[petsc-dev] configure failed after update of OSX

Tue Jan 28 01:39:06 CST 2014

To echo what Aron said, I wouldn't point people at the
hpc.sourceforge.netbuilds. They do install directly into /usr/bin, and
it's a pain in the ass
to undo. The R/AT&T build of gcc was better, but also installed into
/usr/bin, and was also a pain in the ass to uninstall.

Having used both MacPorts (2010-2012) and Homebrew (2012-present), I find
Homebrew to be a better experience, especially if you only need a small
number of packages for development. MacPorts used to insist on its own
stack, which meant that if you wanted gfortran, you also had to install
many other packages.

I generally developed using gcc 4.2 because I found cross-version linking
to be a pain in the ass. I've also installed gcc 4.8 via the
homebrew/versions tap and that's worked well, too.

Python is sort of broken in both MacPorts and Homebrew. If you look at the
GitHub issues, there's been a lot of traffic related to Python in Homebrew
lately because they completely revamped how they handle Python in their
build recipes, which then broke some Python packages installed via
Homebrew. Last I checked, Python was more broken in MacPorts and required
lots of hacks to get things to work, but it's been a while since I've used
MacPorts. I think the best policy is to rely on the package manager for as
little Python software as possible, and install the rest of your Python
stack in an isolated manner; I use pyenv, pip, & virtualenv. Conda sort of
does something similar, but I feel like conda is a great build system with
too many other responsibilities.

On Mon, Jan 27, 2014 at 9:53 PM, Satish Balay <balay at mcs.anl.gov> wrote:

> BTW: gfortran from 'R' would install in /usr. It had an uninstaller
> [so was initially attractive to us].
>
> However if I remember correctly - it overwrote one of the libgcc_xx.a
> stuff that came with Xcode - and uninstalling it resulted in a broken
> gcc [I had to delete/reinstall xcode after that]
>
> There were other issues aswell. Perhaps Sean remembers them better..
> This was many osx/xcode versions ago.
>
> Satish
>
> On Mon, 27 Jan 2014, Satish Balay wrote:
>
> > Yeah - it must have been a while since I last checked on homebrew :)
> >
> > Wrt hpc.sourceforge.net - it installs in /usr/local - so it does not
> > conflict system stuff.
> >
> > Satish
> >
> > On Mon, 27 Jan 2014, Aron Ahmadia wrote:
> >
> > > Satish,
> > >
> > > Yup!  Samuel John switched homebrew over to a modern gfortran in 2012:
> > >
> > >
> https://github.com/Homebrew/homebrew/commit/1751362562f9b5d56708003f0dffb88e5b2418ab
> > >
> > > So it's been at least a year :)
> > >
> > > I don't point people at the hpc.sourceforge builds, if I recall
> correctly
> > > they install right into your /usr/bin, which seems a bit risky to me.
> > >
> > > Cheers,
> > > Aron
> > >
> > >
> > > On Tue, Jan 28, 2014 at 12:27 AM, Satish Balay <balay at mcs.anl.gov>
> wrote:
> > >
> > > > I've generally recommended hpc.sourceforge as its simple, easy to
> > > > install and has worked for me for a long time. [Uninstall requires a
> > > > bit of effort though..]
> > > >
> > > > Sure - if one needs a bunch of packages including fortran -
> > > > homebrew/macports would be the way to go.
> > > >
> > > > We've had quiet a few maint issues with macport conflicts - and Sean
> > > > had been trying to resolve some of them within macpors. [And helping
> > > > folks here on this list]
> > > >
> > > > Previously Homebrew had gfortran-4.2. But that was a buggy version
> and
> > > > broke petsc f90 related functionality - so I didn't recommend it. But
> > > > now I see gfortran-4.8 in homebrew - so perhaps it will work better
> > > > now.
> > > >
> > > > Satish
> > > >
> > > > On Mon, 27 Jan 2014, Aron Ahmadia wrote:
> > > >
> > > > > Mark,
> > > > >
> > > > > You don't have any surprises in your configure file.  I'm not
> surprised
> > > > > that your MacPorts install broke, we saw pretty terrible breakage
> across
> > > > > the Scientific Python community, although I think Homebrew
> weathered the
> > > > > update pretty well.
> > > > >
> > > > > I'd suggest following Sean's instructions so long as you're happy
> with
> > > > Mac
> > > > > Ports.  The most important thing is getting your compiler stack
> sane, and
> > > > > unfortunately when you're compiling Fortran on OS X, you're going
> to have
> > > > > to deal with a half-crazed stack no matter what you do.  See
> Geoff's
> > > > > excellent summary on SciComp for future Fortran compiler options:
> > > > > http://scicomp.stackexchange.com/a/2470/9 -- MacPorts is a
> reasonable
> > > > > choice here.
> > > > >
> > > > > HashDist's main purpose is in helping scientists specify a software
> > > > stack,
> > > > > then reproduce it elsewhere.  It looks to me like PETSc is actually
> > > > > satisfying most of your stack, and the only place where you need a
> little
> > > > > help from MacPorts is the Fortran compiler, so I think HashDist
> would be
> > > > > overkill for your needs here.
> > > > >
> > > > > Cheers,
> > > > > Aron
> > > > >
> > > > >
> > > > > On Mon, Jan 27, 2014 at 6:19 PM, Mark Adams <mfadams at lbl.gov>
> wrote:
> > > > >
> > > > > > Sean, I seem to need to reinstall macorts.  I ran this:
> > > > > >
> > > > > > *Edit:* A binary installer for Mavericks (for the 2.2.1 bugfix
> release)
> > > > > > is now available:
> > > > > >
> > > >
> https://distfiles.macports.org/MacPorts/MacPorts-2.2.1-10.9-Mavericks.pkg.
> > > > > >
> > > > > > And it created a MacPorts directory in Application but this just
> a few
> > > > > > apps but no 'port' command.  Any idea what is going on here?
> > > > > > Thanks,
> > > > > > Mark
> > > > > >
> > > > > >
> > > > > > On Mon, Jan 27, 2014 at 11:44 AM, Sean Farley <
> > > > > > sean.michael.farley at gmail.com> wrote:
> > > > > >
> > > > > >>
> > > > > >> bsmith at mcs.anl.gov writes:
> > > > > >>
> > > > > >> >   I think resolved it by getting rid of some stuff that
> macports
> > > > put in
> > > > > >> maybe
> > > > > >>
> > > > > >> I just *completely* revamped the mpi ports in macports and
> would like
> > > > to
> > > > > >> know if these types of problems still exist.
> > > > > >>
> > > > > >> >   MPICH or libtool assumes certain files are there if other
> files
> > > > are
> > > > > >> there (without checking for them)
> > > > > >> >
> > > > > >> >    Barry
> > > > > >> >
> > > > > >> > On Jan 27, 2014, at 10:36 AM, Satish Balay <balay at mcs.anl.gov
> >
> > > > wrote:
> > > > > >> >
> > > > > >> >> On Mon, 27 Jan 2014, Jed Brown wrote:
> > > > > >> >>
> > > > > >> >>> Mark Adams <mfadams at lbl.gov> writes:
> > > > > >> >>>
> > > > > >> >>>> It seems to want /opt/local/lib/liblzma.la
> > > > > >> >>>> I do have /opt/local/lib/liblzma.a
> > > > > >> >>>
> > > > > >> >>> There is no explicit reference to liblzma in either PETSc or
> > > > MPICH.
> > > > > >>  Can
> > > > > >> >>> you send PETSC_ARCH/externalpackages/mpich*/config.log?
> > > > > >> >>
> > > > > >> >> Ah - perhaps its a buggy libtool. Presumably its picked up
> from
> > > > > >> >> /opt/local/bin/libtool - aka macports - and you have a broken
> > > > macports
> > > > > >> >> install.
> > > > > >> >>
> > > > > >> >> Satish
> > > > > >> >>
> > > > > >> >>
> > > > > >>
> > > > > >>
> > > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
>
>

-- 
Geoffrey Oxberry, Ph.D., E.I.T.
goxberry at gmail.com
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