[petsc-users] osx configuration error

[Satish Balay]

>>>>>>>>
Executing: mpif90  -o /var/folders/sw/67cq0mmx43g93vrb5xkf1j7c0000gn/T/petsc-2z06LS/config.setCompilers/conftest    /var/folders/sw/67cq0mmx43g93vrb5xkf1j7c0000gn/T/petsc-2z06LS/config.setCompilers/conftest.o
Testing executable /var/folders/sw/67cq0mmx43g93vrb5xkf1j7c0000gn/T/petsc-2z06LS/config.setCompilers/conftest to see if it can be run
Executing: /var/folders/sw/67cq0mmx43g93vrb5xkf1j7c0000gn/T/petsc-2z06LS/config.setCompilers/conftest
Executing: /var/folders/sw/67cq0mmx43g93vrb5xkf1j7c0000gn/T/petsc-2z06LS/config.setCompilers/conftest
ERROR while running executable: Could not execute "/var/folders/sw/67cq0mmx43g93vrb5xkf1j7c0000gn/T/petsc-2z06LS/config.setCompilers/conftest":
dyld: Library not loaded: /Users/markadams/homebrew/lib/gcc/x86_64-apple-darwin13.4.0/4.9.1/libgfortran.3.dylib
  Referenced from: /Users/markadams/homebrew/lib/libmpifort.12.dylib
  Reason: image not found
<<<<<<<<<<<

Mostlikely you haven't reinstalled mpich - as its refering to gfortran-4.9.1. Current gfortran is 5.3
GNU Fortran (Homebrew gcc 5.3.0) 5.3.0


This is what I would do to reinstall brew

1. Make list of pkgs to reinstall

brew leaves > reinstall.lst

2. delete all installed brew pacakges.

brew cleanup
brew list > delete.lst
brew remove `cat delete.lst

3. Now reinstall all required packages
brew update
brew install `cat reinstall.lst`


Satish


On Wed, 13 Jan 2016, Mark Adams wrote:

> I'm still having problems.  I have upgraded gcc and mpich. I am now
> upgrading everything from homebrew.  Any ideas on this error?
> thanks,
> 
> On Wed, Jan 13, 2016 at 2:15 AM, Matthew Knepley <knepley at gmail.com> wrote:
> 
> > On Tue, Jan 12, 2016 at 6:31 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> >
> >> > 'file' object has no attribute 'getvalue'  File
> >> "/Users/markadams/Codes/petsc/config/configure.py", line 363, in
> >> petsc_configure
> >>
> >> Hm - have to figure this one out - but the primary issue is:
> >>
> >> > stderr:
> >> > gfortran: warning: couldn't understand kern.osversion '15.2.0
> >> > ld: -rpath can only be used when targeting Mac OS X 10.5 or later
> >>
> >
> > I get this. The remedy I use is to put
> >
> >   MACOSX_DEPLOYMENT_TARGET=10.5
> >
> > in the environment. Its annoying, and quintessentially Mac.
> >
> >   Matt
> >
> >
> >> Perhaps you've updated xcode or OSX - but did not reinstall brew/gfortran.
> >>
> >> > Executing: mpif90 --version
> >> > stdout:
> >> > GNU Fortran (Homebrew gcc 4.9.1) 4.9.1
> >>
> >> I suggest uninstalling/reinstalling homebrew packages.
> >>
> >> Satish
> >>
> >>
> >>
> >> On Tue, 12 Jan 2016, Mark Adams wrote:
> >>
> >> > I did nuke the arch directory.  This has worked in the past and don't
> >> know
> >> > what I might have changed.  it's been awhile since I've reconfigured.
> >> > Thanks,
> >> > Mark
> >> >
> >>
> >>
> >
> >
> > --
> > 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
> >
>