VMD-L Mailing List

From: toshiaki.tomimori_at_uniadex.co.jp
Date: Wed Aug 03 2022 - 06:10:01 CDT

Subject: Multi-core CPU does not work with VMD.

Hi, can anyone advise me to solve these? Just wondering this is not the VMD work usually.

This is what I'm considering using VMD with VMware and NVIDIA vGPU.
The GPU used is NVIDIA A40 and the vGPU profile is nvidia_a40-8q.
There are doubtful points when I try how the VMD work on VDI. If these are not the usual behaviors, I would like to know how to solve these.

The combinations evaluated are as follows:
VMD version 1.9.3 + RHEL 8.4
VMD version 1.9.3 + RHEL 7.9
VMD version 1.9.4 + RHEL 7.9
There are the same results to me, in all conditions.

Looks like CPU is single core processed.
I used MD sample data of just one million atoms. I set to "VDW" as "Drawing Method of Graphics", the drawing performance was significantly slower. In the "top" command confirmed on the RHEL side, the load is leaned only to "Cpu6".

================================================================================
%Cpu0 : 0.0 us, 0.4 sy, 0.0 ni, 99.6 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu1 : 0.0 us, 0.0 sy, 0.0 ni,100.0 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu2 : 0.0 us, 0.4 sy, 0.0 ni, 99.6 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu3 : 0.0 us, 0.0 sy, 0.0 ni,100.0 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu4 : 0.0 us, 0.0 sy, 0.0 ni,100.0 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu5 : 0.0 us, 0.0 sy, 0.0 ni,100.0 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu6 : 99.6 us, 0.4 sy, 0.0 ni, 0.0 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu7 : 0.4 us, 0.4 sy, 0.0 ni, 99.3 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu8 : 0.0 us, 0.4 sy, 0.0 ni, 99.6 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu9 : 0.4 us, 0.0 sy, 0.0 ni, 99.6 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu10 : 0.0 us, 0.4 sy, 0.0 ni, 99.6 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu11 : 0.0 us, 0.0 sy, 0.0 ni,100.0 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu12 : 0.0 us, 0.0 sy, 0.0 ni,100.0 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu13 : 0.0 us, 0.0 sy, 0.0 ni,100.0 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu14 : 0.0 us, 0.0 sy, 0.0 ni,100.0 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
%Cpu15 : 0.0 us, 0.0 sy, 0.0 ni,100.0 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
KiB Mem : 12135108 total, 8341144 free, 2587752 used, 1206212 buff/cache
KiB Swap: 6160380 total, 6160380 free, 0 used. 9199748 avail Mem
=================================================================================

According to the "VMD version 1.9.3 user guide", VMD also supports GPU acceleration using CUDA, and takes advantage of both multi-core CPUs and GPUs for acceleration of electrostatics. I thought the load should balanced to multi CPUs, but it seems like not. Can anyone advise me the setting for making be balanced the load to multi CPUs?

Multi-core CPU and GPU acceleration:
https://www.ks.uiuc.edu/Research/vmd/current/ug/node13.html