[FLASH-USERS] [EXT] HDF5 error

[Marissa B. P. Adams]

Hi Carla,

I would recommend using an older version of HDF5. Since you're using an
older version of FLASH and a very recent release of HDF5, I would recommend
trying to make with an earlier version of HDF5 to see if that alleviates
the error. You may need to use HDF5 1.6 bindings. Take a look at page 174 /
Chapter 9 (IO Unit) of the FLASH user manual on the FLASH Transition. If
you're working on a cluster, I would recommend asking cluster support to
build an older version of HDF5 for you if necessary. I hope this helps.

Marissa

On Tue, Oct 5, 2021 at 10:15 AM Carla Nicolin Schoder <
a01302326 at unet.univie.ac.at> wrote:

> Dear FLASH community,
>
> I hope someone can help me with the following problem.
> I work with FLASH 3.2 and for the Sedov problem I get an HDF5 Error.
>
> my modules:
> hdf5/1.10.5, intel-mpi/2019.5, intel/19, parallel-netcdf/1.11.1, ..
>
> my run:
> ./setup Sedov -auto
> gmake -j 4
> mpirun -np 4 ./flash3  --> ERROR:
>
> the ERROR:
> HDF5-DIAG: Error detected in HDF5 (1.10.5) MPI-process 0:
>    #000: H5Ddeprec.c line 189 in H5Dopen1(): not a location
>      major: Invalid arguments to routine
>      minor: Inappropriate type
>    #001: H5Gloc.c line 246 in H5G_loc(): invalid object ID
>      major: Invalid arguments to routine
>      minor: Bad value
> flash3: io_h5_attribute.c:49: io_h5_attribute_create: Assertion `dsetID
>  >= 0' failed.
> forrtl: error (76): Abort trap signal
> Image              PC                Routine            Line
> Source
> flash3             00000000005AF86B  Unknown               Unknown
> Unknown
> libpthread-2.17.s  00002AD54C3575D0  Unknown               Unknown
> Unknown
> libc-2.17.so       00002AD54C89C207  gsignal               Unknown
> Unknown
> libc-2.17.so       00002AD54C89D8F8  abort                 Unknown
> Unknown
> libc-2.17.so       00002AD54C895026  Unknown               Unknown
> Unknown
> libc-2.17.so       00002AD54C8950D2  Unknown               Unknown
> Unknown
> flash3             00000000004CB40D  Unknown               Unknown
> Unknown
> flash3             00000000004D1EA1  Unknown               Unknown
> Unknown
> flash3             00000000004E0979  Unknown               Unknown
> Unknown
> flash3             000000000044C208  Unknown               Unknown
> Unknown
> flash3             000000000044BC8F  Unknown               Unknown
> Unknown
> flash3             000000000040BC0F  Unknown               Unknown
> Unknown
> flash3             00000000004133E9  Unknown               Unknown
> Unknown
> flash3             0000000000605456  Unknown               Unknown
> Unknown
> libc-2.17.so       00002AD54C8883D5  __libc_start_main     Unknown
> Unknown
> flash3             0000000000407CE9  Unknown               Unknown
> Unknown
>
>
> ===================================================================================
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   RANK 0 PID 4328 RUNNING AT l48
> =   KILLED BY SIGNAL: 6 (Aborted)
>
> ===================================================================================
>
>
> If anyone has an idea, what might causes that error, I would be very
> happy if you would help me to solve this error.
>
> Best, Carla Nicolin Schoder
>


-- 
%---------------------------------------------%
Marissa B. P. Adams
(she/her/hers)
Phd Candidate, University of Rochester
*E-mail:* madams at pas.rochester.edu
*Website:* https://www.pas.rochester.edu/~madams
<http://www.pas.rochester.edu/~madams#>
*Current Location:*
Occupied Seneca Land
471 Bausch and Lomb Hall
University of Rochester
Rochester, NY 14627
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