[FLASH-USERS] 3D resolution

Mon Mar 3 09:17:43 EST 2008

Hi Mousumi,

Yes, there is a way.  In flash.par, specify Nblock(x,y,z) = (some  
number > 1).  This increases the number of blocks in the domain at  
refinement level one.  nxb,nyb,nzb set the number of zones per block.   
You can also go beyond 6 levels of refinement.

Sean

---------------------------------------------
Sean M. Couch
Graduate Research Assistant
Department of Astronomy
The University of Texas at Austin
1 University Station C1400
RLM 15.202A
(512) 471-8316
smc at astro.as.utexas.edu
www.as.utexas.edu/~smc

On Mar 2, 2008, at 11:46 PM, Mousumi Das wrote:

> Hello All,
>  How can one increase resolution in 3D FLASH? I am using  
> nxb=nyb=nz=16 zones with refinement level 6 for box length 0 to  
> 0.01cm. IDL plot gives unifrom grid size 0.195 micron. But I want  
> grid size to be about 0.08micron. Is there any way in FLASH that one  
> can start with small domain with high resolution and then increase  
> the simulation box. Or is there any way that we can modify the  
> checkpoint file from high resolution of small domain calculation and  
> coarsening the data, modify the checkpoint file and feed them back  
> to a large domain 3D run. thanks,
>
> Mousumi
>
> On Fri, 28 Dec 2007, Anshu Dubey wrote:
>
>> Try switching the IO mode between hdf5_serial and hdf5_parallel and  
>> see
>> if you do any better.
>>
>>> Hello All,
>>>    Even if I increase the frequency of the checkpointing, that is  
>>> not
>>> going to help, bacause the code stops running while writting the 2nd
>>> checkpoint file always, chk_0002. Log file shows the follwoing  
>>> error mesg.
>>>
>>>  [ 12-28-2007  01:45.36 ] step: n=163 t=1.969343E-09 dt=8.117542E-12
>>>  [ 12-28-2007  01:47.06 ] step: n=164 t=1.985578E-09 dt=8.124520E-12
>>>  [ 12-28-2007  01:48.50 ] file_wr_open: type=checkpoint
>>> name=Ni_Tem_hdf5_chk_0002
>>>
>>> If I see the output file it gives the error mesg
>>>  [CHECKPOINT_WR] Writing checkpoint file Ni_Tem_hdf5_chk_0002
>>>  Progress:  |.........
>>> Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
>>> Failing at addr:0x2abd18f1e8
>>> *** End of error message ***
>>>
>>> I have checked there is enough space for wrting files. Did anyone  
>>> of you
>>> face such problem before?
>>> thanks,
>>> Mousumi
>>>
>>>
>>> On Mon, 17 Dec 2007, Anshu Dubey wrote:
>>>
>>>> The checkpoint and plotfile numbers are not related to each other.
>>>> For the plotfile, the number only provides the number from where
>>>> the plotfile count starts upon restart.
>>>>
>>>> But if your second checkpoint didn't get written correctly, I am  
>>>> afraid
>>>> you will have to restart from the first checkpoint, and repeat  
>>>> all the
>>>> steps in between. You might want to increase the frequence of
>>>> checkpointing if you are running into IO problems, that way you  
>>>> won't
>>>> have to rollback as much.
>>>>
>>>> Anshu
>>>>>
>>>>>   I am using FLASH2.5. My programme stops while writing a  
>>>>> checkpint
>>>>> file
>>>>> after outputing several plot files, but it has not completed the  
>>>>> run
>>>>> till
>>>>> tstop value.
>>>>>
>>>>>  [ 12-14-2007  21:45.22 ] step: n=364 t=5.630710E-09  
>>>>> dt=1.014811E-11
>>>>>  [ 12-14-2007  21:48.17 ] [AMR_REFINE_DEREFINE]: refinement  
>>>>> initiated
>>>>> at
>>>>> 21:48.1 7
>>>>>  [ 12-14-2007  21:49.17 ] [AMR_REFINE_DEREFINE] blocks   all:
>>>>> min=1326
>>>>> max=1336  tot=13321
>>>>>  [ 12-14-2007  21:49.17 ] [AMR_REFINE_DEREFINE] blocks valid:
>>>>> min=1163
>>>>> max=1167  tot=11656
>>>>>  [ 12-14-2007  21:49.17 ] [AMR_REFINE_DEREFINE]: refinement  
>>>>> complete
>>>>>  [ 12-14-2007  21:49.32 ] file_wr_open: type=checkpoint
>>>>> name=Ni_Tem_hdf5_chk_000 2
>>>>>
>>>>>
>>>>> I want to restart the simulation with previous checkpointpoint  
>>>>> file
>>>>> Ni_Tem_hdf5_chk_0001. According to FLASH manual I change the  
>>>>> restart
>>>>> logical variable to .true.
>>>>> cpunumber I specfied 0001 ( last written checkpointfile)
>>>>> pltnumber 0001 ( last written plotfile number after 0001 check  
>>>>> point)
>>>>>
>>>>> Although the last written pltnumber is 0056. But there is gap  
>>>>> between
>>>>> checkpoint file chk_0001 and chk_0002.
>>>>>
>>>>> But with this I am not able to restart the simulation. How do I  
>>>>> restart
>>>>> the simulation run if I want to get the plotfile (0057) after  
>>>>> the last
>>>>> plotfile generated (0056).
>>>>> thanks,
>>>>> Mousumi
>>>>>
>>>>> On Mon, 17 Dec 2007, Anshu Dubey wrote:
>>>>>
>>>>>> People have used the parallel hdf5 module in Flash2.5 at the  
>>>>>> center
>>>>>> and still do, but on many platforms the restart is extremely  
>>>>>> slow.
>>>>>> We haven't been able to determine the cause. However,  
>>>>>> fortunately,
>>>>>> the problem didn't get carried over to Flash3, so we strongly
>>>>>> recommend switching over to Flash3 if it is possible for you.
>>>>>>
>>>>>> Anshu
>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>>  I have a serious problem when using the parallel hdf5 module to
>>>>>>> restart from a checkpoint file. It takes about half an hour to  
>>>>>>> read a
>>>>>>> single variable to each node for a 1GB file. The same problem  
>>>>>>> was
>>>>>>> reported two year ago
>>>>>>> (http://flash.uchicago.edu/pipermail/flash-users/2005-April/001938.html 
>>>>>>> )
>>>>>>> but I cannot find the follow-ups. Did anyone succeed in using  
>>>>>>> the
>>>>>>> parallel hdf5 module so far? Will the Flash center continue  
>>>>>>> support
>>>>>>> such
>>>>>>> issue on Flash2.5? Thanks!
>>>>>>>
>>>>>>> Bests,
>>>>>>> Shikui
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>>
>>