[gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

[Dallas Warren]

Done Mark, thanks.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 4 October 2017 at 02:37, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> Hi,
>
> I'm sure we have opportunities to improve this code - please do file a
> redmine issue with repro inputs so we can profile and see!
>
> Thanks,
>
> Mark
>
> On Tue, Oct 3, 2017 at 3:05 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/2/17 11:14 PM, Dallas Warren wrote:
>> > Thanks for the reply Justin.
>> >
>> > I am just going to use the largest exclusion bond distance I can, then
>> > ignore the RDF of those beyond that distance.
>> >
>> > Seems curious to me (not actually understanding what grommp is
>> > generating) that the list is so large.  These are linear molecules, 38
>> > atoms, 60 molecules in total.
>>
>> It generates a matrix of all possible exclusions, sorts them, then removes
>> duplicates. So for nrexcl = 37 you need memory on the order of 37 * 37 *
>> 60 * (2
>> * sizeof(int)) - the factor of 2 for the atom numbers comes from the fact
>> that
>> you're actually allocating an array of type "sortable" which is a pair of
>> atom
>> numbers.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
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