[FLASH-USERS] HDF5 serial with LaserSlab

[Christopher Daley]

Hi Robert,

The parallel symbol is present because a FLASH HDF5 parallel I/O
implementation is being selected at FLASH setup time.  Normally +hdf5
will select HDF5 serial I/O, but the presence of the +laser shortcut
(for LaserSlab) is overriding this choice and selecting HDF5 parallel
I/O.

It is possible to run the LaserSlab simulation with HDF5 serial I/O, but
only if you remove the LaserIO sub-unit (which depends on HDF5 parallel
I/O).  Note that removing the sub-unit will mean ray data will not be
written to the plot files.  If this is OK then simply add the
following to your setup line:

--without-unit=physics/sourceTerms/EnergyDeposition/EnergyDepositionMain/Laser/LaserIO

Regards,
Chris


On 04/21/2013 03:34 PM, Robert Crowston wrote:
> Hello,
>
> I'm trying to get FLASH 4.0.1 up and running on Mac OS 10.8.3.
>
> I have "./setup Sedov -auto" and "./setup Sedov -auto +hdf5" running
> no problem and I can examine the output of the latter with VisIt.
>
> Now I'm trying a more intensive problem, the LaserSlab setup from the
> manual. I try to setup with +hdf5 instead of +hdf5typeio, for serial
> HDF5 support instead of parallel HDF5. (I'm having trouble building
> HDF5 with parallel support here, but I understand parallel support
> isn't required.)
>
> However, the linker fails with
> 'Undefined symbols for architecture x86_64: "_H5Pset_dxpl_mpio",
> referenced from  _io_h5read_unknowns_ in io_h5read_unknowns.o [...]'
> _H5Pset ... is a parallel symbol. I'm not sure why it's being called
> ... any ideas??
>
> Thanks!
> Rob
>
> --
> Robert Crowston
> York Plasma Institute, Dept of Physics
> University of York
> Genesis 2, Innovation Way
> YO10 5DQ
> United Kingdom