On 20/09/16 09:30, Justin Chang wrote:
> Hi all,
>
> 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.
>
> However, I get this strange MPI warning/error that I have never before
> seen:
>
> $ 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.

Can you run an mpi4py program?

In the virtualenv:

$ python -c "from mpi4py import MPI; print MPI.COMM_WORLD.rank"

If that fails, try uninstalling mpi4py

$ pip uninstall mpi4py

And then reinstalling, but crucially without using the pip cache:

$ pip install --no-binary :all: mpi4py


Cheers,

Lawrence


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