From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Oct 30 2013 - 11:09:44 CDT
1 - No.
2 - Doesn't matter here most of the cases.
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von James Starlight
Gesendet: Mittwoch, 30. Oktober 2013 14:13
An: Namd Mailing List
Betreff: Re: namd-l: Two GPU-based workstation
Some extra questions-
1- Do I need special drivers optimizing dual GPU in Debian ?
2- Should I compile NAMD from sources for optimal performance ? Previouslu
I've used NAMD from Binaries ( using 1 gPU + 4 cores of i5 )
James
2013/10/29 Norman Geist <norman.geist_at_uni-greifswald.de>
>Just remember, NAMD is very memory bandwidth hungry.
Guess you mean PCIE bandwidth hungry?
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Ajasja Ljubetic
Gesendet: Dienstag, 29. Oktober 2013 14:34
An: James Starlight
Cc: Norman Geist; Namd Mailing List
Betreff: Re: namd-l: Two GPU-based workstation
As I've told I have typical desktop with 6 pci/e slots and 1 coreI7 (4
cores) + 2 GPU + 4 RAM slots (each of 4gb or 8gb I dont remember it now
clearly :) ). I'd like to launch simulations ( water soluble as well as
membrane proteins using NAMD with the explicit solvents (50k and 80k atoms
resp) using both GPUs simultaneously and CPU for one run.
What another extra modification of my desktop as well as simulation
parameters should I take into account? Are any other specified drivers
needed for typical Linux-based multi GPU workstation?
Make sure to pick a motherboard with two 16x speed PCIE ports. (Probably
PCIE 3.0?). Personally I don't think you will see the scaling you desire.
I.e., the GPUs will be underutilized. But then again, YMMV. Just remember,
NAMD is very memory bandwidth hungry.
Best regards,
Ajasja
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