[FLASH-USERS] first model: hdf5 error

[John Zuhone]

HI Peter,

The Makefile.h is in your FLASH object directory itself, not HDF5. 

John

> On Oct 10, 2017, at 10:47 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 <mailto: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.in <http://makefile.h.in/>tel 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 <tel:%28%2B44%29%201334%2046%201681>
> Fax: (+44) 1334 46 3104 <tel:%28%2B44%29%201334%2046%203104>
> 
> 
> 
> 
> -- 
> 
> Mark Richardson
> MAT Postdoctoral Fellow
> Department of Astrophysics
> American Museum of Natural History
> Mark.Richardson.Work at gmail.com <mailto:Mark.Richardson.Work at gmail.com>
> My Website <https://sites.google.com/site/marklarichardson/>
> 212 496 3432

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