I upgraded homebrew on my macbook and had to remove firedrake because the compiled libraries were pointing to old/nonexistent brew packages. So when I tried to install a fresh copy of firedrake, i get this message:
$ python firedrake-install --developer --disable_ssh --log
Installing command line tools...
Installing required packages via homebrew. You can safely ignore warnings that packages are already installed
Creating firedrake virtualenv in 'firedrake'.
/Users/justin/Software/firedrake/bin/pip install -vvv -U pip
Traceback (most recent call last):
File "firedrake-install", line 1016, in <module>
framework = fix_osx_virtualenv_python()
File "firedrake-install", line 973, in fix_osx_virtualenv_python
shutil.copytree(appsrc, appdest)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 208, in copytree
raise Error, errors
shutil.Error: [('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Info.plist', '/Users/justin/Software/firedrake/Python.app/Contents/Info.plist', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/Info.plist'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python', '/Users/justin/Software/firedrake/Python.app/Contents/MacOS/Python', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/MacOS/Python'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS', '/Users/justin/Software/firedrake/Python.app/Contents/MacOS', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/MacOS'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/PkgInfo', '/Users/justin/Software/firedrake/Python.app/Contents/PkgInfo', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/PkgInfo'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources/PythonApplet.icns', '/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonApplet.icns', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonApplet.icns'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources/PythonInterpreter.icns', '/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources', '/Users/justin/Software/firedrake/Python.app/Contents/Resources', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/Resources'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/version.plist', '/Users/justin/Software/firedrake/Python.app/Contents/version.plist', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/version.plist'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents', '/Users/justin/Software/firedrake/Python.app/Contents', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app', '/Users/justin/Software/firedrake/Python.app', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app'")]
And when I run the script again, it installs correctly. I guess this meant the virtualenv was "successfully" installed the first time.
$ python -c "from firedrake import *"
[Justins-MacBook-Pro-2.local:88453] [[15547,0],0] bind() failed on error Address already in use (48)
[Justins-MacBook-Pro-2.local:88453] [[15547,0],0] ORTE_ERROR_LOG: Error in file oob_usock_component.c at line 228
My firedrake programs appear to run without any error, but these messages still seem very suspicious. Any ideas what this could be? My homebrew upgrade/update has now given me Open MPI 2.0.1, and I am wondering if anyone else is having this issue.