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Running meshtools3d on macOS (Apple Silicon)

On Apple Silicon, macOS SIGKILLs the prebuilt meshtools3d arm64 binaries the first time you run them:

zsh: killed     ./meshtools3d-2.0.0-macos-arm64/bin/meshtools3d

This is not a crash in meshtools3d. The arm64 kernel refuses to execute a binary without a valid code signature, and the released tarballs are currently unsigned. Removing the quarantine attribute alone is not enough — the dylibs and binaries must also be ad-hoc re-signed.

Why pycemrg-meshing stops instead of auto-fixing

pycemrg-meshing deliberately does not sign the binaries for you. Doing so would mean the library shells out to codesign/xattr to mutate files it did not build — hidden, side-effecting behavior we would rather keep out of the package. Instead, when the automatic ModelManager download path is used on macOS, the runner stops with a MacOSGatekeeperError that prints the exact commands below and the path of the extracted install.

Preferred workflow: install, sign once, pass the path

The recommended macOS workflow is to install meshtools3d yourself, sign it once, and hand the path to the runner via an explicit override (which skips ModelManager entirely):

# 1. Download + extract the macOS tarball from the meshtools3d release page, e.g.
#    https://github.com/OpenHeartDevelopers/meshtools3d/releases
DIR=$PWD/meshtools3d-2.0.0-macos-arm64

# 2. Strip quarantine and ad-hoc sign the dylibs and binaries
xattr -dr com.apple.quarantine "$DIR"
for f in "$DIR"/lib/*.dylib; do [ -L "$f" ] && continue; codesign --force --sign - "$f"; done
for b in "$DIR"/bin/*; do codesign --force --sign - "$b"; done

# 3. Confirm it runs
"$DIR"/bin/meshtools3d

The [ -L "$f" ] && continue skips symlinked dylibs (sign the real files only). The bin/* loop covers every shipped binary — meshtools3d, laplace_solver, and parfile_builder.

Then point the runner at the signed binary:

pycemrg-meshing run heart.par --binary "$DIR/bin/meshtools3d"
pycemrg-meshing laplace heart.par --binary "$DIR/bin/laplace_solver"

from pycemrg_meshing import MeshtoolsRunner

runner = MeshtoolsRunner(binary_path="/path/to/meshtools3d-2.0.0-macos-arm64/bin/meshtools3d")
runner.run("heart.par")

Once signed and passed explicitly, the run proceeds normally — the ModelManager download path (and its Gatekeeper stop) is never reached again.

Long-term fix

The proper fix lives upstream in the meshtools3d release CI: sign the binaries with a Developer ID certificate and notarize the tarballs. When that ships, downloaded builds will run directly and the MacOSGatekeeperError guard in logic/runners.py can be removed.