[petsc-dev] Fwd: [petsc-users] cannot find 'libz.a' when configuring

[Matthew Knepley]

On Thu, Apr 11, 2013 at 9:48 AM, Satish Balay <balay at mcs.anl.gov> wrote:

> On Thu, 11 Apr 2013, Matthew Knepley wrote:
>
> > On Thu, Apr 11, 2013 at 9:38 AM, Satish Balay <balay at mcs.anl.gov> wrote:
> >
> > > On Thu, 11 Apr 2013, Matthew Knepley wrote:
> > >
> > > > On Thu, Apr 11, 2013 at 9:17 AM, Satish Balay <balay at mcs.anl.gov>
> wrote:
> > > >
> > > > > On Thu, 11 Apr 2013, Matthew Knepley wrote:
> > > > >
> > > > > > On Wed, Apr 10, 2013 at 7:53 PM, Satish Balay <balay at mcs.anl.gov
> >
> > > wrote:
> > > > > >
> > > > > > > How do we handle these packages with complicated dependencies
> [they
> > > > > > > are complicated as petsc dependencies?]
> > > > > > >
> > > > > > > In this report hdf5 was built with szip-2.1 and zlib-1.2.7. So
> how
> > > > > > > does petsc configure automatically detect this?
> > > > > > >
> > > > > > > And I've recently used the following for hdf5/necddf5 on fusion
> > > [with
> > > > > > > the extra implicit depenceny of hdf5 on zlib, and netcdf5 on
> hdf5
> > > from
> > > > > > > within configure]
> > > > > > >
> > > > > > >     '--with-hdf5-lib=-L/soft/hdf5/1.8.6-parallel/lib -lhdf5_hl
> > > -lhdf5
> > > > > > > -lgpfs',
> > > > > > >
> > > > > > >     '--with-netcdf-lib=-L/soft/netcdf/4.1.1-parallel/lib
> -lnetcdff
> > > > > > > -lnetcdf -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5
> > > > > -lk5crypto
> > > > > > > -lcom_err -lidn -lssl -lcrypto -lz',
> > > > > > >
> > > > > > > Yeah - things work if the user knows the dependencies and the
> link
> > > > > > > command for those dependencies - and specify it to petsc
> configure
> > > as
> > > > > > > above. But I'm not sure how to autodetect this.
> > > > > > >
> > > > > > > Also currently -lz is handled in package.py with
> > > > > > > 'self.needsCompression' similar to 'self.needsMath' with the
> > > detection
> > > > > > > of -lz in libraires.py:checkCompression() - but one can't
> specify a
> > > > > > > --with-zlib-lib option this way. I guess this part can be
> fixed by
> > > > > > > migrating it a standalone package z.py. [And somehow handle the
> > > > > > > optional part of this dependency for hdf5]
> > > > > >
> > > > > >
> > > > > > We already have a mechanism for this. Lots of packages depend on
> > > > > > other packages. This is just screwed up in the case of libz
> because
> > > > > > someone (maybe me) did not want to write an entire package file
> for
> > > > > > it, and instead copped out with the needsCompression.
> > > > >
> > > > > Currently we handle 'mandatory' dependencies properly - and
> optional
> > > > > >depencencies for --download-pakcage somewhat - but not for
> > > > > --with-package-dir
> > > > >
> > > > > For hdf5 - handling just zlib.py is not sufficient. Do we add
> szip.py,
> > > > > zlib.py, gpfs.py [and perhaps more] for hdf5? And somehow use
> these as
> > > > > optionaly when testing for user provided --with-hdf5? Which package
> > > > > currently implements this usage [to check for this optionaly
> > > > > dependency - and give the correct error]?
> > > > >
> > > > > i.e In this case - when the user specified --with-hdf5-dir option.
> We
> > > > > had to print an error.:
> > > > >  * please provide --with-zlib-dir and --with-szip-dir options.
> > > > > [For a different user - with the same usage - there would be no
> error]
> > > > >
> > > > > For netcdf above one would have kerbros.py, curl.py and perhaps
> more?
> > > >
> > > >
> > > > We have had this same discussion a million times, and we always
> > > eventually
> > > > get to the same answer and forget. Do we need our own error message
> for
> > > > petsc-dev?
> > > >
> > > > We cannot possibly guess everything that can go wrong. What we need
> is a
> > > > system
> > > > where the user can specify what he actually wants and we check it.
> So,
> > > zlib
> > > > and
> > > > everything else are optional dependencies for hdf5. If something is
> not
> > > > specified, it
> > > > fails, and the user goes back and specifies the right thing.
> > >
> > > Sure - but specify how? specify everything with
> > > --with-hdf5-lib,--with-hdf5-include options?
> > >
> > > Or somehow he knows that he has to specify
> > > --with-zlib-include/-with-zlib-lib options?
> > >
> >
> > This. It would be nice if HDF5 would tell us about its dependencies, but
> if
> > it does not, then
> > the user has to, and this is our system (packages).
>
> So we would start adding zlib.py, szip.py and manymore [and support
> --download-zlib --download-szip]. And if user gets the error:
>
> --with-hdf5-dir=/foo/bar does not work.
>
> So he/she send us configure.log
>
> Then we look at it and respond saying: you need to specify --with-zlib-dir
> --with-szip-dir options aswell.
>
> Does this look right?


Yes, that is what I think makes sense.

We can always try to add another layer that 'greps' for libz in the hdf5
error message and guesses that
the user forgot it, but hopefully before we get to it, a sane storage
library appears, or HDF5 gets its act
together.

   Matt


>
> Satish
>
> >
> >    Matt
> >
> >
> > > This thread started becasue one expected --with-hdf5-dir to be
> > > sufficient - and its not.  current workarround [becuase of
> > > self.needsCompression] is to specify zlib with LIBS otpions - and all
> > > other dependencies with --with-hdf5-lib. It works - but if were were
> > > satisfactory - this whole thread on petsc-dev wouldn't arise.
> > >
> > > Satish
> > >
> >
> >
> >
> >
>
>


-- 
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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