[FLASH-USERS] How to generate big checkpoint files in FLASH

[Dean Townsley]

Zheng,

Also, if you are testing compression algorithms, you should consider the 
physical state of the data you are compressing.

The initial conditions or state after only a few time steps of something 
like the Sod problem or Sedov will be very easily compressible because 
there are large regions on the grid that are in a spatially uniform 
state.  Conversely, a fully developed turbulence field (e.g. StirTurb 
run for a decent fraction of a turnover time) is likely to be harder to 
compress.

Dean

On 03/02/2016 11:47 AM, Zheng Yuan wrote:
> Thanks Klaus! I will use 3D instead of 2D. Someone also suggested that 
> larger values of lrefine_min & lrefine_max results in larger 
> checkpoint file sizes. I will use 3D & larger Irefine_min&max, while 
> keeping nxb*nyb*nzb = 8*8*8.
>
> Best
> Zheng
>
> On 3/2/16 11:23 AM, Klaus Weide wrote:
>> On Tue, 1 Mar 2016, Zheng Yuan wrote:
>>
>>> Dear all,
>>>
>>> My goal is to run FLASH using 1K MPI processes and get large 
>>> checkpoint files
>>> (500 GB each. These large checkpoint files will be used as the test 
>>> data of a
>>> parallel data compression algorithm proposed by our group.). Does 
>>> anybody know
>>> how to set the parameters to run FLASH in large scale and get large 
>>> checkpoint
>>> files?
>> Hello,
>>
>> If you really "just" want large checkpoint files, you should start 
>> with a 3D
>> setup!
>>
>>
>>> Currently, I am trying to run FLASH/Sedov to generate large 
>>> checkpoint files.
>>> However, FLASH reports an error when I increase the dimension of the 
>>> grid.
>>>
>>> I configured FLASH using:
>>>
>>> ./setup Sedov -auto +pnetcdf -objdir=sedov_2d 
>>> -parfile=sedov_io_69b_2d.par -2d
>>> -nxb=64 -nyb=64 -maxblocks=200
>>>
>>> To run more iterations, I changed the 'nend' parameter to 10 in
>>> sedov_2d/flash.par and make sedov_2d
>>>
>>> I run flash using command:
>>>
>>> mpirun -n 4 ./flash4
>>>
>>>
>>> FLASH terminate at the third iteration. The error is:
>>   *** Wrote plotfile to sedov_2d_6lev_ncmpi_plt_cnt_0001 ****
>>         n          t         dt  (         x, y,          z) |  dt_hydro
>>         1 2.0000E-10 2.5000E-05  ( 4.993E-01,  4.875E-01, 0.000E+00) 
>> |  1.265E-05
>>   *** Wrote checkpoint file to sedov_2d_6lev_ncmpi_chk_0001 ****
>>   *** Wrote plotfile to sedov_2d_6lev_ncmpi_plt_cnt_0002 ****
>>         2 5.0000E-05 2.5000E-05  ( 5.134E-01,  5.017E-01, 0.000E+00) 
>> |  8.673E-06
>>   *** Wrote checkpoint file to sedov_2d_6lev_ncmpi_chk_0002 ****
>>   *** Wrote plotfile to sedov_2d_6lev_ncmpi_plt_cnt_0003 ****
>>         3 1.0000E-04 2.5000E-05  ( 5.139E-01,  4.988E-01, 0.000E+00) 
>> |  6.407E-07
>>   *** Wrote checkpoint file to sedov_2d_6lev_ncmpi_chk_0003 ****
>>      Nonconvergence in subroutine rieman
>>   .....
>>
>>
>> By increasing NXB and NYB, you have increased the resolution. This
>> requires a smaller timestep for stability, see "dt_hydro" column.  But
>> your flash.par fixes dtmin and dtmax at 2.5e-5, the direct effect of
>> this can be seen in the "dt" column. So you are forcing FLASH to do
>> Hydro advances with a time step that is too large for stability.
>> So it is not surprising that the simulation fails after a few steps.
>>
>> Basically, aking your runtime parameter "dtmin" much smaller should
>> get you a simulation that runs.
>>
>> Btw, a more common way to increase resolution (thus file sizes) would
>> be to increase lrefine_in and/or lrefine_max and/or Nblock{X,Y,Z},
>> rather than keep increasing the block size.
>>
>> Klaus
>
>