From: Anna Modzelewska (modzelewska.namd_at_gmail.com)
Date: Mon Jul 28 2014 - 05:56:05 CDT
I am trying to run accelerated MD for the first time.
I have run several classic MD before, sometimes with errors, but usually I
could identify their source.
Now, I get "segmentation fault" message in my terminal window and no other
NAMD output just cut with no error message after bellow section:
Info: Entering startup at 2.94229 s, 2181.94 MB of memory in use
Info: Startup phase 0 took 0.000176191 s, 2181.94 MB of memory in use
Info: Startup phase 1 took 0.080847 s, 2218.17 MB of memory in use
Info: Startup phase 2 took 0.00411892 s, 2218.17 MB of memory in use
Info: Startup phase 3 took 0.000150919 s, 2218.17 MB of memory in use
Info: PATCH GRID IS 7 (PERIODIC) BY 4 (PERIODIC) BY 9 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY -0.0255745 0.0124505 -0.0060263
Info: LARGEST PATCH (141) HAS 644 ATOMS
Info: Startup phase 4 took 0.0501051 s, 2241.56 MB of memory in use
Info: PME using 26 and 24 processors for FFT and reciprocal sum.
Info: PME USING 1 GRID NODES AND 1 TRANS NODES
Info: PME GRID LOCATIONS: 1 2 3 4 5 6 7 9 10 11 ...
Info: PME TRANS LOCATIONS: 1 2 3 4 5 6 8 9 10 12 ...
Info: Startup phase 5 took 0.00427699 s, 2241.56 MB of memory in use
Info: Startup phase 6 took 0.00360703 s, 2241.56 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 7 took 0.004668 s, 2241.56 MB of memory in use
Info: CREATING 4998 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Input structure comes from 100ns classic MD simulation, configuration file
is the same as for cMD, just aMD section is added.
I run it on the same workstation as cMD, I use
NAMD_2.9_Linux-x86_64-multicore and NAMD_2.9_Linux-x86_64-multicore-CUDA
versions, it crashes on both.
Could anyone help me to identify the source of error?
I know there were few very similar questions on the list, but with no reply.
Thanks and regards
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