Installing with pip

[asher-pembroke]

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]

Thanks Asher.

Since you have the terminal command can’t you invoke that from setup.py?

I believe there is a post-install trigger in setuptools and the package has the paths and such the final code is, or will be, when installed.

On Oct 9, 2019, at 5:25 PM, Asher Pembroke notifications@github.com<mailto:notifications@github.com> wrote:

I ran into problems installing with pip involving the notorious libgfortran rpath bughttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FContinuumIO%2Fanaconda-issues%2Fissues%2F739&data=02%7C01%7Crstoneba%40utdallas.edu%7Ca340e93046f74b7db90808d74d07840f%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C0%7C637062566996679415&sdata=rc%2FB%2FjvgNM5g9Bqqg18SM35sz%2FwZAT9A0%2BnIgCHgO%2B8%3D&reserved=0 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...

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[dcsozturk]

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 https://github.com/pymc-devs/pymc/issues/119

[rstoneback]

Thanks for the report.

Cheers

[asher-pembroke]

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.

[asher-pembroke]

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]

The delocate looks like it would be helpful for pip.

[asher-pembroke]

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]

Does it work in python 3? If it’s good then I think we are good.

Cheers, Russell

On Nov 4, 2019, at 11:41 AM, Asher Pembroke notifications@github.com wrote:



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 .)

@rstonebackhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Frstoneback&data=02%7C01%7Crstoneba%40utdallas.edu%7Cb069f242f989454df8a508d7615696cb%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C0%7C637084896840415726&sdata=Bl8QmPA%2Fl4M4J42nXjrokOeJegJzySj2Via2ZNGLtug%3D&reserved=0 Anything left to do here?

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[asher-pembroke]

Yep, it works with python3 as well.

[rstoneback]

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

[aburrell]

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]

Great!