VMD-L Mailing List

From: jrhau lung (jrhaulung_at_gmail.com)
Date: Thu Jan 31 2019 - 05:43:53 CST

Dear VMD friends:
    In order to run simulation on new Geforce RTX20 vedio card, a NAMD was
compiled from nightly build Git source to generate a
Linux-x86_64-multicore-CUDA
<https://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1584>
suported NAMD accroding to the recommend process in the relase note. The
compile was successful without any error and should be successful as the
Linux-x86_64-multicore
<https://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1584>
verion NAMD was also compiled before generating the CUDA supported version
and multicore version works fine with QwikMD in MD simulation.
Unfortunately, running MD simulation using the self-built CUDA NAMD, the
simulation aborted shortly after launch with the follwing messages. Any
suggestions and hints would be highly appreciated.

Info) Using multithreaded IMD implementation.
------------- Processor 64 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: ComputeBondedCUDA::copyTupleData, invalid number of
exclusions
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html

Charm++ fatal error:
FATAL ERROR: ComputeBondedCUDA::copyTupleData, invalid number of exclusions
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html

Info) IMD connection ended unexpectedly; connection terminated.

   Another issue would like to have your comments is the simulation speed
uisng self-built Linux-x86_64-multicore
<https://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1584>
NAMD is significantly slower than of the 2.13 multicore version. What
woulld be the potential causes for this? Is this related to the comfiling
tools or libs? Thanks

sincerely,

Jrhau