Hi all, Upon experimenting with Joe’s python3 version of kwant on OS X I found that mumps has a well maintained homebrew formula of its own in the homebrew/science tap: https://github.com/Homebrew/homebrew-science/blob/master/mumps.rb I think it might be useful to simplify the kwant installation on OS X. Also the tinyarray and kwant version are outdated on https://github.com/michaelwimmer/homebrew-kwant Updating tinyarray via pip doesn’t work: bnijholt:~> pip install tinyarray -U Collecting tinyarray Installing collected packages: tinyarray Found existing installation: tinyarray 1.0.2 DEPRECATION: Uninstalling a distutils installed project (tinyarray) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project. Uninstalling tinyarray-1.0.2: Successfully uninstalled tinyarray-1.0.2 Rolling back uninstall of tinyarray Exception: Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/pip/basecommand.py", line 223, in main status = self.run(options, args) File "/usr/local/lib/python2.7/site-packages/pip/commands/install.py", line 299, in run root=options.root_path, File "/usr/local/lib/python2.7/site-packages/pip/req/req_set.py", line 646, in install **kwargs File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 813, in install self.move_wheel_files(self.source_dir, root=root) File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 1008, in move_wheel_files isolated=self.isolated, File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 339, in move_wheel_files clobber(source, lib_dir, True) File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 317, in clobber shutil.copyfile(srcfile, destfile) File "/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 83, in copyfile with open(dst, 'wb') as fdst: IOError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/tinyarray.so' Changing the kwant tarball to the 1.0.4 file on the brew formula also doesn’t work (https://github.com/basnijholt/homebrew-kwant/blob/master/kwant.rb): bnijholt:~> brew install kwant ==> Installing kwant from basnijholt/homebrew-kwant ==> Using Homebrew-provided fortran compiler. This may be changed by setting the FC environment variable. ==> Building with an alternative Fortran compiler This is unsupported. Warning: No Fortran optimization information was provided. You may want to consider setting FCFLAGS and FFLAGS or pass the `--default-fortran-flags` option to `brew install` if your compiler is compatible with GCC. If you like the default optimization level of your compiler, ignore this warning. ==> Downloading pypi.python.org/packages/source/k/kwant/kwant-1.0.4.tar.gz Already downloaded: /Library/Caches/Homebrew/kwant-1.0.4.tar.gz ==> Patching patching file build.conf ==> python setup.py install --prefix=/usr/local/Cellar/kwant/1.0.4 Build configuration was: User-configured LAPACK and BLAS User-configured MUMPS ********************************************************************** error: command 'clang' failed with exit status 1 READ THIS: https://git.io/brew-troubleshooting If reporting this issue please do so at (not Homebrew/homebrew): https://github.com/basnijholt/homebrew-kwant/issues Best Bas
Hi Bas, I don't have a mac, but it appears that you executed the first command without the superuser permissions. It also tries to modify the python 2.7 installation instead of 3.4, so you're definitely not doing what you want. Probably replacing pip with pip3 or python with python3 would help (if it's pip that you're using). As far as the second command goes, did you try following the suggestion and using the fortran flags option? Best, Anton On Sun, Aug 9, 2015 at 10:44 PM, Bas Nijholt <basnijholt@gmail.com> wrote:
Hi all,
Upon experimenting with Joe’s python3 version of kwant on OS X I found that mumps has a well maintained homebrew formula of its own in the homebrew/science tap: https://github.com/Homebrew/homebrew-science/blob/master/mumps.rb
I think it might be useful to simplify the kwant installation on OS X.
Also the tinyarray and kwant version are outdated on https://github.com/michaelwimmer/homebrew-kwant
Updating tinyarray via pip doesn’t work:
bnijholt:~> pip install tinyarray -U Collecting tinyarray Installing collected packages: tinyarray Found existing installation: tinyarray 1.0.2 DEPRECATION: Uninstalling a distutils installed project (tinyarray) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project. Uninstalling tinyarray-1.0.2: Successfully uninstalled tinyarray-1.0.2 Rolling back uninstall of tinyarray Exception: Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/pip/basecommand.py", line 223, in main status = self.run(options, args) File "/usr/local/lib/python2.7/site-packages/pip/commands/install.py", line 299, in run root=options.root_path, File "/usr/local/lib/python2.7/site-packages/pip/req/req_set.py", line 646, in install **kwargs File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 813, in install self.move_wheel_files(self.source_dir, root=root) File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 1008, in move_wheel_files isolated=self.isolated, File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 339, in move_wheel_files clobber(source, lib_dir, True) File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 317, in clobber shutil.copyfile(srcfile, destfile) File "/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 83, in copyfile with open(dst, 'wb') as fdst: IOError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/tinyarray.so'
Changing the kwant tarball to the 1.0.4 file on the brew formula also doesn’t work (https://github.com/basnijholt/homebrew-kwant/blob/master/kwant.rb):
bnijholt:~> brew install kwant ==> Installing kwant from basnijholt/homebrew-kwant ==> Using Homebrew-provided fortran compiler. This may be changed by setting the FC environment variable. ==> Building with an alternative Fortran compiler This is unsupported. Warning: No Fortran optimization information was provided. You may want to consider setting FCFLAGS and FFLAGS or pass the `--default-fortran-flags` option to `brew install` if your compiler is compatible with GCC.
If you like the default optimization level of your compiler, ignore this warning. ==> Downloading pypi.python.org/packages/source/k/kwant/kwant-1.0.4.tar.gz Already downloaded: /Library/Caches/Homebrew/kwant-1.0.4.tar.gz ==> Patching patching file build.conf ==> python setup.py install --prefix=/usr/local/Cellar/kwant/1.0.4 Build configuration was: User-configured LAPACK and BLAS User-configured MUMPS ********************************************************************** error: command 'clang' failed with exit status 1
READ THIS: https://git.io/brew-troubleshooting If reporting this issue please do so at (not Homebrew/homebrew): https://github.com/basnijholt/homebrew-kwant/issues
Best Bas
Hi Anton, I probably wasn't clear on this, but I was addressing different points, the "old" kwant py2 installation, can't be updated. A Mac related thing; if you installed python with brew, it's recommended that you install everything without sudo rights. Best, Bas On Mon, Aug 10, 2015 at 11:05 AM, Anton Akhmerov <anton.akhmerov@gmail.com> wrote:
Hi Bas, I don't have a mac, but it appears that you executed the first command without the superuser permissions. It also tries to modify the python 2.7 installation instead of 3.4, so you're definitely not doing what you want. Probably replacing pip with pip3 or python with python3 would help (if it's pip that you're using). As far as the second command goes, did you try following the suggestion and using the fortran flags option? Best, Anton On Sun, Aug 9, 2015 at 10:44 PM, Bas Nijholt <basnijholt@gmail.com> wrote:
Hi all,
Upon experimenting with Joe’s python3 version of kwant on OS X I found that mumps has a well maintained homebrew formula of its own in the homebrew/science tap: https://github.com/Homebrew/homebrew-science/blob/master/mumps.rb
I think it might be useful to simplify the kwant installation on OS X.
Also the tinyarray and kwant version are outdated on https://github.com/michaelwimmer/homebrew-kwant
Updating tinyarray via pip doesn’t work:
bnijholt:~> pip install tinyarray -U Collecting tinyarray Installing collected packages: tinyarray Found existing installation: tinyarray 1.0.2 DEPRECATION: Uninstalling a distutils installed project (tinyarray) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project. Uninstalling tinyarray-1.0.2: Successfully uninstalled tinyarray-1.0.2 Rolling back uninstall of tinyarray Exception: Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/pip/basecommand.py", line 223, in main status = self.run(options, args) File "/usr/local/lib/python2.7/site-packages/pip/commands/install.py", line 299, in run root=options.root_path, File "/usr/local/lib/python2.7/site-packages/pip/req/req_set.py", line 646, in install **kwargs File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 813, in install self.move_wheel_files(self.source_dir, root=root) File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 1008, in move_wheel_files isolated=self.isolated, File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 339, in move_wheel_files clobber(source, lib_dir, True) File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 317, in clobber shutil.copyfile(srcfile, destfile) File "/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 83, in copyfile with open(dst, 'wb') as fdst: IOError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/tinyarray.so'
Changing the kwant tarball to the 1.0.4 file on the brew formula also doesn’t work (https://github.com/basnijholt/homebrew-kwant/blob/master/kwant.rb):
bnijholt:~> brew install kwant ==> Installing kwant from basnijholt/homebrew-kwant ==> Using Homebrew-provided fortran compiler. This may be changed by setting the FC environment variable. ==> Building with an alternative Fortran compiler This is unsupported. Warning: No Fortran optimization information was provided. You may want to consider setting FCFLAGS and FFLAGS or pass the `--default-fortran-flags` option to `brew install` if your compiler is compatible with GCC.
If you like the default optimization level of your compiler, ignore this warning. ==> Downloading pypi.python.org/packages/source/k/kwant/kwant-1.0.4.tar.gz Already downloaded: /Library/Caches/Homebrew/kwant-1.0.4.tar.gz ==> Patching patching file build.conf ==> python setup.py install --prefix=/usr/local/Cellar/kwant/1.0.4 Build configuration was: User-configured LAPACK and BLAS User-configured MUMPS ********************************************************************** error: command 'clang' failed with exit status 1
READ THIS: https://git.io/brew-troubleshooting If reporting this issue please do so at (not Homebrew/homebrew): https://github.com/basnijholt/homebrew-kwant/issues
Best Bas
I probably wasn't clear on this, but I was addressing different points, the "old" kwant py2 installation, can't be updated.
I see.
A Mac related thing; if you installed python with brew, it's recommended that you install everything without sudo rights.
Right, but since there was a permission denied, it appears that you cannot remove the file. You can double-check the permissions or even manually remove the offending file. Anton
Best, Bas
On Mon, Aug 10, 2015 at 11:05 AM, Anton Akhmerov <anton.akhmerov@gmail.com> wrote:
Hi Bas,
I don't have a mac, but it appears that you executed the first command without the superuser permissions. It also tries to modify the python 2.7 installation instead of 3.4, so you're definitely not doing what you want. Probably replacing pip with pip3 or python with python3 would help (if it's pip that you're using).
As far as the second command goes, did you try following the suggestion and using the fortran flags option?
Best, Anton
On Sun, Aug 9, 2015 at 10:44 PM, Bas Nijholt <basnijholt@gmail.com> wrote:
Hi all,
Upon experimenting with Joe’s python3 version of kwant on OS X I found that mumps has a well maintained homebrew formula of its own in the homebrew/science tap: https://github.com/Homebrew/homebrew-science/blob/master/mumps.rb
I think it might be useful to simplify the kwant installation on OS X.
Also the tinyarray and kwant version are outdated on https://github.com/michaelwimmer/homebrew-kwant
Updating tinyarray via pip doesn’t work:
bnijholt:~> pip install tinyarray -U Collecting tinyarray Installing collected packages: tinyarray Found existing installation: tinyarray 1.0.2 DEPRECATION: Uninstalling a distutils installed project (tinyarray) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project. Uninstalling tinyarray-1.0.2: Successfully uninstalled tinyarray-1.0.2 Rolling back uninstall of tinyarray Exception: Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/pip/basecommand.py", line 223, in main status = self.run(options, args) File "/usr/local/lib/python2.7/site-packages/pip/commands/install.py", line 299, in run root=options.root_path, File "/usr/local/lib/python2.7/site-packages/pip/req/req_set.py", line 646, in install **kwargs File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 813, in install self.move_wheel_files(self.source_dir, root=root) File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 1008, in move_wheel_files isolated=self.isolated, File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 339, in move_wheel_files clobber(source, lib_dir, True) File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 317, in clobber shutil.copyfile(srcfile, destfile) File
"/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 83, in copyfile with open(dst, 'wb') as fdst: IOError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/tinyarray.so'
Changing the kwant tarball to the 1.0.4 file on the brew formula also doesn’t work (https://github.com/basnijholt/homebrew-kwant/blob/master/kwant.rb):
bnijholt:~> brew install kwant ==> Installing kwant from basnijholt/homebrew-kwant ==> Using Homebrew-provided fortran compiler. This may be changed by setting the FC environment variable. ==> Building with an alternative Fortran compiler This is unsupported. Warning: No Fortran optimization information was provided. You may want to consider setting FCFLAGS and FFLAGS or pass the `--default-fortran-flags` option to `brew install` if your compiler is compatible with GCC.
If you like the default optimization level of your compiler, ignore this warning. ==> Downloading pypi.python.org/packages/source/k/kwant/kwant-1.0.4.tar.gz Already downloaded: /Library/Caches/Homebrew/kwant-1.0.4.tar.gz ==> Patching patching file build.conf ==> python setup.py install --prefix=/usr/local/Cellar/kwant/1.0.4 Build configuration was: User-configured LAPACK and BLAS User-configured MUMPS ********************************************************************** error: command 'clang' failed with exit status 1
READ THIS: https://git.io/brew-troubleshooting If reporting this issue please do so at (not Homebrew/homebrew): https://github.com/basnijholt/homebrew-kwant/issues
Best Bas
Hi Bas, - thanks for bringing up the mumps formula. The problem is that this formula is for both the mpi and non-mpi (sequential) variant. Kwant only runs with the sequential version, but it is not possible to require such a specific variant in homebrew. Hence, if someone has already installed the mpi version, kwant would be linked against this one, and it would not work. This is why we made our own formula. But you can easily upgrade this one to Mumps 5 yourself, if you would like to check kwant-compatibility, I haven't had the time yet (some small things have been changed in mumps) - tinyarray: seems something went wrong with permissions, did you maybe use sudo at some point? - kwant 1.0.4, it seems you used the old 1.0.2 formula to update. Use my new 1.0.3 formula and it should work. Kwant 1.0.4 came out when I went on holiday, the official update must wait until I'm back ;) Best, Michael
Am 9 aug. 2015 um 22:44 schrieb Bas Nijholt <basnijholt@gmail.com>:
Hi all,
Upon experimenting with Joe’s python3 version of kwant on OS X I found that mumps has a well maintained homebrew formula of its own in the homebrew/science tap: https://github.com/Homebrew/homebrew-science/blob/master/mumps.rb
I think it might be useful to simplify the kwant installation on OS X.
Also the tinyarray and kwant version are outdated on https://github.com/michaelwimmer/homebrew-kwant
Updating tinyarray via pip doesn’t work:
bnijholt:~> pip install tinyarray -U Collecting tinyarray Installing collected packages: tinyarray Found existing installation: tinyarray 1.0.2 DEPRECATION: Uninstalling a distutils installed project (tinyarray) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project. Uninstalling tinyarray-1.0.2: Successfully uninstalled tinyarray-1.0.2 Rolling back uninstall of tinyarray Exception: Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/pip/basecommand.py", line 223, in main status = self.run(options, args) File "/usr/local/lib/python2.7/site-packages/pip/commands/install.py", line 299, in run root=options.root_path, File "/usr/local/lib/python2.7/site-packages/pip/req/req_set.py", line 646, in install **kwargs File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 813, in install self.move_wheel_files(self.source_dir, root=root) File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 1008, in move_wheel_files isolated=self.isolated, File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 339, in move_wheel_files clobber(source, lib_dir, True) File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 317, in clobber shutil.copyfile(srcfile, destfile) File "/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 83, in copyfile with open(dst, 'wb') as fdst: IOError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/tinyarray.so'
Changing the kwant tarball to the 1.0.4 file on the brew formula also doesn’t work (https://github.com/basnijholt/homebrew-kwant/blob/master/kwant.rb):
bnijholt:~> brew install kwant ==> Installing kwant from basnijholt/homebrew-kwant ==> Using Homebrew-provided fortran compiler. This may be changed by setting the FC environment variable. ==> Building with an alternative Fortran compiler This is unsupported. Warning: No Fortran optimization information was provided. You may want to consider setting FCFLAGS and FFLAGS or pass the `--default-fortran-flags` option to `brew install` if your compiler is compatible with GCC.
If you like the default optimization level of your compiler, ignore this warning. ==> Downloading pypi.python.org/packages/source/k/kwant/kwant-1.0.4.tar.gz Already downloaded: /Library/Caches/Homebrew/kwant-1.0.4.tar.gz ==> Patching patching file build.conf ==> python setup.py install --prefix=/usr/local/Cellar/kwant/1.0.4 Build configuration was: User-configured LAPACK and BLAS User-configured MUMPS ********************************************************************** error: command 'clang' failed with exit status 1
READ THIS: https://git.io/brew-troubleshooting If reporting this issue please do so at (not Homebrew/homebrew): https://github.com/basnijholt/homebrew-kwant/issues
Best Bas
participants (3)
-
Anton Akhmerov -
Bas Nijholt -
Michael Wimmer