Arbor playground prebuilt

Versions

• arbor 0.7.1-dev (491a0d648b8e245d04842f5ffed5ba9e3d087d48)
• emscripten 3.1.21
• python 3.10.2
• pyodide 0.22.0a1

Live version (v0.2 beta): https://llandsmeer.github.io/arbor-online/

Custom mechanisms go in the catalogue directory

Build instructions

For if you want to port a new arbor version. The build process is very version dependent, you'll probably have to adapt it to new releases.

1. Download and unpack a pyodide release, both the xbuildenv-*.tar.bz2 and pyodide-*.tar.bz2 files.
2. Find out the emscripten version, eg. by running make -f Makefile.envs .output_vars | grep PYODIDE_EMSCRIPTEN_VERSION in xbuildenv-*/pyodide-root
3. Download the latest emsdk release
4. Install the correct (same as pyodide) emscripten version using emsdk install/activate and the new paths to you environment. If you don't do this you'll get an infinite stream of annoying type errors.
5. Download/git clone the arbor repository
6. Build a regular (native) modcc binary
   • mkdir build; cd build
   • cmake .. -DCMAKE_INSTALL_PREFIX=$(realpath prefix) -DARB_USE_BUNDLED_LIBS=ON
   • make modcc
   • make install
7. Build emscripten arbor libraries (without python or neuroml support) and using the modcc previously built to generate the C++ mechanism files. Now currently this doesn't work because of a bug in the CMakeLists.txt, you need to manually disable building modcc and update the modcc variable to point to your previously built modcc binary there. Also there is a error in the Random123 library that you need to remove from the source code in the gcc-intrinsics file. We use ARB_ARCH=generic because the default native
   • mkdir build-emscripten; cd build-emscripten
   • source "path/to/emsdk_env.sh"
   • cmake .. --toolchain path/to/the/emsdk/Emscripten.cmake -DCMAKE_INSTALL_PREFIX=$(realpath prefix) -DARB_USE_BUNDLED_LIBS=ON -DARB_MODCC=../build/prefix/bin/modcc -DARB_ARCH=generic
   • make -j10
   • make install
8. Build the python .so file. The standard pyodide-build method doesn't work
   • mkdir build-empy; cd build-empy
   • source "path/to/emsdk_env.sh"
   • (See em++ invocation below)
9. Build the wheel file
   • Copy the .so to a directory name arbor in the pyodide dist root
   • Copy the VERSION, __init__ files from a normal python arbor compilation to the arbor directory.
   • Make a arbor.dist-info directory, copy the METADATA file there and create a WHEEL file with contents as below
   • zip -r arbor-0.7-py3-none-any.whl arbor arbor.dist-info

em++ command to build the python .so file

    em++ \
        ../python/*.cpp \
        -I ../ext/pybind11/include/ \
        -I path/to/xbuildenv/pyodide-root/cpython/installs/python-3.10.2/include/python3.10/ \
        -I ../build-emscripten/prefix/include \
        -std=c++20 \
        ../build-emscripten-3.1.12/prefix/lib/libarbor* \
        -o _arbor.cpython-310-wasm32-emscripten.so \
        -shared -fPIC \
        -s ALLOW_MEMORY_GROWTH=1 \
        -s FORCE_FILESYSTEM=1 \
        -s LINKABLE=1 \
        -s USE_SDL=0 \
        -s SIDE_MODULE=1 \
        -s MODULARIZE=1 \
        -s WASM_BIGINT=1 \
        -g0 \
        -O2

WHEEL file contents

Wheel-Version: 1.0
Generator: manual 1.0
Root-Is-Purelib: false
Tag: py3-none-any