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

Dallas Warren dallas.warren at monash.edu
Thu Oct 5 00:33:31 CEST 2017


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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