[FLASH-USERS] H5Screate_simple(): zero sized dimension for non-unlimited dimension

[kunal rao]

Yes, Got it !! Thanks Sam and Anshu for your prompt response.

Regards,
Kunal

On Thu, Jun 3, 2010 at 5:07 PM, Anshu Dubey <dubey at flash.uchicago.edu>wrote:

> Kunal,
>
> The following message in your log file is the key :
>
> WARNING : Adaptive Grid did not find any variable to refine
>
> Since there is no refinement, the number of blocks stays at 1, and so the second processor has no blocks. Make sure that you have the following lines in your flash.par :
>
>
> refine_var_1 = "dens"
> refine_var_2 = "pres"
>
> Anshu
>
>
>
> On Thu, Jun 3, 2010 at 3:58 PM, kunal rao <kunalgrao at gmail.com> wrote:
>
>> Hi,
>>
>> I am running FLASH 3.2 on my laptop on a virtual machine running Ubuntu
>> 9.10. I have configured the code using:
>> $./setup Sedov -auto -makefile=gfortran
>>
>> I am able to run the executable for a single process using $./flash3 . But
>> when I try to run it on 2 processes using
>>
>> $mpirun -np 2 ./flash3
>>
>> I get the following error:
>>
>> Driver_abortC called
>> Error: negative return from memspace H5Screate_simple
>> Calling MPI_Abort for immediate shutdown
>> HDF5-DIAG: Error detected in HDF5 library version: 1.6.10 thread 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
>>
>> This problem was addressed in one of the previous archived emails. The
>> response to that by Chris was that:
>>
>> -------------------------------------------------
>>
>> 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.
>>
>> -------------------------
>>
>> I checked in my sedov.log file and it is 0. This is what i see in the sedov.log file:
>>
>> ----------------------------
>>
>> WARNING : Adaptive Grid did not find any variable to refine
>>  [ 06-03-2010  11:55:51.588 ] [GRID amr_refine_derefine]: initiating refinement
>>
>>
>>
>>
>>  [GRID amr_refine_derefine] min blks 0    max blks 1    tot blks 1
>>  [GRID amr_refine_derefine] min leaf blks 0    max leaf blks 1    tot leaf blks 1
>>  [ 06-03-2010  11:55:51.616 ] [GRID amr_refine_derefine]: refinement complete
>>
>>
>>
>>
>>  [ 06-03-2010  11:55:51.743 ] [GRID gr_expandDomain]: iteration=1, create level=2
>>
>> -----------------------------------------------------------
>>
>> The temporary workaround was to use fewer processes. But I am not able to run on even 2 processes.
>>
>> Can you please tell me if there is a solution for this.
>>
>> Thanks & Regards,
>> Kunal
>>
>
>
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