bs-mbpr85:Applications baracd$ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" python firedrake-install
Installing command line tools...
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
Homebrew 1.1.12
Homebrew/homebrew-core (git revision 3ab9; last commit 2017-04-06)
Installing required packages via homebrew. You can safely ignore warnings that packages are already installed
/usr/local/Cellar/gcc/6.3.0_1/bin/c++-6
/usr/local/Cellar/gcc/6.3.0_1/bin/cpp-6
/usr/local/Cellar/gcc/6.3.0_1/bin/g++-6
/usr/local/Cellar/gcc/6.3.0_1/bin/gcc-6
/usr/local/Cellar/gcc/6.3.0_1/bin/gcc-ar-6
/usr/local/Cellar/gcc/6.3.0_1/bin/gcc-nm-6
/usr/local/Cellar/gcc/6.3.0_1/bin/gcc-ranlib-6
/usr/local/Cellar/gcc/6.3.0_1/bin/gcov-6
/usr/local/Cellar/gcc/6.3.0_1/bin/gcov-tool-6
/usr/local/Cellar/gcc/6.3.0_1/bin/gfortran
/usr/local/Cellar/gcc/6.3.0_1/bin/gfortran-6
/usr/local/Cellar/gcc/6.3.0_1/bin/x86_64-apple-darwin16.3.0-c++-6
/usr/local/Cellar/gcc/6.3.0_1/bin/x86_64-apple-darwin16.3.0-g++-6
/usr/local/Cellar/gcc/6.3.0_1/bin/x86_64-apple-darwin16.3.0-gcc-6
/usr/local/Cellar/gcc/6.3.0_1/bin/x86_64-apple-darwin16.3.0-gcc-6.3.0
/usr/local/Cellar/gcc/6.3.0_1/bin/x86_64-apple-darwin16.3.0-gcc-ar-6
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/usr/local/Cellar/gcc/6.3.0_1/bin/x86_64-apple-darwin16.3.0-gcc-ranlib-6
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/usr/local/Cellar/gcc/6.3.0_1/include/c++/ (757 files)
/usr/local/Cellar/gcc/6.3.0_1/lib/gcc/ (629 files)
/usr/local/Cellar/gcc/6.3.0_1/libexec/gcc/ (13 files)
/usr/local/Cellar/gcc/6.3.0_1/share/gcc-6.3.0/ (4 files)
/usr/local/Cellar/gcc/6.3.0_1/share/man/ (8 files)
/usr/local/Cellar/open-mpi/2.1.0/bin/mpic++
/usr/local/Cellar/open-mpi/2.1.0/bin/mpicc
/usr/local/Cellar/open-mpi/2.1.0/bin/mpicxx
/usr/local/Cellar/open-mpi/2.1.0/bin/mpiexec
/usr/local/Cellar/open-mpi/2.1.0/bin/mpif77
/usr/local/Cellar/open-mpi/2.1.0/bin/mpif90
/usr/local/Cellar/open-mpi/2.1.0/bin/mpifort
/usr/local/Cellar/open-mpi/2.1.0/bin/mpirun
/usr/local/Cellar/open-mpi/2.1.0/bin/ompi-clean
/usr/local/Cellar/open-mpi/2.1.0/bin/ompi-dvm
/usr/local/Cellar/open-mpi/2.1.0/bin/ompi-ps
/usr/local/Cellar/open-mpi/2.1.0/bin/ompi-server
/usr/local/Cellar/open-mpi/2.1.0/bin/ompi-submit
/usr/local/Cellar/open-mpi/2.1.0/bin/ompi-top
/usr/local/Cellar/open-mpi/2.1.0/bin/ompi_info
/usr/local/Cellar/open-mpi/2.1.0/bin/opal_wrapper
/usr/local/Cellar/open-mpi/2.1.0/bin/orte-clean
/usr/local/Cellar/open-mpi/2.1.0/bin/orte-dvm
/usr/local/Cellar/open-mpi/2.1.0/bin/orte-info
/usr/local/Cellar/open-mpi/2.1.0/bin/orte-ps
/usr/local/Cellar/open-mpi/2.1.0/bin/orte-server
/usr/local/Cellar/open-mpi/2.1.0/bin/orte-submit
/usr/local/Cellar/open-mpi/2.1.0/bin/orte-top
/usr/local/Cellar/open-mpi/2.1.0/bin/ortecc
/usr/local/Cellar/open-mpi/2.1.0/bin/orted
/usr/local/Cellar/open-mpi/2.1.0/bin/orterun
/usr/local/Cellar/open-mpi/2.1.0/etc/ (3 files)
/usr/local/Cellar/open-mpi/2.1.0/include/openmpi/ (2 files)
/usr/local/Cellar/open-mpi/2.1.0/include/ (23 files)
/usr/local/Cellar/open-mpi/2.1.0/lib/libmca_common_sm.20.dylib
/usr/local/Cellar/open-mpi/2.1.0/lib/libmpi.20.dylib
/usr/local/Cellar/open-mpi/2.1.0/lib/libmpi_mpifh.20.dylib
/usr/local/Cellar/open-mpi/2.1.0/lib/libmpi_usempi_ignore_tkr.20.dylib
/usr/local/Cellar/open-mpi/2.1.0/lib/libmpi_usempif08.20.dylib
/usr/local/Cellar/open-mpi/2.1.0/lib/libompitrace.20.dylib
/usr/local/Cellar/open-mpi/2.1.0/lib/libopen-pal.20.dylib
/usr/local/Cellar/open-mpi/2.1.0/lib/libopen-rte.20.dylib
/usr/local/Cellar/open-mpi/2.1.0/lib/openmpi/ (95 files)
/usr/local/Cellar/open-mpi/2.1.0/lib/pkgconfig/ (7 files)
/usr/local/Cellar/open-mpi/2.1.0/lib/ (8 other files)
/usr/local/Cellar/open-mpi/2.1.0/share/man/ (445 files)
/usr/local/Cellar/open-mpi/2.1.0/share/openmpi/ (71 files)
/usr/local/Cellar/python/2.7.13/bin/2to3
/usr/local/Cellar/python/2.7.13/bin/2to3-2
/usr/local/Cellar/python/2.7.13/bin/2to3-2.7
/usr/local/Cellar/python/2.7.13/bin/easy_install
/usr/local/Cellar/python/2.7.13/bin/easy_install-2.7
/usr/local/Cellar/python/2.7.13/bin/idle
/usr/local/Cellar/python/2.7.13/bin/idle2
/usr/local/Cellar/python/2.7.13/bin/idle2.7
/usr/local/Cellar/python/2.7.13/bin/pip
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/usr/local/Cellar/python/2.7.13/bin/pip2.7
/usr/local/Cellar/python/2.7.13/bin/pydoc
/usr/local/Cellar/python/2.7.13/bin/pydoc2
/usr/local/Cellar/python/2.7.13/bin/pydoc2.7
/usr/local/Cellar/python/2.7.13/bin/python
/usr/local/Cellar/python/2.7.13/bin/python-config
/usr/local/Cellar/python/2.7.13/bin/python2
/usr/local/Cellar/python/2.7.13/bin/python2-config
/usr/local/Cellar/python/2.7.13/bin/python2.7
/usr/local/Cellar/python/2.7.13/bin/python2.7-config
/usr/local/Cellar/python/2.7.13/bin/pythonw
/usr/local/Cellar/python/2.7.13/bin/pythonw2
/usr/local/Cellar/python/2.7.13/bin/pythonw2.7
/usr/local/Cellar/python/2.7.13/bin/smtpd.py
/usr/local/Cellar/python/2.7.13/bin/smtpd2.7.py
/usr/local/Cellar/python/2.7.13/bin/smtpd2.py
/usr/local/Cellar/python/2.7.13/bin/wheel
/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/ (2295 files)
/usr/local/Cellar/python/2.7.13/IDLE.app/Contents/ (8 files)
/usr/local/Cellar/python/2.7.13/lib/pkgconfig/ (3 files)
/usr/local/Cellar/python/2.7.13/libexec/pip/ (540 files)
/usr/local/Cellar/python/2.7.13/libexec/setuptools/ (272 files)
/usr/local/Cellar/python/2.7.13/libexec/wheel/ (93 files)
/usr/local/Cellar/python/2.7.13/Python Launcher.app/Contents/ (17 files)
/usr/local/Cellar/python/2.7.13/share/man/ (3 files)
/usr/local/Cellar/python/2.7.13/share/python/ (315 files)
/usr/local/Cellar/autoconf/2.69/bin/autoconf
/usr/local/Cellar/autoconf/2.69/bin/autoheader
/usr/local/Cellar/autoconf/2.69/bin/autom4te
/usr/local/Cellar/autoconf/2.69/bin/autoreconf
/usr/local/Cellar/autoconf/2.69/bin/autoscan
/usr/local/Cellar/autoconf/2.69/bin/autoupdate
/usr/local/Cellar/autoconf/2.69/bin/ifnames
/usr/local/Cellar/autoconf/2.69/share/autoconf/ (42 files)
/usr/local/Cellar/autoconf/2.69/share/emacs/ (4 files)
/usr/local/Cellar/autoconf/2.69/share/info/autoconf.info
/usr/local/Cellar/autoconf/2.69/share/man/ (9 files)
/usr/local/Cellar/automake/1.15/bin/aclocal
/usr/local/Cellar/automake/1.15/bin/aclocal-1.15
/usr/local/Cellar/automake/1.15/bin/automake
/usr/local/Cellar/automake/1.15/bin/automake-1.15
/usr/local/Cellar/automake/1.15/share/aclocal/ (2 files)
/usr/local/Cellar/automake/1.15/share/aclocal-1.15/ (33 files)
/usr/local/Cellar/automake/1.15/share/automake-1.15/ (76 files)
/usr/local/Cellar/automake/1.15/share/doc/automake/amhello-1.0.tar.gz
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/usr/local/Cellar/cmake/3.7.2/bin/ctest
/usr/local/Cellar/cmake/3.7.2/share/aclocal/cmake.m4
/usr/local/Cellar/cmake/3.7.2/share/cmake/ (2107 files)
/usr/local/Cellar/cmake/3.7.2/share/doc/ (6 files)
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/usr/local/Cellar/cmake/3.7.2/share/man/ (19 files)
/usr/local/Cellar/libtool/2.4.6_1/bin/glibtool
/usr/local/Cellar/libtool/2.4.6_1/bin/glibtoolize
/usr/local/Cellar/libtool/2.4.6_1/include/libltdl/ (3 files)
/usr/local/Cellar/libtool/2.4.6_1/include/ltdl.h
/usr/local/Cellar/libtool/2.4.6_1/lib/libltdl.7.dylib
/usr/local/Cellar/libtool/2.4.6_1/lib/ (2 other files)
/usr/local/Cellar/libtool/2.4.6_1/share/aclocal/ (7 files)
/usr/local/Cellar/libtool/2.4.6_1/share/info/ (3 files)
/usr/local/Cellar/libtool/2.4.6_1/share/libtool/ (42 files)
/usr/local/Cellar/libtool/2.4.6_1/share/man/ (2 files)
/usr/local/Cellar/mercurial/4.1.2/bin/chg
/usr/local/Cellar/mercurial/4.1.2/bin/hg
/usr/local/Cellar/mercurial/4.1.2/etc/bash_completion.d/hg-completion.bash
/usr/local/Cellar/mercurial/4.1.2/lib/python2.7/ (430 files)
/usr/local/Cellar/mercurial/4.1.2/share/man/ (3 files)
/usr/local/Cellar/mercurial/4.1.2/share/zsh/site-functions/_hg
Creating firedrake virtualenv in '/Users/baracd/Applications/firedrake'.
/Users/baracd/Applications/firedrake/bin/pip install -U setuptools
Collecting setuptools
  Using cached setuptools-34.4.1-py2.py3-none-any.whl
Collecting packaging>=16.8 (from setuptools)
  Using cached packaging-16.8-py2.py3-none-any.whl
Collecting appdirs>=1.4.0 (from setuptools)
  Using cached appdirs-1.4.3-py2.py3-none-any.whl
Collecting six>=1.6.0 (from setuptools)
  Using cached six-1.10.0-py2.py3-none-any.whl
Collecting pyparsing (from packaging>=16.8->setuptools)
  Using cached pyparsing-2.2.0-py2.py3-none-any.whl
Installing collected packages: six, pyparsing, packaging, appdirs, setuptools
  Found existing installation: setuptools 28.8.0
    Uninstalling setuptools-28.8.0:
      Successfully uninstalled setuptools-28.8.0
Successfully installed appdirs-1.4.3 packaging-16.8 pyparsing-2.2.0 setuptools-34.4.1 six-1.10.0
/Users/baracd/Applications/firedrake/bin/pip install -U pip
Requirement already up-to-date: pip in ./firedrake/lib/python2.7/site-packages
[('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/_CodeSignature/CodeResources', '/Users/baracd/Applications/firedrake/Python.app/Contents/_CodeSignature/CodeResources', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/_CodeSignature/CodeResources'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/_CodeSignature', '/Users/baracd/Applications/firedrake/Python.app/Contents/_CodeSignature', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/_CodeSignature'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Info.plist', '/Users/baracd/Applications/firedrake/Python.app/Contents/Info.plist', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/Info.plist'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python', '/Users/baracd/Applications/firedrake/Python.app/Contents/MacOS/Python', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/MacOS/Python'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS', '/Users/baracd/Applications/firedrake/Python.app/Contents/MacOS', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/MacOS'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/PkgInfo', '/Users/baracd/Applications/firedrake/Python.app/Contents/PkgInfo', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/PkgInfo'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources/PythonApplet.icns', '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources/PythonApplet.icns', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources/PythonApplet.icns'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources/PythonInterpreter.icns', '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources', '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/version.plist', '/Users/baracd/Applications/firedrake/Python.app/Contents/version.plist', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/version.plist'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents', '/Users/baracd/Applications/firedrake/Python.app/Contents', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app', '/Users/baracd/Applications/firedrake/Python.app', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app'")]
Traceback (most recent call last):
  File "firedrake-install", line 1140, 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
Error: [('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/_CodeSignature/CodeResources', '/Users/baracd/Applications/firedrake/Python.app/Contents/_CodeSignature/CodeResources', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/_CodeSignature/CodeResources'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/_CodeSignature', '/Users/baracd/Applications/firedrake/Python.app/Contents/_CodeSignature', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/_CodeSignature'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Info.plist', '/Users/baracd/Applications/firedrake/Python.app/Contents/Info.plist', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/Info.plist'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python', '/Users/baracd/Applications/firedrake/Python.app/Contents/MacOS/Python', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/MacOS/Python'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS', '/Users/baracd/Applications/firedrake/Python.app/Contents/MacOS', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/MacOS'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/PkgInfo', '/Users/baracd/Applications/firedrake/Python.app/Contents/PkgInfo', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/PkgInfo'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources/PythonApplet.icns', '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources/PythonApplet.icns', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources/PythonApplet.icns'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources/PythonInterpreter.icns', '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources', '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/version.plist', '/Users/baracd/Applications/firedrake/Python.app/Contents/version.plist', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents/version.plist'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents', '/Users/baracd/Applications/firedrake/Python.app/Contents', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app/Contents'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app', '/Users/baracd/Applications/firedrake/Python.app', "[Errno 1] Operation not permitted: '/Users/baracd/Applications/firedrake/Python.app'")]
Cloning firedrake

Warning: Permanently added the RSA host key for IP address '192.30.253.113' to the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone firedrake using ssh, falling back to https.
Successfully cloned repository firedrake.
Checking out branch master
Successfully checked out branch master
Cloning the dependencies of firedrake
Cloning ufl

Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone ufl using ssh, falling back to https.
Successfully cloned repository ufl.
Checking out branch master
Successfully checked out branch master
Cloning fiat

Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone fiat using ssh, falling back to https.
Successfully cloned repository fiat.
Checking out branch master
Successfully checked out branch master
Cloning FInAT

Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone FInAT using ssh, falling back to https.
Successfully cloned repository FInAT.
Checking out branch master
Successfully checked out branch master
Cloning tsfc

Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone tsfc using ssh, falling back to https.
Successfully cloned repository tsfc.
Checking out branch master
Successfully checked out branch master
Cloning PyOP2

Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone PyOP2 using ssh, falling back to https.
Successfully cloned repository PyOP2.
Checking out branch master
Successfully checked out branch master
Cloning the dependencies of PyOP2
Cloning petsc

Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone petsc using ssh, falling back to https.
Successfully cloned repository petsc.
Checking out branch firedrake
Successfully checked out branch firedrake
Cloning petsc4py

Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone petsc4py using ssh, falling back to https.
Successfully cloned repository petsc4py.
Checking out branch firedrake
Successfully checked out branch firedrake
Cloning COFFEE

Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Failed to clone COFFEE using ssh, falling back to https.
Successfully cloned repository COFFEE.
Checking out branch master
Successfully checked out branch master
/Users/baracd/Applications/firedrake/bin/pip install --no-binary mpi4py Cython>=0.22

dyld: Library not loaded: @executable_path/../.Python
  Referenced from: /Users/baracd/Applications/firedrake/bin/python
  Reason: image not found
Traceback (most recent call last):
  File "firedrake-install", line 1238, in <module>
    run_pip_install(["Cython>=0.22"])
  File "firedrake-install", line 548, in run_pip_install
    check_call(pipinstall + pipargs)
  File "firedrake-install", line 369, in check_call
    subprocess.check_call(arguments, env=env)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 540, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/Users/baracd/Applications/firedrake/bin/pip', 'install', '--no-binary', 'mpi4py', 'Cython>=0.22']' returned non-zero exit status -6
bs-mbpr85:Applications baracd$