[FLASH-USERS] [EXT] Fwd: Some Problem when restart the StirTurb

Tue May 25 04:30:22 EDT 2021

Hi Tristan,

I second Marissa’s suggestion to use the ‘FromFile’ unit for turbulence driving. It has been extensively tested and was used in a number of previous works (most recently in https://ui.adsabs.harvard.edu/abs/2021NatAs...5..365F/abstract <https://ui.adsabs.harvard.edu/abs/2021NatAs...5..365F/abstract>). There were some issues in the ‘generate’ unit when I first started using it in FLASH (was still FLASH v3 then :-), which I used as a template to make the ‘FromFile’ unit, and fixed some bugs and added some functionality, such as the decomposition into solenoidal and compressive parts, and the restarting issues you discovered. Using ‘FromFile’ is explained in detail in the flash user guide, but please let me know if you have any questions about it.

Best regards,
Christoph

> On 25 May 2021, at 11:24, Tristan <juwj at mail2.sysu.edu.cn> wrote:
> 
> Hi,everyone:
> 
> I tried to add the two runtime parameters in my flash.par
> 	```
> 	st_saveReproducible = .true.
> 	st_reproducible = .true.
> 	```
>  It could generate the “saved_random_numbers” in the object directory, but when I want to restart from the generated seed file, It didn’t wrong as same as before. It says "Attempt to DEALLOCATE unallocated ‘st_randseed’ “. 
> 
> Also, I took your advice and tried the FromFile unit, it works well.
> But We have used the StirTurb unit for two months, our work is also based on the StirTurb, Is there any difference between the two units?  Because my boss may not be willing to turn to a new unit. Because he used the StirTurb unit during his PhD career 15 years ago. We are working on the characteristic of the high Mach turbulence, If FromFile behaves better in this aspect, I will turn on it.
>> Begin forwarded message:
>> 
>> From: "Marissa B. P. Adams" <madams at pas.rochester.edu <mailto:madams at pas.rochester.edu>>
>> Subject: Re: [EXT] [FLASH-USERS] Fwd: Some Problem when restart the  
>> Date: May 25, 2021 at 5:05:58 AM GMT+8
>> To: Tristan <juwj at mail2.sysu.edu.cn <mailto:juwj at mail2.sysu.edu.cn>>
>> Cc: flash-users <flash-users at flash.uchicago.edu <mailto:flash-users at flash.uchicago.edu>>
>> 
>> Hi Tristan,
>> 
>> I will admit I did not look at your log file, however I can assume based on the error you're using the Stir unit's "generate" unit. I would recommend trying the Stir "FromFile" implementation instead for now. 
>> 
>> The generate sub-unit seems to have issues with restarts/reading in the random seed from the file you can generate to store the random seeds in (take a look at the Config file in the sub-unit). I've attempted to think of a fix for this but came to the conclusion it'd take some time to renovate (I could be wrong though ofc!).
>> 
>> Best,
>> Marissa
>> 
>> 
>> 
>> On Mon, May 24, 2021 at 12:25 PM Tristan <juwj at mail2.sysu.edu.cn <mailto:juwj at mail2.sysu.edu.cn>> wrote:
>> Additionally, I may not receive the mail from the flash-user mail list. I try to join the mail list. If you have any idea about the question, please CC to me at juwj at mail2.sysu.edu.cn <mailto:juwj at mail2.sysu.edu.cn>.  Thanks everyone !
>> Best wishes! 
>> 
>>> Begin forwarded message:
>>> 
>>> From: Tristan <juwj at mail2.sysu.edu.cn <mailto:juwj at mail2.sysu.edu.cn>>
>>> Subject: Some Problem when restart the StirTurb
>>> Date: May 25, 2021 at 12:18:44 AM GMT+8
>>> To: flash-users at flash.uchicago.edu <mailto:flash-users at flash.uchicago.edu>
>>> 
>>> Hello, everyone:
>>> 	When I run the Flash code with the StirTrub unit for my turbulence simulation, it works well.But when I want to restart from a checkpointfile , something went wrong.
>>> 	To restart from a CheckPointFile, I changed my flash.par :
>>> 	```
>>> 	restart    =    .true.
>>> 	checkpointFileNumber  = 5
>>> 	plotFileNumber    = 10
>>> 	```
>>> The total number of CheckPointFile is 10, and for plotfile is 20 when I run the code first time. So I just want to restart from half the number
>>> That is the error I met :
>>> ```
>>>  [io_readData] Opening driventurb_3d_hdf5_chk_0005 for restart
>>>  Progress:   seed length =            0
>>>  Random seed =
>>>  nmodes =          188
>>>  Source terms initialized
>>>   Finished with Grid_initDomain, restart
>>>  Ready to call Hydro_init
>>>  Hydro initialized
>>>  Gravity initialized
>>>  Initial dt verified
>>>  *** Wrote plotfile to driventurb_3d_forced_hdf5_plt_cnt_0000 ****
>>>  Initial plotfile written
>>>  Driver init all done
>>>        n          t         dt  (         x,          y,          z) |
>>>      106 2.5417E+00 4.9986E-02  (  999.    ,   999.    ,   999.    ) |
>>>      107 2.5917E+00 9.9972E-02  (  999.    ,   999.    ,   999.    ) |
>>>      108 2.6916E+00 1.9994E-01  (  999.    ,   999.    ,   999.    ) |
>>>  *** Wrote plotfile to driventurb_3d_hdf5_plt_cnt_0010 ****
>>>      109 2.8916E+00 3.9989E-01  (  999.    ,   999.    ,   999.    ) |
>>>  *** Wrote plotfile to driventurb_3d_hdf5_plt_cnt_0011 ****
>>>      110 3.2915E+00 7.9977E-01  (  999.    ,   999.    ,   999.    ) |
>>>  *** Wrote checkpoint file to driventurb_3d_hdf5_chk_0006 ****
>>>  *** Wrote plotfile to driventurb_3d_hdf5_plt_cnt_0012 ****
>>>      111 4.0912E+00 1.5995E+00  (  999.    ,   999.    ,   999.    ) |
>>>  *** Wrote checkpoint file to driventurb_3d_hdf5_chk_0007 ****
>>>  *** Wrote plotfile to driventurb_3d_hdf5_plt_cnt_0013 ****
>>>      112 5.6908E+00 3.1991E+00  (  999.    ,   999.    ,   999.    ) |
>>>  *** Wrote checkpoint file to driventurb_3d_hdf5_chk_0008 ****
>>>  *** Wrote plotfile to driventurb_3d_hdf5_plt_cnt_0014 ****
>>>      113 8.8899E+00 6.3982E+00  (  999.    ,   999.    ,   999.    ) |
>>>  *** Wrote checkpoint file to driventurb_3d_hdf5_chk_0009 ****
>>>  *** Wrote plotfile to driventurb_3d_hdf5_plt_cnt_0015 ****
>>>      114 1.5288E+01 1.2796E+01  (  999.    ,   999.    ,   999.    ) |
>>>  *** Wrote checkpoint file to driventurb_3d_hdf5_chk_0010 ****
>>>  exiting: reached max SimTime
>>>  *** Wrote plotfile to driventurb_3d_forced_hdf5_plt_cnt_0001 ****
>>> At line 25 of file Stir_finalize.F90
>>> Fortran runtime error: Attempt to DEALLOCATE unallocated 'st_randseed'
>>> At line 25 of file Stir_finalize.F90
>>> Fortran runtime error: Attempt to DEALLOCATE unallocated 'st_randseed'
>>> At line 25 of file Stir_finalize.F90
>>> Fortran runtime error: Attempt to DEALLOCATE unallocated 'st_randseed'
>>> At line 25 of file Stir_finalize.F90
>>> Fortran runtime error: Attempt to DEALLOCATE unallocated 'st_randseed'
>>> At line 25 of file Stir_finalize.F90
>>> Fortran runtime error: Attempt to DEALLOCATE unallocated 'st_randseed'
>>> At line 25 of file Stir_finalize.F90
>>> Fortran runtime error: Attempt to DEALLOCATE unallocated 'st_randseed'
>>> At line 25 of file Stir_finalize.F90
>>> Fortran runtime error: Attempt to DEALLOCATE unallocated 'st_randseed'
>>> At line 25 of file Stir_finalize.F90
>>> Fortran runtime error: Attempt to DEALLOCATE unallocated ‘st_randseed'
>>> ```
>>> The file Stir_finalize.F90 is below:
>>> 
>>> !!****if* source/physics/sourceTerms/Stir/StirMain/Generate/Stir_finalize
>>>   !!
>>>   !! NAME
>>>   !!
>>>   !!  Stir_finalize
>>>   !!
>>>   !! SYNOPSIS
>>>   !!
>>>   !!  call Stir_finalize()
>>>   !!
>>>   !! ARGUMENTS
>>>   !!
>>>   !!  none
>>>   !!
>>>   !! DESCRIPTION
>>>   !!
>>>   !!  Clean up the Stir unit
>>>   !!
>>>   !!***
>>> 
>>>   subroutine Stir_finalize()
>>>     use Stir_data, ONLY : st_randseed, st_reproducible, &
>>>          st_saveReproducible, st_randomSaveUnit
>>>     implicit none
>>>     deallocate(st_randseed)        !!!!!!!! This is the 25th line.
>>>     if(st_reproducible.or.st_saveReproducible)&
>>>          close(unit=st_randomSaveUnit)
>>>     return
>>>   end subroutine Stir_finalize
>>> 
>>> 
>>> I have updated the log file for you to check my work. If someone met the some questions, let me know. 
>> 
>> 
> 

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