Re: domain decomposition problem

From: Javiera Guedes <javiera_at_ucolick.org>
Date: Tue, 17 Apr 2007 10:10:02 -0700

Thanks Yves,

I have tried increasing the TreeAllocFactor but I got the same error. I
run the same simulation before on my desktop computer for a few hours
and it run just fine. I don't understand why it doesn't run as smoothly
on a supercomputer cluster....
-Javiera

Yves Revaz wrote:
>
> Javiera,
>
> This problem occurs typically when the distance between two or more
> particles is to small compared to the system size. In this case, the
> tree must be
> very deep and the allocated memory is not large enough to contain it.
>
> If possible, you should increase the allocated memory to the tree
> construction,
> by increasing the parameter TreeAllocFactor.
>
> However, in some cases, especially when you have a very dissipative
> component, some particles may form clumps and it will be difficult to
> avoid the problem.
>
> Regards,
>
> Yves
>
>
>
>
> Javiera Guedes wrote:
>
>>
>> Hi all,
>>
>> I'm trying to use Gadget2 to evolve a galaxy with halo, gas, and star
>> particles. I was running this on a single processor until I got an
>> account at the Pleiades, a brand new supercomputer at UCSC. I get the
>> following error:
>>
>> **********************************************************
>> This is Gadget, version `2.0'.
>>
>> Running on 8 processors.
>>
>> Allocated 50 MByte communication buffer per processor.
>>
>> Communication buffer has room for 1008246 particles in gravity
>> computation
>> Communication buffer has room for 409600 particles in density
>> computation
>> Communication buffer has room for 327680 particles in hydro computation
>> Communication buffer has room for 304818 particles in domain
>> decomposition
>>
>>
>> Hubble (internal units) = 4.13479
>> G (internal units) = 0.999652
>> UnitMass_in_g = 6.30712e+48
>> UnitTime_in_s = 1.27586e+18
>> UnitVelocity_in_cm_per_s = 6.91e+07
>> UnitDensity_in_cgs = 9.20417e-30
>> UnitEnergy_in_cgs = 3.01153e+64
>>
>> Task=0 FFT-Slabs=32
>> Task=1 FFT-Slabs=32
>> Task=2 FFT-Slabs=32
>> Task=3 FFT-Slabs=32
>> Task=4 FFT-Slabs=32
>> Task=5 FFT-Slabs=32
>> Task=6 FFT-Slabs=32
>> Task=7 FFT-Slabs=32
>>
>> Allocated 8.0625 MByte for FFT kernel(s).
>>
>>
>> Allocated 20.0963 MByte for particle storage. 80
>>
>> Allocated 4.09163 MByte for storage of SPH data. 84
>>
>>
>> reading file `/home/javiera/ICs/MW1.bh.000.gadget' on task=0
>> (contains 1404834 particles.)
>> distributing this file to tasks 0-7
>> Type 0 (gas): 272409 (tot= 0000272409) masstab=0
>> Type 1 (halo): 951539 (tot= 0000951539) masstab=0
>> Type 2 (disk): 0 (tot= 0000000000) masstab=0
>> Type 3 (bulge): 0 (tot= 0000000000) masstab=0
>> Type 4 (stars): 180886 (tot= 0000180886) masstab=0
>> Type 5 (bndry): 0 (tot= 0000000000) masstab=0
>>
>> reading done.
>> Total number of particles : 0001404834
>>
>> allocated 0.0762939 Mbyte for ngb search.
>>
>> Allocated 15.6342 MByte for BH-tree. 64
>>
>> domain decomposition...
>> NTopleaves= 834
>>
>> *No domain decomposition that stays within memory bounds is possible.*
>>
>> **************************************************************
>>
>> The relevant options on my parameter files are:
>>
>> % Memory allocation
>>
>> PartAllocFactor 1.5
>> TreeAllocFactor 0.8
>> BufferSize 50 % in MByte
>>
>>
>> And my makefile options are:
>> OPT += -DUNEQUALSOFTENINGS
>> OPT += -DPEANOHILBERT
>> OPT += -DWALLCLOCK OPT += -DSYNCHRONIZATION
>>
>> Any suggestions would be much appreciated.
>>
>> Thanks,
>> -- Javiera
>>
>> -----------------------------------
>> Javiera Guedes UCSC Astronomy Department
>> javiera_at_astro.ucsc.edu
>> ph: (831) 459-5722 fax: (831) 459-5265
>> -----------------------------------
>>
>>
>>
>>
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>
>
>

-- 
-----------------------------------
        Javiera Guedes        
   UCSC Astronomy Department
    javiera_at_astro.ucsc.edu
     ph:  (831) 459-5722      
     fax: (831) 459-5265      
-----------------------------------
Received on 2007-04-17 19:10:06

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