[petsc-dev] configure failed after update of OSX

[Satish Balay]

On Tue, 28 Jan 2014, Geoff Oxberry wrote:

> 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.

Just reiterating my previous e-mails. hpc installs in /usr/local/bin
and does not touch stuff in /usr/bin

> 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.

Our experience is R/AT&T build is worse wrt PETSc. Will never
recommend it. [and will never recommend gfortran-4.2 as this early
version has bugs in some of its f90 implementation affecting petsc's
f90 interface]

> 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.

One more reason to prefer hpc.sourceforge [gfortran only] install -
wrt PETSc.

> 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.

Sounds like you are adding more reasons to prefer hpc.sourceforge gfortran
[for petsc usage]

Obviously - if one needs more than just gfortran - they would have to
use Macports or homebrew - and deal with all the issues they
have. [Just like the issue Mark is currently having - hence this
e-mail thread]

I'll add one more note here: Its possible to cleanly uninstal hpc
stuff - but its not simple. One would have to keep the tarball arround
[or store the tarball table of contents in a file] - and use this
info to remove files.

cd /
sudo tar -tf ~/Downloads/gfortran-mlion.tar | xargs rm
sudo tar -tf ~/Downloads/gfortran-mlion.tar | xargs rmdir
sudo tar -tf ~/Downloads/gfortran-mlion.tar | xargs rmdir
...

Satish

> 
> 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
> > > > > > >> >>
> > > > > > >> >>
> > > > > > >>
> > > > > > >>
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> >
> >
> 
> 
>