, 44500.0 ps).
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090605
Source code file: md.c, line: 2169
Fatal error:
NaN detected at step 22250000
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 1, will try to stop all the nodes
Halting parallel program mdrun on CPU 1 out of 4
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090605
Source code file: md.c, line: 2169
Fatal error:
NaN detected at step 22250000
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 2, will try to stop all the nodes
Halting parallel program mdrun on CPU 2 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
gcq#0: Thanx for Using GROMACS - Have a Nice Day
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 1
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090605
Source code file: md.c, line: 2169
Fatal error:
NaN detected at step 22250000
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 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
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090605
Source code file: md.c, line: 2169
Fatal error:
NaN detected at step 22250000
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 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
[05:02:19] Completed 0 out of 250000 steps (0%)
[05:02:23] CoreStatus = FF (255)
[05:02:23] Client-core communications error: ERROR 0xff
[05:02:23] Deleting current work unit & continuing...
[0]0:Return code = 0, signaled with Quit
[0]1:Return code = 0, signaled with Quit
[05:02:37] - Warning: Could not delete all work unit files (0): Core file absent
[05:02:37] Trying to send all finished work units
[05:02:37] + No unsent completed units remaining.
[05:02:37] - Preparing to get new work unit...
[05:02:37] + Attempting to get work packet
[05:02:37] - Will indicate memory of 7200 MB
[05:02:37] - Connecting to assignment server
[05:02:37] Connecting to http://assign.stanford.edu:8080/
[05:02:37] Posted data.
[05:02:37] Initial: 43AB; - Successful: assigned to (171.67.108.24).
[05:02:37] + News From Folding@Home: Welcome to Folding@Home
[05:02:37] Loaded queue successfully.
[05:02:37] Connecting to http://171.67.108.24:8080/
[05:02:45] Posted data.
[05:02:45] Initial: 0000; - Receiving payload (expected size: 1507339)
[05:02:48] - Downloaded at ~490 kB/s
[05:02:48] - Averaged speed for that direction ~463 kB/s
[05:02:48] + Received work.
[05:02:48] + Closed connections
[05:02:53]
[05:02:53] + Processing work unit
[05:02:53] Core required: FahCore_a2.exe
[05:02:53] Core found.
[05:02:53] Working on Unit 01 [September 11 05:02:53]
[05:02:53] + Working ...
[05:02:53] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 01 -checkpoint 15 -verbose -lifeline 2780 -version 602'
[05:02:53]
[05:02:53] *------------------------------*
[05:02:53] Folding@Home Gromacs SMP Core
[05:02:53] Version 2.10 (Sun Aug 30 03:43:28 CEST 2009)
[05:02:53]
[05:02:53] Preparing to commence simulation
[05:02:53] - Ensuring status. Please wait.
[05:03:02] - Looking at optimizations...
[05:03:02] - Working with standard loops on this execution.
[05:03:02] - Files status OK
[05:03:03] - Expanded 1506827 -> 24012993 (decompressed 1593.6 percent)
[05:03:03] Called DecompressByteArray: compressed_data_size=1506827 data_size=24012993, decompressed_data_size=24012993 diff=0
[05:03:03] - Digital signature verified
[05:03:03]
[05:03:03] Project: 2671 (Run 12, Clone 40, Gen 89)
[05:03:03]
[05:03:03] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=tinalinux
NNODES=4, MYRANK=2, HOSTNAME=tinalinux
NNODES=4, MYRANK=3, HOSTNAME=tinalinux
NNODES=4, MYRANK=1, HOSTNAME=tinalinux
NODEID=0 argc=20
NODEID=1 argc=20
NODEID=2 argc=20
NODEID=3 argc=20
Reading file work/wudata_01.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 '22884 system in water'
22500000 steps, 45000.0 ps (continuing from step 22250000, 44500.0 ps).
[05:03:29] Completed 0 out of 250000 steps (0%)
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090605
Source code file: md.c, line: 2169
Fatal error:
NaN detected at step 22250000
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 2, will try to stop all the nodes
Halting parallel program mdrun on CPU 2 out of 4
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090605
Source code file: md.c, line: 2169
Fatal error:
NaN detected at step 22250000
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 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
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090605
Source code file: md.c, line: 2169
Fatal error:
NaN detected at step 22250000
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 1, will try to stop all the nodes
Halting parallel program mdrun on CPU 1 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090605
Source code file: md.c, line: 2169
Fatal error:
NaN detected at step 22250000
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 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
gcq#0: Thanx for Using GROMACS - Have a Nice Day
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 1
[05:03:33] CoreStatus = FF (255)
[05:03:33] Client-core communications error: ERROR 0xff
[05:03:33] Deleting current work unit & continuing...
[0]0:Return code = 0, signaled with Quit
[0]1:Return code = 0, signaled with Quit
[05:03:47] - Warning: Could not delete all work unit files (1): Core file absent
[05:03:47] Trying to send all finished work units
[05:03:47] + No unsent completed units remaining.
[05:03:47] - Preparing to get new work unit...
[05:03:47] + Attempting to get work packet
[05:03:47] - Will indicate memory of 7200 MB
[05:03:47] - Connecting to assignment server
[05:03:47] Connecting to http://assign.stanford.edu:8080/
[05:03:47] Posted data.
[05:03:47] Initial: 43AB; - Successful: assigned to (171.67.108.24).
[05:03:47] + News From Folding@Home: Welcome to Folding@Home
[05:03:48] Loaded queue successfully.
[05:03:48] Connecting to http://171.67.108.24:8080/
[05:03:56] Posted data.
[05:03:56] Initial: 0000; - Receiving payload (expected size: 1507339)
[05:03:59] - Downloaded at ~490 kB/s
[05:03:59] - Averaged speed for that direction ~469 kB/s
[05:03:59] + Received work.
[05:03:59] + Closed connections
[05:04:04]
[05:04:04] + Processing work unit
[05:04:04] Core required: FahCore_a2.exe
[05:04:04] Core found.
[05:04:04] Working on Unit 02 [September 11 05:04:04]
[05:04:04] + Working ...
[05:04:04] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 02 -checkpoint 15 -verbose -lifeline 2780 -version 602'
[05:04:04]
[05:04:04] *------------------------------*
[05:04:04] Folding@Home Gromacs SMP Core
[05:04:04] Version 2.10 (Sun Aug 30 03:43:28 CEST 2009)
[05:04:04]
[05:04:04] Preparing to commence simulation
[05:04:04] - Ensuring status. Please wait.
[05:04:13] - Looking at optimizations...
[05:04:13] - Working with standard loops on this execution.
[05:04:13] - Files status OK
[05:04:14] - Expanded 1506827 -> 24012993 (decompressed 1593.6 percent)
[05:04:14] Called DecompressByteArray: compressed_data_size=1506827 data_size=24012993, decompressed_data_size=24012993 diff=0
[05:04:14] - Digital signature verified
[05:04:14]
[05:04:14] Project: 2671 (Run 12, Clone 40, Gen 89)
[05:04:14]
[05:04:14] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=tinalinux
NNODES=4, MYRANK=1, HOSTNAME=tinalinux
NNODES=4, MYRANK=2, HOSTNAME=tinalinux
NNODES=4, MYRANK=3, HOSTNAME=tinalinux
NODEID=0 argc=20
NODEID=1 argc=20
NODEID=2 argc=20
Reading file work/wudata_02.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=3 argc=20
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 '22884 system in water'
22500000 steps, 45000.0 ps (continuing from step 22250000, 44500.0 ps).
-----------------------------------[05:04:40] Completed 0 out of 250000 steps (0%)
[05:04:40]
[05:04:40] Folding@home Core Shutdown: INTERRUPTED
--------------------
Program mdrun, VERSION 4.0.99_development_20090605
Source code file: md.c, line: 2169
Fatal error:
NaN detected at step 22250000
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 1, will try to stop all the nodes
Halting parallel program mdrun on CPU 1 out of 4
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090605
Source code file: md.c, line: 2169
Fatal error:
NaN detected at step 22250000
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 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
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
gcq#0: Thanx for Using GROMACS - Have a Nice Day
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 1
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090605
Source code file: md.c, line: 2169
Fatal error:
NaN detected at step 22250000
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 2, will try to stop all the nodes
Halting parallel program mdrun on CPU 2 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
[05:04:44] CoreStatus = FF (255)
[05:04:44] Client-core communications error: ERROR 0xff
[05:04:44] - Attempting to download new core...
[05:04:44] + Downloading new core: FahCore_a2.exe
[05:04:44] Downloading core (/~pande/Linux/x86/Core_a2.fah from http://www.stanford.edu)
[05:04:44] Initial: AFDE; + 10240 bytes downloaded
[05:04:44] Initial: E2DE; + 20480 bytes downloaded
[05:04:45] Initial: 10DD; + 30720 bytes downloaded