VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Jan 31 2019 - 09:04:40 CST

Hi Jrhau,

Thank you for reporting the error. The error that you are seeing is related
to the system size and the number of CPU cores+GPU that you selected to run
your simulation. I would guess that the system you are running is not that
big to justify many cores plus a GPU. Reduce the number of CPU cores and
the simulation should run smoothly.

Now, on the performance of the multicore version of VMD, did you run
exactly the same configuration file?

Please allow me to add some notes about the configuration files produced by
QwikMD. QwikMD has a lot of ludic behavior in the selection of the MD
parameters in the config files, namely, high frequency of energy outputs
and trajectory saving frequency (dcd freq), which is useful when you are
starting running simulations but has high penalties in the NAMD
performance. Also, running your simulations with the option "Live view"
mode (Interactive Molecular Dynamics activated) also decreases your
performance substantially, as NAMD-VMD communication occurs every so often.

In summary, if you are trying to squeeze the most ns/day from your machine,
please increase periods of saving frames (dcd freq) and output events
(outputpressure, outputenergies and etc.) and run your simulations in the
background (Live view off == IMDon off).

I hope this helps and I am also copying the NAMD developers on this thread
so they can comment further on the NAMD issues and how to improve NAMD
performance.

Best

Joao

On Thu, Jan 31, 2019 at 5:44 AM jrhau lung <jrhaulung_at_gmail.com> wrote:

> 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
>
>
> 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851