[gmx-developers] GROMACS 4.0.1 still broken on Bluegene

Erik Lindahl lindahl at cbr.su.se
Sun Nov 9 16:27:19 CET 2008


Nope, for BG we currently rely on people like you testing it :-)

Please keep sending your patches!

You might want to hold off with the 4.0.2 I just put on the website.  
Apparently somebody has been committing stuff that disables the water- 
water detection & optimization. Trying to debug it now...



On Nov 9, 2008, at 3:32 PM, Mark Abraham wrote:

> Erik Lindahl wrote:
>> Hi,
>> Sorry, me too - I always use the default settings when retrieving  
>> my to-do list, so I too missed it.
>> I'll see if I can make an instant 4.0.2 tomorrow, that also has  
>> makefiles for windows. Then it's binary time!
> Erik's helpfully fixed the earlier issues I've noted with BlueGene,  
> along with some more I found today at http://bugzilla.gromacs.org/show_bug.cgi?id=250 
>  and http://bugzilla.gromacs.org/show_bug.cgi?id=252
> There can't have been any kind of real-world testing of this code:
> * Any non-solvent charge groups in a neighbour-list of more than 6  
> atoms would have produced erroneous Coulomb energies and forces for  
> a third of the interactions. (In my case, an equilibrated system  
> blew up in under 20 steps.)
> * I suspect RF and cutoff have a sign error in generating fscal, but  
> haven't tested or analysed the code to my satisfaction yet.
> * Any double-precision build would have failed.
> However, once I applied some fixes, a no-solvent-loop simulation of  
> 50K atoms under PME is running stably on 32 processors under both  
> single and double precision.
> I haven't gotten around to looking at the water-optimized loops yet,  
> but I will, and will test things out with gmxtest.pl as well.
> Mark
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