[FLASH-BUGS] problems running flash3

[Chris Daley]

Hi Manami,

You have compiled your application with HD5-1.6.10, but are loading
HDF5-1.8.1 at runtime.  Modify your FLASH Makefile.h so you have:

HDF5_PATH = /your/path/to/HDF5-1.8.1
CFLAGS_HDF5 = -I${HDF5_PATH}/include -DH5_USE_16_API

You can leave your LD_LIBRARY_PATH as it is.

Chris

Manami Sasaki wrote:
> 
> Dear Chris,
> 
> Thank you for the quick reply. I included the options and it seems to 
> have resolved the issue with MPI_Allreduce. However, now I get the 
> following message
> 
> Warning! ***HDF5 library version mismatched error***
> The HDF5 header files used to compile this application do not match
> the version used by the HDF5 library to which this application is linked.
> Data corruption or segmentation faults may occur if the application 
> continues.
> You should recompile the application or check your shared library related
> settings such as 'LD_LIBRARY_PATH'.
> You can, at your own risk, disable this warning by setting the environment
> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
> Setting it to 2 will suppress the warning messages totally.
> Headers are 1.6.10, library is 1.8.1
> Bye...
> rank 0 in job 15  aitp28_40893   caused collective abort of all ranks
>   exit status of rank 0: killed by signal 9
> 
> Thanks
> Manami
> 
> 
> On Mon, 24 Jan 2011, Christopher Daley wrote:
> 
>> Hi Manami,
>>
>> It looks like FLASH is failing on the first floating point MPI
>> communication, so I suspect that you have not promoted Fortran
>> reals to double precision.  If you are using gfortran compiler
>> then the FFLAGS macros in your FLASH Makefile.h should have
>> -fdefault-real-8 -fdefault-double-8 options.  Do you have these
>> compiler options in your Makefile.h?
>>
>> Chris
>>
>>
>> On Mon, 2011-01-24 at 08:06 +0100, Manami Sasaki wrote:
>>> Hi,
>>>
>>> I have downloaded FLASH3.3 and also installed mpich and hdf5.
>>>> ./setup Sedov -auto
>>> works fine. However, if I try to run flash with
>>>> mpirun -np 1 /home/sasaki/soft/flash/FLASH3.3/object/flash3
>>> I get the result shown below and could not figure out how to
>>> revolve this. I'm working on a PC with openSUSE 11.1 (Linux
>>> 2.6.27.56-0.1-default x86_64) installed.
>>>
>>> Thank you for your help.
>>> Best regards,
>>> Manami
>>>
>>>
>>> ---------------------------------------------------------------
>>> Fatal error in MPI_Allreduce: Internal MPI error!, error stack:
>>> MPI_Allreduce(826).......: MPI_Allreduce(sbuf=0x7fffa0b3d938,
>>> rbuf=0x7fffa0b3d93c, count=1, MPI_DOUBLE_PRECISION, MPI_MIN,
>>> MPI_COMM_WORLD)
>>> failed
>>> MPIR_Allreduce_impl(684).:
>>> MPIR_Allreduce_intra(279):
>>> MPIR_Localcopy(349)......: memcpy arguments alias each other,
>>> dst=0x7fffa0b3d93c src=0x7fffa0b3d938 len=8
>>>   WARNING : Adaptive Grid did not find any refinement variables
>>>   MaterialProperties initialized
>>>   Cosmology initialized
>>>   Source terms initialized
>>>    iteration, no. not moved =            0           0
>>>   refined: total leaf blocks =            1
>>>   refined: total blocks =            1
>>>    starting MORTON ORDERING
>>>    tot_blocks after            1
>>>    max_blocks 2           1
>>>    min_blocks 2           1
>>>   INFO: Grid_fillGuardCells is ignoring masking.
>>>    Finished with Grid_initDomain, no restart
>>>   Ready to call Hydro_init
>>>   Info: Hydro_init has set hy_specialFluxVar to            3
>>>   Hydro initialized
>>>   Gravity initialized
>>> rank 0 in job 9  aitp28_40893   caused collective abort of all ranks
>>>    exit status of rank 0: killed by signal 9
>>
>>
>>