From: yjcoshc (yjcoshc_at_gmail.com)
Date: Fri Jul 31 2020 - 14:43:11 CDT
Hi Michael,
Thanks for sharing the files! I can reproduce the error and I think it
is probably related to the water molecule.
Haochuan Chen
在 2020/7/31 上午11:01, Michael Von Domaros 写道:
> Thanks to both of you for offering to help!
>
> I uploaded all relevant files to this github repository:
> https://github.com/mvondomaros/namd3_test
>
> Cheers,
> Michael
>
> On Fri, Jul 31, 2020 at 5:01 AM De Carvalho Maia, Julio Daniel
> <jmaia_at_illinois.edu <mailto:jmaia_at_illinois.edu>> wrote:
>
> Hi Michael,
>
> Thanks for trying the offloaded integrator.
> If you can send me your files, I can quickly take a look at what’s
> wrong and get back to you ASAP.
>
> Best,
>
> ------------------------------------------------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu>
> <owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu>> on
> behalf of Michael Von Domaros <mvondoma_at_uci.edu
> <mailto:mvondoma_at_uci.edu>>
> *Sent:* Thursday, July 30, 2020 6:43:15 PM
> *To:* namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
> <namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>>
> *Subject:* namd-l: [3.0alpha5] Low global CUDA exclusion count.
> System is stable without cudaSOAIntegrate or without rigidBonds.
>
> Hi everyone,
> I'm simulating a single TIP3P water molecule in some lipids (PME,
> NPT, ambient conditions). The system has been running stable on
> CPUs for over 20 ns with NAMD 2.14b2. It is also running with NAMD
> 3.0alpha5 on a GPU if I use the old offloading scheme. Finally, it
> continues to run well with these versions/configs.
> Once I turn on cudaSOAIntegrate, set margin to 4, and remove the
> pair list updating settings, as recommended, I immediately get:
> FATAL ERROR: Low global CUDA exclusion count! (136304 vs 136307)
> System unstable or pairlistdist or cutoff too small.
> If I turn off rigidBonds, everything is fine again.
> Exactly the same system, but with small organic molecules instead
> of water, is running stable with 3.0alpha5 and with
> cudaSOAIntegrate + rigidBonds on.
> So I thought something might be broken with water, but I can
> simulate both the apoa1 benchmark and an isolated water molecule
> (with NAMD 3.0alpha5, cudaSOAIntegrate + rigidBonds on).
> I tried increasing pairListDist to 16, reducing the timestep to
> 0.1 (and at the same time using equal timesteps for all forces),
> increasing margin to 8, all without success. Visual inspection of
> the starting structure did not reveal anything odd to me.
> Does anyone have suggestions on what else I could try?
> Thanks a bunch for your help,
> Michael
> I uploaded the config and output files to:
> https://gist.github.com/mvondomaros/0430f2ed7a8409522e3f1f49e897766e
>
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