123 mac m1 installation

[sy-cui]

Fix #123

The source of dependencies PyFFTW and pystencils are set to two temporary git repositories.
PyFFTW: https://github.com/tp5uiuc/pyFFTW/tree/macos_fix
pystencils: https://github.com/sy-cui/pystencils/tree/macos_fix

The modifed PyFFTW looks up fftw library in /opt/homebrew/lib on macos platforms.

In pystencils, the shared object (.so) file is not dynamically linked to OpenMP properly on Apple M1. Restricting the -fopenmp compiler option to the linking stage alone seems to resolve this issue. For our purpose, it is also plausible to compile in one step instead of two

clang++ -shared -o object.so object.cpp -fopenmp -undefined dynamic_lookup [other options]

but we don't do it for now.

A new environment.yml file is provided to integrate poetry into conda environment.
(curtesy of https://stackoverflow.com/questions/70851048/does-it-make-sense-to-use-conda-poetry)

Poetry version is restricted to below 1.6 to avoid a known issue with version control.

Edit:
The changes regarding -fopenmp on pystencils is reverted as multithreading isn't enabled if the flag isn't passed. Instead the clang compiler flag -Xclang is removed as it prevents -fopenmp from being recognized as a regular command line option.

[bhosale2]

LGTM

[bhosale2]

@armantekinalp please take a look again and merge accordingly.

[armantekinalp]

I think this is not working yet. Songyuan was planning to test on different machines. @sy-cui can you confirm?

[sy-cui]

After the most recent push everything should be fine now. I have tested on Bridges and Expanse and they install without issue. We could (and should) let people in the lab try installing now because I made the dependency sources platform dependent, and we might not catch some issues with just clusters.

[armantekinalp]

Okay let me try on my system as well, then we can proceed

[bhosale2]

@sy-cui and @armantekinalp current installation instructions on this branch didnt work on my machine (pyfftw issue I think):

[bhosale2]

ok I just realized the issue. The install instructions don't tell to install fftw via brew first. @sy-cui lets add it somewhere then? or what if we integrate it in conda env?

Also we need instructions to install llvm and link it properly. @sy-cui please discuss with @armantekinalp and figure out a solution accordingly.

basically current instructions dont work off the bat, some more details are needed

[sy-cui]

@armantekinalp @bhosale2 can we merge this?

[armantekinalp]

LGTM

[bhosale2]

LGTM