[FLASH-USERS] 3D resolution

[Mousumi Das]

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
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>>
>>
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