python-inferno

Partly adapted from https://code.metoffice.gov.uk/svn/utils/inferno_py (joaoteixeira)

Use git submodule update --init --recursive to recursively update git submodules, e.g. the GPU code project which contains a submodule itself.

Install py_gpu_inferno using the following steps:

mkdir build
cd build
cmake ..
make py_gpu_inferno
make install

Useful environment variables

KMP_WARNINGS=off
LOGURU_LEVEL=WARNING

rpy2

A separate miniconda installation was used for rpy2 since it was found that installing rpy2 broke pyenv. This used the conda requirements file: arm64_requirements_rpy2.yaml.

See: https://mac.r-project.org/openmp/ regarding R installation on MAC M1. Note also the following contents of ~/.R/Makevars:

BLDSHARED=clang -bundle -undefined
CC=clang
CCBASE=clang
CLANG=clang
CLINKERBASE=clang
CPP=clang -E
CXX11=clang++
CXX14=clang++
CXX17=clang++
CXX20=clang++
CXX=clang++ -std=gnu++14
CXXBASE=clang++
CXXLINKERBASE=clang++
LDCXXSHARED=clang++ -bundle -undefined
LDSHARED=clang -bundle -undefined dynamic_lookup
LINKCC=clang
LTCC=clang
MAINCC=clang
OBJC=clang
OBJCXX=clang++
ccompiler=clang
cppcompiler=clang++
CPPFLAGS+=-Xclang -fopenmp
LDFLAGS+=-lomp

Note that <miniconda_dir>/envs/python-inferno/lib/R/etc/Makeconf and similar files were modified to use clang, clang++ (instead of equivalent names prefixed like 'arm64-...' or similar), and -fopenmp -> -Xclang -fopenmp.

Run install.packages(c("mgcv", "import", "purrr"), dependencies=TRUE) to install R dependencies.

See also https://github.com/kharchenkolab/conos/wiki/Installing-Conos-for-Mac-OS.