AFNI 25.2.00 macOS ARM64 clang build, repack 2

AFNI macOS ARM64 Clang Build

This is an unofficial AFNI macOS ARM64 build made for the Apple Silicon Mac where the standard binary/install path was not ideal. It uses Apple clang, M2-targeted optimization, Homebrew jpeg-turbo, Homebrew zlib-ng-compat, and Apple system expat/libiconv.

Why

This build was created because:

• The available AFNI macOS binary was not the right fit for my Apple Silicon Macbook.
• AFNI's Apple Silicon installation path depends on Homebrew/XQuartz/Mesa behavior. AFNI's own macOS ARM setup script currently pins Mesa through an AFNI tap for SUMA support.
• The goal was a reproducible arm64 build using Apple clang and M2-aware flags, without Homebrew GCC.

The result keeps practical optimization while preserving AFNI's macOS plugin ABI. ThinLTO and dead_strip were not included because they broke runtime plugin loading.

Tested System

• Hardware: 2023 MacBook Pro, Apple M2 Max
• OS: macOS 26.5.1, arm64
• Compiler: /usr/bin/clang
• AFNI source: afni_src
• Output tree: afni_src/macos_13_ARM
• X11: XQuartz with /opt/X11/lib/flat_namespace
• Homebrew prefix: /opt/homebrew

Build Choices

Dependency choices:

• zlib-ng-compat replaces zlib through the zlib-compatible libz ABI. zlib-ng documents a zlib-compatible API and CPU-intrinsic acceleration paths.
• jpeg-turbo replaces libjpeg for JPEG support. libjpeg-turbo documents SIMD acceleration and compatibility with the traditional libjpeg API.
• Apple system expat and libiconv reduce Homebrew runtime coupling.

Key Makefile settings:

LOCAL_CC_PATH ?= /usr/bin/clang
CCMIN  = $(LOCAL_CC_PATH) -arch arm64 -DDARWIN -DARM_M1
OPTFLAGS = -O3 -mcpu=apple-m2 -pipe
LDFLAGS_OPT = -arch arm64

ZLIB_NG_ROOT = /opt/homebrew/opt/zlib-ng-compat
LZLIB = $(ZLIB_NG_ROOT)/lib/libz.dylib

JPEG_TURBO_ROOT = /opt/homebrew
XLIBS = -lXm $(JPEG_TURBO_ROOT)/lib/libjpeg.dylib -lXt

MACOS_SDKROOT ?= $(shell xcrun --show-sdk-path)
LGIFTI = $(MACOS_SDKROOT)/usr/lib/libexpat.tbd

AFNI_LDFLAGS = -Wl,-export_dynamic
PLUGIN_LFLAGS = -m64 -bundle -flat_namespace -undefined suppress -Wl,-x $(LDFLAGS_OPT)

Avoid these flags for this AFNI plugin build:

-flto=thin
-Wl,-dead_strip

They can be valid for other projects, but here they hid or stripped symbols needed by AFNI's flat-namespace plugin bundles.

Runtime Requirements

This package was checked with otool -L across 447 Mach-O files in ~/abin.

Minimal practical Homebrew install set for running this AFNI package:

brew install openmotif mesa-glu gsl glib libomp libxpm zlib-ng-compat

Those top-level formulae provide or pull the runtime libraries used by the binaries. The direct Homebrew dylib formulae found by otool were:

fontconfig
glib
gsl
jpeg-turbo
libomp
libpng
libx11
libxext
libxft
libxmu
libxp
libxpm
libxt
mesa
mesa-glu
openmotif
zlib-ng-compat

Apple system libraries used at runtime:

/usr/lib/libSystem.B.dylib
/usr/lib/libc++.1.dylib
/usr/lib/libexpat.1.dylib
/usr/lib/libiconv.2.dylib
/usr/lib/libz.1.dylib

Not needed just to run this packaged build: pkgconf, autoconf, cmake, and netpbm. Those were build-time tools or source-build dependencies, not runtime dylibs in this package.

XQuartz is still needed for interactive AFNI/SUMA GUI display. If plugins fail to load under the GUI, use the XQuartz flat-namespace path:

export DYLD_LIBRARY_PATH="/opt/X11/lib/flat_namespace:${DYLD_LIBRARY_PATH}"

R is needed for AFNI's R-based programs, but not for the core C/C++ AFNI binaries to run.

Build

From the workspace root:

/afni_src
export PATH="/opt/homebrew/bin:/opt/homebrew/opt/pkgconf/bin:$PATH"
export SDKROOT="$(xcrun --show-sdk-path)"
make -f Makefile.macos_13_ARM clean
make -f Makefile.macos_13_ARM vastness

Output:

/afni_src/macos_13_ARM

Validation

Local version:

Precompiled binary macos_13_ARM: Jun 17 2026 (Version AFNI_25.2.00 'Gordian I')

Architecture checks:

afni:   Mach-O 64-bit executable arm64
3dinfo: Mach-O 64-bit executable arm64
suma:   Mach-O 64-bit executable arm64

Dependency checks confirmed:

• libz.1.dylib from /opt/homebrew/opt/zlib-ng-compat
• libjpeg.8.dylib from /opt/homebrew/opt/jpeg-turbo
• libiconv.2.dylib from /usr/lib
• libexpat.1.dylib from /usr/lib
• no GCC-14 runtime, libgomp, or gfortran runtime in checked binaries

Plugin checks confirmed that afni exports:

_first_plugin_check
_AFNI_driver_register
_PLUTO_set_sequence
_PLUTO_prefix_ok
_PLUTO_popup_worker

GUI/plugin smoke test:

plug_3dsvm.so loaded successfully
PLUG_get_many_plugins -- found 49 plugins

Program-help validation:

found 623 good progs and 20 issues out of 643

The remaining 20 issues were R-dependent AFNI programs or wrappers.

Functional smoke test:

printf '0 0 0 7\n1 1 1 3\n' > vox.1D
3dUndump -overwrite -dimen 2 2 2 -ijk -datum short -prefix vox vox.1D
3dcalc -overwrite -a vox+orig -expr 'a*2' -prefix vox2
3dBrickStat -sum vox2+orig

Expected result:

20

Package

Packaged artifact:

dist/macos_13_ARM.AFNI_25.2.00.m2clang.2.tgz

Size:

416 MB

SHA-256:

25a0a3c205e4b1e5897feeb15ce6be584ac1f828b6f7aa6b5c4ec6f14d95ceaa

Checksum file:

dist/macos_13_ARM.AFNI_25.2.00.m2clang.2.tgz.sha256

The archive contains a top-level macos_13_ARM/ directory. It was repacked from ~/abin after removing Python cache files and adding missing atlas/template/support assets from ~/abin3. It was extracted into /private/tmp and re-tested successfully.

Package contents:

• 2120 files
• no __pycache__ files
• includes atlas/template/refacer support assets, including MNI152_2009_template_SSW.nii.gz, Julich_MNI2009c_v3.1.nii.gz, and R_io.so
• preserves the python symlink

Install From The Package

Example user install:

mkdir -p "$HOME/abin"
tar -xzf macos_13_ARM.AFNI_25.2.00.m2clang.2.tgz -C "$HOME/abin" --strip-components=1
echo 'export PATH="$HOME/abin:$PATH"' >> "$HOME/.zshrc"
echo 'export DYLD_LIBRARY_PATH="/opt/X11/lib/flat_namespace:${DYLD_LIBRARY_PATH}"' >> "$HOME/.zshrc"

Open a new terminal and check:

afni -ver
afni_system_check.py -check_all

References