From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Wed Dec 05 2012 - 10:43:57 CST
Greetings,
Although I can run unbiased MD in implicit solvent with NAMD2.9
CVS-2012-11-19 Linux-x86_64-multicore using multiple threads, when I switch
to aMD I get a segmentation fault. However, I can run aMD in serial mode.
Below are the last lines of NAMD output. Does anyone have any idea what may
be wrong?
$ namd2 +setcpuaffinity +p8 ./prod.amber.GB.aMD.namd
..
Info: Reading from binary file ../../cMD/extendedEnds/cMDrun1.restart.coor
Info:
Info: Entering startup at 0.0573871 s, 598.43 MB of memory in use
Info: Startup phase 0 took 7.39098e-05 s, 598.43 MB of memory in use
Info: ADDED 0 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 0.00340199 s, 598.867 MB of memory in use
Info: Startup phase 2 took 5.31673e-05 s, 598.867 MB of memory in use
Info: Startup phase 3 took 4.48227e-05 s, 598.867 MB of memory in use
Info: Startup phase 4 took 0.000200033 s, 598.867 MB of memory in use
Info: Startup phase 5 took 5.4121e-05 s, 598.867 MB of memory in use
Info: PATCH GRID IS 2 BY 2 BY 2
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: Reading from binary file ../../cMD/extendedEnds/cMDrun1.restart.vel
Info: REMOVING COM VELOCITY -0.109981 0.0393109 0.148996
patch 0 (0 0 0) has 350 atoms
patch 1 (1 0 0) has 349 atoms
patch 2 (0 1 0) has 349 atoms
patch 3 (1 1 0) has 349 atoms
patch 4 (0 0 1) has 350 atoms
patch 5 (1 0 1) has 349 atoms
patch 6 (0 1 1) has 350 atoms
patch 7 (1 1 1) has 350 atoms
Info: LARGEST PATCH (0) HAS 350 ATOMS
assignPatchesRecursiveBisection
Info: Startup phase 6 took 0.00205994 s, 599.555 MB of memory in use
Info: Startup phase 7 took 5.60284e-05 s, 599.555 MB of memory in use
Info: Startup phase 8 took 0.000134945 s, 599.555 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 9 took 0.000128031 s, 599.555 MB of memory in use
Info: CREATING 116 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000290327 AT 0.251946
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0136312 AT 12.9976
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.0596145 AT 12.9976
Info: useSync: 1 useProxySync: 0
Info: Startup phase 10 took 0.0014329 s, 599.914 MB of memory in use
Info: Startup phase 11 took 0.000105143 s, 599.914 MB of memory in use
Info: Startup phase 12 took 7.39098e-05 s, 599.914 MB of memory in use
Info: Finished startup at 0.0652061 s, 599.914 MB of memory in use
TCL: Running for 10000000 steps
Segmentation fault (core dumped)
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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