Problem with installation on MacOS M1

Problem:

Date: Mon, 25 Nov 2024
From: Marite Cardenas Gomez marite.cardenas@ehu.eus

I have to install BornAgain on my work computer but I have encounter problems, see error [as attached text file].
I have installed python 3 using the Mac terminal and ran the different packages mentioned in the bornagain website but still cannot manage to make it work, my computer is an Apple M1.

mac_m1_error.log

The key part of the error report is the following:

EXC_BAD_ACCESS (SIGKILL (Code Signature Invalid))

The reported problem on newer Mac architectures (M1 and more recent ones) is known (see issue #585 (closed)). It is an issue due to the increased security measures of MacOS which does not allow an application without a certified Apple signature to run on the machine and this prevents BornAgain GUI from execution when installed via the .dmg installer.

A possible way is to build BornAgain locally on the target machine.

Building BornAgain on MacOS M1

Open the terminal and enter the commands given below.

OS and machine architecture

Check the OS,

sw_vers

and machine architecture,

uname -m

sysctl machdep.cpu.brand_string

which will yield, e.g., macOS 15.1.1 Sequoia for OS and arm64 and Apple M1 for the architecture.

Xcode

Verify that xcode is installed, for instance, by using

/usr/bin/xcode-select -p

If xcode is not available, install it; see https://apps.apple.com/us/app/xcode/id497799835

Homebrew

Homebrew package manager should be installed. Verify the installed version,

brew -v

and the Homebrew prefix:

brew --prefix

BornAgain dependencies

Install BornAgain dependencies via Homebrew (see https://bornagainproject.org/21/installation/building/unix/):

brew install git cmake fftw gsl libcerf boost libtiff qt6 python

Python dependencies

The version of Python must be >= 3.8. Check Python version via

python3 --version

Make a temporary Python virtual environment (eg., in ~/Documents/venvs), activate it and install the required Python packages

python3 -m venv ~/Documents/venvs
source ~/Documents/venvs/bin/activate
python3 -m pip install wheel numpy matplotlib

Build and install libheinz

cd /tmp/
git clone -b v2.0.0 --single-branch --depth 1 https://jugit.fz-juelich.de/mlz/libheinz
cd libheinz
cmake -S. -B build
cmake --build build -j8
sudo cmake --install build

Build and install libformfactor

cd /tmp/
git clone -b v0.3.0 --single-branch --depth 1 https://jugit.fz-juelich.de/mlz/libformfactor
cd libformfactor
cmake -S. -B build
cmake --build build -j8
sudo cmake --install build

Build BornAgain (release 21)

cd /tmp/
git clone -b r21 --single-branch --depth 1 https://jugit.fz-juelich.de/mlz/bornagain
cd bornagain
cmake -S. -B build
cmake --build build -j8

Test the BornAgain build (optional)

ctest --test-dir build -j8 -C Release

Install the BornAgain GUI

Install BornAgain in a custom folder, say ~/Documents/bornagain_21:

cmake --install /tmp/bornagain/build/ --prefix ~/Documents/bornagain_21

Create the BornAgain Python wheel (optional)

BornAgain Python wheel (standard Python package) can be built via:

python3 -m pip wheel /tmp/bornagain/build/PythonPackage/py311/ --no-deps --wheel /tmp/ba_wheel/

The wheel is created for Python 3.11 in the folder /tmp/ba_wheel with a name like BornAgain-21.2-cp311-cp311-macosx_13_0_arm64.whl. For a different Python version the name of the directory and the wheel name will differ.

Install the BornAgain Python wheel (optional):

python3 -m pip install /tmp/ba_wheel/BornAgain-21.2-cp311-cp311-macosx_13_0_arm64.whl

Run BornAgain GUI

cd ~/Documents/bornagain_21
bin/bornagain

Use the BornAgain Python package (optional)

Start the Python interpreter:

python3

Test the BornAgain Python package inside the Python interpreter:

import bornagain as ba
print(ba.deg)

which will display a floating-point number 0.017453292519943295.

added OS:Mac deployment labels

assigned to @a.nejati

Problem with the Python package (Python 3.13):

>>> import bornagain as ba

Traceback (most recent call last):

  File "<python-input-0>", line 1, in <module>

    import bornagain as ba

  File "/Users/myfolder/venvs/lib/python3.13/site-packages/bornagain/__init__.py", line 17, in <module>

    from .lib import *

  File "/Users/myfolder/venvs/lib/python3.13/site-packages/bornagain/lib/__init__.py", line 28, in <module>

    from .libBornAgainBase import *

  File "/Users/myfolder/venvs/lib/python3.13/site-packages/bornagain/lib/libBornAgainBase.py", line 8, in <module>

    import _libBornAgainBase

ImportError: dlopen(/Users/myfolder/venvs/lib/python3.13/site-packages/bornagain/lib/_libBornAgainBase.so, 0x0002): Library not loaded: @rpath/Python

  Referenced from: <66CE1D5C-73E0-33FF-844D-8D8382DE79FF> /Users/myfolder/venvs/lib/python3.13/site-packages/bornagain/lib/_libBornAgainBase.so

  Reason: tried: '/Users/myfolder/venvs/lib/python3.13/site-packages/bornagain/lib/Python' (no such file), '/Users/myfolder/venvs/lib/python3.13/site-packages/bornagain/lib/extra/Python' (no such file), '/usr/local/Library/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/Library/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/opt/homebrew/opt/python@3.13/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/opt/python@3.13/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/usr/local/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/Library/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/opt/homebrew/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/Users/myfolder/venvs/lib/python3.13/site-packages/bornagain/lib/Python' (no such file), '/Users/myfolder/venvs/lib/python3.13/site-packages/bornagain/lib/extra/Python' (no such file), '/usr/local/Library/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/Library/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/opt/homebrew/opt/python@3.13/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/opt/python@3.13/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/usr/local/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/Library/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/opt/homebrew/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/Frameworks/Python.framework/Versions/3.13/lib/Python' (no such file), '/opt/homebrew/lib/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/Python' (no such file), '/opt/homebrew/lib/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/Python' (no such file)

It seems that the package production script has not worked properly to replace @rpath/Python with @rpath/libpython3.13.dylib.

The reason is a lack of a valid Apple signature in the libraries within the Python wheel. The full crash report can be found in the folder ~/Library/Logs/DiagnosticReports/.

The International Scattering Alliance is able to provide signing certificates for macOS apps if the BornAgain team are interested.

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changed milestone to %v22