pysat/pysatCDF

Installing with pip

Closed this issue · 12 comments

asher-pembroke commented

I ran into problems installing with pip involving the notorious libgfortran rpath bug on mac.

To reproduce,

  1. pip pysatCDF on a mac anaconda/miniconda environment (python 2.7)
  2. import pysatCDF
  3. raises something like this
ImportError: dlopen(/Users/apembrok/Library/Caches/Python-Eggs/pysatCDF-0.3.0-py2.7-macosx-10.6-x86_64.egg-tmp/pysatCDF/fortran_cdf.so, 2): Library not loaded: @rpath/./libgfortran.3.dylib
  Referenced from: /Users/apembrok/Library/Caches/Python-Eggs/pysatCDF-0.3.0-py2.7-macosx-10.6-x86_64.egg-tmp/pysatCDF/fortran_cdf.so
  Reason: image not found

To resolve:

  1. verify the existing library names assigned to fortran_cdf.so:
    otool -L ${CONDA_PREFIX}/lib/python2.7/site-packages/pysatCDF/fortran_cdf.so
  2. modify the library names with install_name_tool:
install_name_tool -change @rpath/./libgfortran.3.dylib ${CONDA_PREFIX}/lib/libgfortran.dylib -change @rpath/./libquadmath.0.dylib ${CONDA_PREFIX}/lib/libquadmath.0.dylib fortran_cdf.so ${CONDA_PREFIX}/lib/python2.7/site-packages/pysatCDF/fortran_cdf.so

Conda package installers usually fix the rpath issue automagically. Not sure how to do this with setuptools...

rstoneback commented
dcsozturk commented

Hi, I also run into a problem trying to install pysat, pysatCDF, and pysatMagVect with pip. It is not directly relevant but I was hesitant to start a new issue, since it is technically an "installation with pip issue". Please feel free to move/edit as you see fit.

I have the following:

  • macOS v.10.14.6
  • gcc 9.2.0_1 (installed with Brew)
  • python2.7.15 (also tried this in python3)

I get a bunch of warnings during installation, all seem to be related with the incompatibility between Apple clang and gfortran versions I installed with Homebrew. To fix I had to define new aliases in my bashrc file to point the gcc and gfortran installed by brew in my /usr/local/bin/.

The problem is similar to pymc-devs/pymc#119

rstoneback commented
asher-pembroke commented

A lot of places suggest the delocate tool which makes pip wheels portable. That would at least solve the issue where users aren't able to install with pip.

  • 👍1
asher-pembroke commented

Also, note that install_name_tool requires users to have the xcode developer tools installed so putting the command in setup.py may not help: https://stackoverflow.com/a/11598098

rstoneback commented

The delocate looks like it would be helpful for pip.

asher-pembroke commented

I found a lot of issues with clang as well, but gcc seems to work better.

I'm able to install from setup.py using the following environment setup

conda create -n pysatCDF python=2.7
conda install -c anaconda gcc
conda install -c anaconda numpy
pip install pysat (or setup.py after cloning pysat)

Then, from pysatCDF directory:

python setup.py install (or pip install .)

@rstoneback Anything left to do here?

rstoneback commented
asher-pembroke commented

Yep, it works with python3 as well.

rstoneback commented

I've uploaded delocated versions of pysatCDF to pypi for macosx. python 2 and 3.8 are currently supported.

aburrell commented

I was finally able to fix various issues and got pysatCDF to install on my laptop (OSX Mojave) with python 2.7, 3.7, and 3.8.

rstoneback commented