[CP2K:3629] NEB: number of replicas, cpus and input files

Teodoro Laino teodor... at gmail.com
Thu Nov 24 06:39:05 CET 2011


Hi Jörg,

both you and Carlo are correct. That's the way replica/nproc_rep are working.
If the error you get is in : neb_utils:build_replica_coords, then your problem is somewhere else.

Posting the motion section online it would help a lot!
Thanks,
Teo

On Nov 24, 2011, at 12:48 AM, Jörg Saßmannshausen wrote:

> Hi Carlo,
> 
> gosh that was quick!
> 
> I got 8 cores per box, so that is where the cores come from.
> I got 17 points I want to run, hence the 17 files.
> 
> Right now I only got 32 cores alltogether.
> 
> So my train of thoughts were similar to yours: 8 replicas and each replica is 
> using 4 cores adds up to 32 cores. 
> However, that crashed with that error message:
> ERRORL2 in neb_utils:build_replica_coords processor
> 
> So in the end I decided to use 32 replicas and 32 nproc_rep for the 32 cores I 
> have. I guess one could do better. ,-)
> 
> All the best
> 
> Jörg
> 
> 
> On Mittwoch 23 November 2011 c.pignedoli wrote:
>> Ciao Joerg,
>> why 17 files an 8 replicas?
>> 
>> If i remember well:
>> if you have 8 replicas an specify 100 nproc_rep
>> then if you run with 200 cores
>> 
>> you will have two replicas done at a time (each with 100 cores), then other
>> two then other two finally the last two
>> 
>> and you cicle.
>> 
>> if you run with 800 cores all replicas will proceed in parallel
>> 
>> Ciao
>> 
>> Carlo
>> 
>> On 24/nov/2011, at 00:05, Jörg Saßmannshausen <j.sassma... at ucl.ac.uk> 
> wrote:
>>> Dear all,
>>> 
>>> I am a bit confused.
>>> When I am running a frequency calculation or a NEB calculation, I can
>>> specify the number of replicas (NUMBER_OF_REPLICA) and the number of
>>> processors (NPROC_REP) in the MOTION section. Now, lets say I got 32
>>> cores on my hands and I got 17 files which I want to use for the NEB
>>> calculation. Now, my understanding was that I could run say 8 replicas
>>> and each replica is using 4 cores. That would add up to the 32 cores I
>>> have alltogether. However, that does not work out. It appears I got to
>>> use 32 replicas and 32 cores for all 32 cores I have available. What is
>>> the relationship between replicas and cores (in the input file) with the
>>> cores I have available on the machine (an in relation to the number of
>>> coordinate files I have). A similar observation was made for a frequency
>>> calculation.
>>> 
>>> I seem to have somehow a wrong understanding here :-/
>>> 
>>> All the best from a foggy London
>>> 
>>> Jörg
>>> 
>>> 
>>> --
>>> *************************************************************
>>> Jörg Saßmannshausen
>>> University College London
>>> Department of Chemistry
>>> Gordon Street
>>> London
>>> WC1H 0AJ
>>> 
>>> email: j.sassma... at ucl.ac.uk
>>> web: http://sassy.formativ.net
>>> 
>>> Please avoid sending me Word or PowerPoint attachments.
>>> See http://www.gnu.org/philosophy/no-word-attachments.html
>>> 
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> 
> 
> 
> -- 
> *************************************************************
> Jörg Saßmannshausen
> University College London
> Department of Chemistry
> Gordon Street
> London
> WC1H 0AJ 
> 
> email: j.sassma... at ucl.ac.uk
> web: http://sassy.formativ.net
> 
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
> 
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