Add Mac OS specific installation instructions

[terotik]

No description provided.

[billlyzhaoyh]

I am using Mac OS here and created a new conda env and download all the packages in the requirement.txt but not the apt-get packages.

This is the thing I got after reinstalling numpy (the version from the git throws error that the Apple Accelerate backend might be at fault)

Hope to have a Mac OS installation instruction soon so I can start playing around the model!

Error compiling Cython file:

...

cython: language_level=3

from numpy.random cimport bitgen_t
^

cythonsim/simrandom.pxd:2:0: 'numpy/random.pxd' not found

Error compiling Cython file:

...

cython: language_level=3

from numpy.random cimport bitgen_t
^

cythonsim/simrandom.pxd:2:0: 'numpy/random/bitgen_t.pxd' not found

Error compiling Cython file:

...
from numpy.random cimport bitgen_t

cdef class RandomPool:
cdef object gen
cdef bitgen_t *rng
^

cythonsim/simrandom.pxd:7:9: 'bitgen_t' is not a type identifier

Error compiling Cython file:

...
from numpy.random import PCG64
import numpy as np

from cpython.pycapsule cimport PyCapsule_IsValid, PyCapsule_GetPointer
from numpy.random cimport bitgen_t
from numpy.random.c_distributions cimport random_lognormal, random_gamma_f
^

cythonsim/simrandom.pyx:11:0: 'numpy/random/c_distributions.pxd' not found

Error compiling Cython file:

...
from numpy.random import PCG64
import numpy as np

from cpython.pycapsule cimport PyCapsule_IsValid, PyCapsule_GetPointer
from numpy.random cimport bitgen_t
from numpy.random.c_distributions cimport random_lognormal, random_gamma_f
^

[terotik]

@billlyzhaoyh just a quick note here that might help before we get the more official process in the documentation

Reina is using dev version of numpy that needs to be compiled, here's how I managed to get it done on Mac:

brew install libomp cmake gcc llvm redis
CC=/usr/local/opt/llvm/bin/clang++ python -m calc.simulation

Also you need to have redis cache running before launching the model

echo 'REDIS_URL=redis://' > .env
brew services start redis

[billlyzhaoyh]

The errors I encountered with the newest version of numpy is this:

RuntimeError: Polyfit sanity test emitted a warning, most likely due to using a buggy Accelerate backend. If you compiled yourself, see site.cfg.example for information. Otherwise report this to the vendor that provided NumPy.
RankWarning: Polyfit may be poorly conditioned

By tracking the changes on github this seems to be something that was added this version. Do you have any idea why?

[billlyzhaoyh]

I have fixed the numpy import problem by using openblas and I followed your instructions and used this command to execute with redis running:
CC=/usr/local/Cellar/llvm/10.0.0_1/bin/clang++ python -m calc.simulation

The error messages generated are attached below:
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
/Users/billyzhaoyh/.pyxbld/temp.macosx-10.9-x86_64-3.7/pyrex/cythonsim/main.c:6939:13: warning:
code will never be executed [-Wunreachable-code]
__pyx_r = 0;
^
1 warning generated.
ld: unknown option: -platform_version
clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
Traceback (most recent call last):
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/unixccompiler.py", line 205, in link
self.spawn(linker + ld_args)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/ccompiler.py", line 910, in spawn
spawn(cmd, dry_run=self.dry_run)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/spawn.py", line 36, in spawn
_spawn_posix(cmd, search_path, dry_run=dry_run)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/spawn.py", line 159, in _spawn_posix
% (cmd, exit_status))
distutils.errors.DistutilsExecError: command '/usr/local/Cellar/llvm/10.0.0_1/bin/clang++' failed with exit status 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/site-packages/pyximport/pyximport.py", line 215, in load_module
inplace=build_inplace, language_level=language_level)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/site-packages/pyximport/pyximport.py", line 191, in build_module
reload_support=pyxargs.reload_support)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/site-packages/pyximport/pyxbuild.py", line 102, in pyx_to_dll
dist.run_commands()
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/site-packages/Cython/Distutils/old_build_ext.py", line 186, in run
_build_ext.build_ext.run(self)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/command/build_ext.py", line 340, in run
self.build_extensions()
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/site-packages/Cython/Distutils/old_build_ext.py", line 195, in build_extensions
_build_ext.build_ext.build_extensions(self)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/command/build_ext.py", line 449, in build_extensions
self._build_extensions_serial()
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/command/build_ext.py", line 474, in _build_extensions_serial
self.build_extension(ext)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/command/build_ext.py", line 559, in build_extension
target_lang=language)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/ccompiler.py", line 717, in link_shared_object
extra_preargs, extra_postargs, build_temp, target_lang)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/unixccompiler.py", line 207, in link
raise LinkError(msg)
distutils.errors.LinkError: command '/usr/local/Cellar/llvm/10.0.0_1/bin/clang++' failed with exit status 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/Users/billyzhaoyh/Desktop/Simulation/reina-model/calc/simulation.py", line 8, in
from cythonsim import model
File "/Users/billyzhaoyh/Desktop/Simulation/reina-model/cythonsim/init.py", line 6, in
from . import main as model
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/site-packages/pyximport/pyximport.py", line 462, in load_module
language_level=self.language_level)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/site-packages/pyximport/pyximport.py", line 231, in load_module
raise exc.with_traceback(tb)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/site-packages/pyximport/pyximport.py", line 215, in load_module
inplace=build_inplace, language_level=language_level)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/site-packages/pyximport/pyximport.py", line 191, in build_module
reload_support=pyxargs.reload_support)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/site-packages/pyximport/pyxbuild.py", line 102, in pyx_to_dll
dist.run_commands()
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/site-packages/Cython/Distutils/old_build_ext.py", line 186, in run
_build_ext.build_ext.run(self)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/command/build_ext.py", line 340, in run
self.build_extensions()
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/site-packages/Cython/Distutils/old_build_ext.py", line 195, in build_extensions
_build_ext.build_ext.build_extensions(self)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/command/build_ext.py", line 449, in build_extensions
self._build_extensions_serial()
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/command/build_ext.py", line 474, in _build_extensions_serial
self.build_extension(ext)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/command/build_ext.py", line 559, in build_extension
target_lang=language)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/ccompiler.py", line 717, in link_shared_object
extra_preargs, extra_postargs, build_temp, target_lang)
File "/Users/billyzhaoyh/anaconda/envs/simulation/lib/python3.7/distutils/unixccompiler.py", line 207, in link
raise LinkError(msg)
ImportError: Building module cythonsim.main failed: ["distutils.errors.LinkError: command '/usr/local/Cellar/llvm/10.0.0_1/bin/clang++' failed with exit status 1\n"]

Do you know why clang++ is not executing in this case?

[jukvalim]

@terotic I added support for running with Docker here, which works fine with Mac OS as well other platforms: https://github.com/jukvalim/reina-model

I created a PR for it, just in case it's something you'd like to have.

[terotik]

Fantastic, thank you @jukvalim ! This is now merged.

Ping: @billlyzhaoyh