From: Éric Germaneau (germaneau_at_sjtu.edu.cn)
Date: Mon Mar 21 2016 - 22:20:54 CDT
This is really helpful, thank you so munch.
On 03/21/2016 04:31 PM, Norman Geist wrote:
> Ok in that case: The STMV and APOA1 benchmarks are widely used as
> reference for large and medium sized systems. Scaling one and the same
> system isn’t that straight forward, or reasonable. If you want an easy
> to scale system, you could build systems of just water for different
> box sizes, this can be done using VMD and the Solvate plugin for
> instance. In case you want to benchmark on GPUs, you may want to test
> the impact of “twoaway[xyz] yes” consecutive in the namd job script
> aswell as +ignoresharing on the commandline.
> Best of luck
> Norman Geist
> *Von:*Eric Germaneau [mailto:germaneau_at_sjtu.edu.cn]
> *Gesendet:* Montag, 21. März 2016 09:15
> *An:* Norman Geist <norman.geist_at_uni-greifswald.de>
> *Cc:* namd-l_at_ks.uiuc.edu
> *Betreff:* Re: AW: namd-l: Testing NAMD scalability
> I didn't say I don't have any MD experience, I'm just not a namd user.
> Sent using CloudMagic Email
> On Mon, Mar 21, 2016 at 3:46 PM, Norman Geist
> <mailto:norman.geist_at_uni-greifswald.de>> wrote:
> Similar question have been asked in the past. Maybe search the
> mailing list archive. Away from that, the NAMD folks do offer
> benchmark systems of various size for download, which are a
> good point to start.
> BTW. as I pointed out in earlier posts, I highly doubt that
> anybody without MD experience can carry out reliable benchmarks.
> Norman Geist
> [mailto:owner-namd-l_at_ks.uiuc.edu] *Im Auftrag von *Éric Germaneau
> *Gesendet:* Samstag, 19. März 2016 02:32
> *An:* namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
> *Betreff:* namd-l: Testing NAMD scalability
> Dear all,
> I'm not a NAMD user but I nned to test its scalability on our
> Can someone tell me how to generate different size of the same
> Can I take any of those case studies
> <https://www-s.ks.uiuc.edu/Training/CaseStudies/> and scale them?
> Thank you.
> Éric Germaneau (艾海克), Specialist
> Center for High Performance Computing
> Shanghai Jiao Tong University
> Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China
> Email:germaneau_at_sjtu.edu.cn Mobi:+86-136-4161-6480
-- Éric Germaneau (艾海克), Specialist Center for High Performance Computing Shanghai Jiao Tong University Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China Email:germaneau_at_sjtu.edu.cn Mobi:+86-136-4161-6480 http://hpc.sjtu.edu.cn
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