Re: [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds.

From: yjcoshc (
Date: Thu Jul 30 2020 - 20:17:40 CDT

Hi Michael,

Are you able to share a test case for reproducing the error and
debugging? The logs look fine.


Haochuan Chen

在 2020/7/30 下午6:43, Michael Von Domaros 写道:
> 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:

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:13 CST