[FLASH-USERS] first model: hdf5 error

[Peter Woitke]

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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