[gmx-users] using dual CPU's

[pbuscemi at q.com]

Szilard,

I get an "unknown command " gpustasks  in :

'mdrun -ntmpi N -npme 1 -nb gpu -pme gpu -gpustasks TASKSTRING 

where > typically N = 4, 6, 8 are worth a try (but N <= #cores) and the > TASKSTRING should have N digits with either N-1 zeros and the last 1 
> or N-2 zeros and the last two 1, i.e..

Would you please complete the i.e...

Thanks again,
Paul



-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of paul buscemi
Sent: Tuesday, December 11, 2018 5:56 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] using dual CPU's

Szilard,

Thank you vey much for the information and I apologize how the text appeared - internet demons at work.

The computer described in the log files is a basic test rig which we use to iron out models. The workhorse is a many core AMD with now one and hopefully soon to be two 2080ti’s,  It will have to handle several 100k particles and at the moment do not think the simulation could be divided. These are essentially of  a multi component ligand adsorption from solution onto a substrate  including evaporation of the solvent.

I saw from a 2015 paper form your group  “ Best bang for your buck: GPU nodes for GROMACS biomolecular simulations “ that I should expect maybe a 50% improvement for 90k atoms ( with  2x  GTX 970 ) What bothered me in my initial attempts was that my simulations became slower by adding the second GPU - it was frustrating to say the least

I’ll give your suggestions a good workout, and report on the results when I hack it out..

Bes
Paul

> On Dec 11, 2018, at 12:14 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:
> 
> Without having read all details (partly due to the hard to read log 
> files), what I can certainly recommend is: unless you really need to, 
> avoid running single simulations with only a few 10s of thousands of 
> atoms across multiple GPUs. You'll be _much_ better off using your 
> limited resources by running a few independent runs concurrently. If 
> you really need to get maximum single-run throughput, please check 
> previous discussions on the list on my recommendations.
> 
> Briefly, what you can try for 2 GPUs is (do compare against the 
> single-GPU runs to see if it's worth it):
> mdrun -ntmpi N -npme 1 -nb gpu -pme gpu -gpustasks TASKSTRING where 
> typically N = 4, 6, 8 are worth a try (but N <= #cores) and the 
> TASKSTRING should have N digits with either N-1 zeros and the last 1 
> or N-2 zeros and the last two 1, i.e..
> 
> I suggest to share files using a cloud storage service like google 
> drive, dropbox, etc. or a dedicated text sharing service like 
> paste.ee, pastebin.com, or termbin.com -- especially the latter is 
> very handy for those who don't want to leave the command line just to 
> upload a/several files for sharing (i.e. try "echo "foobar" | nc 
> termbin.com 9999)
> 
> --
> Szilárd
> On Tue, Dec 11, 2018 at 2:44 AM paul buscemi <pbuscemi at q.com> wrote:
>> 
>> 
>> 
>>> On Dec 10, 2018, at 7:33 PM, paul buscemi <pbuscemi at q.com> wrote:
>>> 
>>> 
>>> Mark, attached are the tail ends of three  log files for the same 
>>> system but run on an AMD 8  Core/16 Thread 2700x, 16G ram In 
>>> summary:
>>> for ntpmi:ntomp of 1:16 , 2:8, and auto selection (4:4) are 12.0, 8.8 , and 6.0 ns/day.
>>> Clearly, I do not have a handle on using 2 GPU's
>>> 
>>> Thank you again, and I'll keep probing the web for more understanding.
>>> I’ve propbably sent too much of the log, let me know if this is the 
>>> case
>> Better way to share files - where is that friend ?
>>> 
>>> Paul
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