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kausaltech / reina-model

Agent-based simulation model for COVID-19 spread in society and patient outcomes
https://reina.kausal.tech/
GNU Affero General Public License v3.0
30 stars 14 forks source link

Add Mac OS specific installation instructions #12

Open terotik opened 4 years ago

billlyzhaoyh commented 4 years ago

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 commented 4 years ago

@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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

@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 commented 4 years ago

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

Ping: @billlyzhaoyh