[FLASH-USERS] H5Screate_simple: zero sized dimension
Mateusz Ruszkowski
mateuszr at umich.edu
Tue Nov 3 00:17:41 EST 2009
Hi Chris,
you are absolutely right. This is how I dealt with this problem initially
and it worked.
thanks for the confirmation,
Mateusz
On Mon, 2 Nov 2009, Christoper Daley wrote:
> Mateusz Ruszkowski wrote:
>>
>>
>> Hi all,
>>
>> [apologies if you are getting this message more then once; we had some
>> trouble sending the e-mail]
>>
>> We are getting a runtime error related to hdf5. The crash occurs the
>> moment the code is attempting to write the initial conditions. The
>> standard output includes the following error messages:
>>
>> .
>> .
>> .
>> Initial dt verified
>> Driver_abortC called
>> Error: negative return from memspace H5Screate_simple
>> Calling MPI_Abort for immediate shutdown
>>
>> and:
>>
>> .
>> .
>> .
>> HDF5-DIAG: Error detected in HDF5 library version 1.6.6-snap21 MPI-process
>> 0. Back trace follows.
>> #000: H5S.c line 1595 in H5Screate_simple(): zero sized dimension for
>> non-unlimited dimension
>> major(01): Function arguments
>> minor(05): Bad value
>> MPI: On host columbia1, Program
>> /u/.realmounts/home7/nieusma/Flash/Planet_IR, Rank 0, Process 8697
>> 1 called MPI_Abort(<communicator>, 1)
>>
>>
>> A similar error was reported on the FLASH mailing list in the past and a
>> suggestion was made that this could be due to (min refinement) > (max
>> refinement) in flash.par. We checked the refinement levels and this does
>> not appear to be a problem in the above run so the cause of this problem
>> is probably different in our case. Did anybody encounter similar issues?
>>
>>
>> thanks,
>> Mateusz & Justin
>>
>
> Hi Mateusz, Justin,
>
> I think this is happening because there are zero blocks on at least
> one processor. You can check whether this is the case by looking in
> the flash log file from your run. Look for the last
> amr_refine_derefine message of the form:
>
> [GRID amr_refine_derefine] min blks 17 max blks 18 tot blks 69
>
> I expect there is a min blks 0 in your message. A temporary
> workaround is to run your application on fewer processors.
>
> Regards,
> Chris
>
>
>
>
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