[FLASH-USERS] first model: hdf5 error

[Ryan Farber]

Hi Peter,

I believe Mark was referring to Makefile.h in the sites directory. Unless
you are on a system known by FLASH, the relevant Makefile.h should be
located at

/PATH_TO_FLASH/sites/Prototypes/Linux/Makefile.h

Best,
--------
Ryan

On Tue, Oct 10, 2017 at 7:47 AM, Peter Woitke <pw31 at st-andrews.ac.uk> wrote:

> Hi Mark,
>
>
> thanks for that. However, I cannot find any Makefile.h, not before nor
> after ./configure  --prefix=/home/star/pw31/software/hdf5
> --enable-fortran --enable-parallel.
> All I see is a Makefile.in and a Makefile, but none of them have entries
> as you listed.
>
> Any idea?
>
>
>   Peter
>
>
> ------------------------------
> *From:* Mark Richardson <mark.richardson.work at gmail.com>
> *Sent:* 10 October 2017 15:38
> *To:* Peter Woitke
> *Cc:* flash-users
> *Subject:* Re: [FLASH-USERS] first model: hdf5 error
>
> Hi Peter,
>
>   it might be because you haven't flagged HDF5 to use the version 1.6
> setup. In my Makefile.h I add DH5_USE_16_API to the following definitions:
>      F90FLAGS
>      CFLAGS_HDF5
>
> Perhaps that will solve your problem,
>    -Mark
>
> On 10 October 2017 at 10:33, Peter Woitke <pw31 at st-andrews.ac.uk> wrote:
>
>> Hi there,
>>
>> I just downloaded and compiled mpich, hdf5 and flash, and I am getting
>> run-time error ...
>>
>> HDF5-DIAG: Error detected in HDF5 (1.10.1) MPI-process 0:
>>   #000: H5Ddeprec.c line 128 in H5Dcreate1(): not a location ID
>>     major: Invalid arguments to routine
>>     minor: Inappropriate type
>>   #001: H5Gloc.c line 251 in H5G_loc(): invalid object ID
>>     major: Invalid arguments to routine
>>     minor: Bad value
>> flash4: io_h5create_dataset.c:57: io_h5create_dataset: Assertion `dataset
>>
>>> = 0'
>>>
>>
>> I have tested my mpich and hdf5 installations and they have passed all
>> tests. I am listing my installation commands below. Maybe "enable-parallel"
>> is not a good idea? My runSedov directory has
>> ugo+rw permissions.
>>
>> I read in another FLASH-USER entry that one should try
>>
>> ./setup -auto Sedov +ug
>>>
>>
>> This results in another run-time error ...
>>
>> [Driver_init] Must set runtime parameters iProcs, jProcs, kProcs, and
>> meshCopyCount so that iProcs*jProcs*kProcs*meshCopyCount equals number
>> of processors
>> Calling MPI_Abort() for immediate shutdown!
>>
>> Thank you for your help,
>>
>>   Peter Woitke
>>
>>
>> ----------------------------------------------------------
>>
>>> cd ~/software/hdf5-1.10.1
>>> setenv CC  mpicc
>>> setenv CXX mpicxx
>>> setenv FC  mpif90
>>> ./configure --help
>>> ./configure --prefix=/home/star/pw31/software/hdf5
>>>
>>               --enable-fortran --enable-parallel
>>
>>> make
>>> make check
>>> make install
>>> make check-install
>>>
>> add /home/star/pw31/software/hdf5/lib to LD_LIBRARY_PATH
>> ----------------------------------------------------------
>>
>>> cd ~/flash4.4/sites
>>> mkdir prodimo
>>> cp Prototypes/Linux/Makefile.h.intel prodimo/Makefile.h
>>> cd prodimo
>>> emacs Makefile.h ...
>>> cd ~/flash4.4
>>> ./setup -auto Sedov cd object
>>> make
>>>
>> SUCCESS
>>
>>> mkdir ../runSedov
>>> cd ../runSedov
>>> cp ../source/Simulation/SimulationMain/SedovChamber/flash.par .
>>> mpirun -np 7 ../object/flash4
>>>
>> ----------------------------------------------------------
>>
>>
>>
>> Dr. Peter Woitke
>> St Andrews University
>> School of Physics & Astronomy
>> top floor, room 306
>> North Haugh
>> KY16 9SS
>> St Andrews, UK
>> Tel: (+44) 1334 46 1681
>> Fax: (+44) 1334 46 3104
>>
>>
>
>
> --
>
> Mark Richardson
> MAT Postdoctoral Fellow
> Department of Astrophysics
> American Museum of Natural History
> Mark.Richardson.Work at gmail.com
> My Website <https://sites.google.com/site/marklarichardson/>
> 212 496 3432 <(212)%20496-3432>
>
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