[petsc-users] Configure/make with "--download-hdf5" or "--with-hdf5-dir=" crashes

[Matthew Knepley]

On Mon, Sep 1, 2014 at 6:57 AM, Åsmund Ervik <asmund.ervik at ntnu.no> wrote:

>
> On 01. sep. 2014 13:52, Matthew Knepley wrote:
> > On Mon, Sep 1, 2014 at 6:18 AM, Åsmund Ervik <asmund.ervik at ntnu.no>
> wrote:
> >
> >>
> >>
> >> On 01. sep. 2014 12:51, Matthew Knepley wrote:
> >>> On Mon, Sep 1, 2014 at 3:22 AM, Åsmund Ervik <asmund.ervik at ntnu.no>
> >> wrote:
> >>>
> >>>>
> >>>> Subsequently I installed HDF5 v. 1.8.12 using my OS package manager
> and
> >>>> then tried to configure with "--with-hdf5
> >>>> --with-hdf5-dir=/path/to/system/hdf5" using PETSc 3.5.1. This time
> both
> >>>> configure and make were successful, but "make test" fails with loads
> of
> >>>> undefined references to PETSc HDF5 stuff (see below). configure.log
> and
> >>>> make.log attached also for this case (error-with-hdf5.tar.gz)
> >>>>
> >>>
> >>> It did not build src/sys/classes/viewer/impls/hdf5/, clearly from the
> >> log.
> >>> However, it
> >>> should have. We have been trying to understand why Make behaves in a
> bad
> >> way
> >>> after configuration failure. It should go away with make clean and
> >> another
> >>> make.
> >>
> >> Thanks Matt, make clean and then make did result in make test passing
> >> all tests.
> >>
> >> However, I am still unable to use HDF5 functionality. When I compile and
> >> run e.g. vec/vec/examples/tutorials/ex10.c it works fine with binary
> >> output, but with HDF5 I get the error message below.
> >>
> >> I'm guessing this is some incompatibility between the various MPI, HDF5
> >> and PETSc versions, i.e. that the HDF5 from my OS is not using the same
> >> MPI as PETSc. Is it simple to edit something in PETSc and have
> >> "./configure --download-hdf5" get the most recent HDF5 library which
> >> compiles on my machine?
> >>
> >
> > Yes, I cannot reproduce, so it must be something like that. Can you
> > reconfigure
> > using the --download version?
>
> No, I am not able to, that is why I switched to "--with-hdf5-dir=". Like
> I said in the first email, the version of HDF5 (1.8.10) that ships with
> PETSc 3.5.1 does not compile on my machine. This is apparently a known
> bug that was fixed upstream, cf.
>
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=711777
>
> This is the reason why I asked whether I can somehow tell
> "--download-hdf5" to download a more recent version. 1.8.11 should do it.


People who leave commented out code in there should be tarred, feathered,
and run out of town on a rail. You can just go in and delete that line, and
then
reconfigure. It will use the source that is already downloaded.

Satish, can we patch our download source? I can do it, but I am not sure of
the process for HDF5.

  Thanks,

     Matt


>
> Åsmund
>
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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