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 <[email protected]> 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 <[email protected]> > > 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 <[email protected]> > > 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 < > > > > > > > [email protected]> wrote: > > > > > > > > > > > > > >> > > > > > > >> [email protected] 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 <[email protected] > > > > > > > > wrote: > > > > > > >> > > > > > > > >> >> On Mon, 27 Jan 2014, Jed Brown wrote: > > > > > > >> >> > > > > > > >> >>> Mark Adams <[email protected]> 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 > > > > > > >> >> > > > > > > >> >> > > > > > > >> > > > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
