Error on first run after new installation (Mac OS, f2py, arm64 CPU problem)

[jan-eberhardt]

I installed the latest version on my machine (MacBook Pro M2, macOS 13.4.1) by Git-cloning and doing

pip install build
cd exostriker
python3 -m build
pip install .

in a new virtual environment with Python 3.11.0.

This worked without problems and installed all needed dependencies (including numpy 1.26.1). I installed gfortran version 12.1.0 and tried to run ExoStriker by just typing exostriker and ran into the following problem:

FileNotFoundError: [Errno 2] No such file or directory: '/opt/miniconda3/envs/exostriker/lib/python3.11/site-packages/exostriker/lib/RV_mod/rvmod/rvmod_for/.libs'

Abort trap: 6

However, there is no folder named 'rvmod_for' inside 'lib/RV_mod/rvmod'.
Help would be greatly appreciated!

[jan-eberhardt]

The initial problem was located in exostriker/exostriker/lib/RV_mod/rvmod/__init__.py in f_compile().
It was checking the operating system to be Windows (if "win" in sys.platform:) but sys.platform is "darwin" in my case, so that triggered the Windows flag.
A hotfix from @3fon3fonov ( if "win" in sys.platform[0:3]:) fixed this issue but led to a different one on line 761 when trying to import rvmod_for:

ImportError: dlopen(/Users/eberhardt/Documents/PhD/WINE_paper_02/exostriker/exostriker/lib/RV_mod/rvmod/rvmod_for.cpython-311-darwin.so, 0x0002): tried: '/Users/eberhardt/Documents/PhD/WINE_paper_02/exostriker/exostriker/lib/RV_mod/rvmod/rvmod_for.cpython-311-darwin.so' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/eberhardt/Documents/PhD/WINE_paper_02/exostriker/exostriker/lib/RV_mod/rvmod/rvmod_for.cpython-311-darwin.so' (no such file), '/Users/eberhardt/Documents/PhD/WINE_paper_02/exostriker/exostriker/lib/RV_mod/rvmod/rvmod_for.cpython-311-darwin.so' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64'))

Abort trap: 6

which appears to be a problem related to the Apple Silicon chip.

[3fon3fonov]

I wonder if this can be reproduced by NOT using Anaconda.... In the past, we had quite a lot of problems with the gfortran compiler that comes with Anaconda installation. The solution was to install system wide gfortran. People on MAC with M1 & M2 chips must test, I only have Intel based Mac's

[vvkrddy]

On an arm64 Mac, I installed Exostriker by cloning the repository and building it in an Anaconda environment with Python 3.11 installation. I get the following errors:

Click to see Traceback

(exostriker)$> exostriker
Traceback (most recent call last):
  File "/Users/username/anaconda3/envs/exostriker/bin/exostriker", line 5, in <module>
    from exostriker.gui import main
  File "/Users/username/anaconda3/envs/exostriker/lib/python3.11/site-packages/exostriker/__init__.py", line 1, in <module>
    from exostriker import gui
  File "/Users/username/anaconda3/envs/exostriker/lib/python3.11/site-packages/exostriker/gui.py", line 50, in <module>
    import RV_mod as rv
  File "/Users/username/anaconda3/envs/exostriker/lib/python3.11/site-packages/exostriker/lib/RV_mod/__init__.py", line 25, in <module>
    import celerite
  File "/Users/username/anaconda3/envs/exostriker/lib/python3.11/site-packages/celerite/__init__.py", line 29, in <module>
    from . import terms, solver, modeling
  File "/Users/username/anaconda3/envs/exostriker/lib/python3.11/site-packages/celerite/terms.py", line 18, in <module>
    from .solver import get_kernel_value, get_psd_value, check_coefficients
ImportError: dlopen(/Users/username/anaconda3/envs/exostriker/lib/python3.11/site-packages/celerite/solver.cpython-311-darwin.so, 0x0002): Library not loaded: @rpath/libc++.1.dylib
  Referenced from: <AA2C24F3-6060-32F7-A9D3-047FEAAB84FB> /Users/username/anaconda3/envs/exostriker/lib/python3.11/site-packages/celerite/solver.cpython-311-darwin.so
  Reason: tried: '/Users/username/anaconda3/envs/exostriker/lib/libc++.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/username/anaconda3/envs/exostriker/lib/libc++.1.dylib' (no such file), '/Users/username/anaconda3/envs/exostriker/lib/libc++.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/username/anaconda3/envs/exostriker/lib/libc++.1.dylib' (no such file), '/Users/username/anaconda3/envs/exostriker/bin/../lib/libc++.1.dylib' (no such file), '/Users/username/anaconda3/envs/exostriker/bin/../lib/libc++.1.dylib' (no such file)

I then installed gfortran using the conda-forge channel. I cannot find a 12.1.0 version mentioned by @jan-eberhardt but on installing 13.2.0 (latest available), I am able to open the exostriker GUI despite many warnings in shell.

[3fon3fonov]

@vvkrddy But does the e.g., RV fitting works? Can you import a data set (you can find .vels files in the datafiles root directory), and tell what you see? You may get a lot of stdout/stderr output at first start, but the second one you should not get any warnings. Thus, any input you could provide is vital.

[vvkrddy]

@3fon3fonov On fitting, I can see the best-fit parameters in the stdout/stderr section of the GUI.

[3fon3fonov]

@vvkrddy, if there is no error on the stdout, and you see the fit and its best fit parameters, then you are all set! I would appreciate it if you share more details of your anaconda, gfortran, Python and OS system setup.

Cheers,
Trifon

[vvkrddy]

Conda version: 23.7.2
Python version: 3.11.0
GFortran version: 13.2.0
Platform: osx-arm64
OS: macOS 14.0

[jan-eberhardt]

@vvkrddy Where did you get your Conda version from? I found installers specifically for arm64 but I have trouble installing them. They either tell me they're not compatible with my OS version of just produce an error during installation and leave an incomplete Conda installation

[vvkrddy]

@jan-eberhardt I used the M1 (command line) installer from the official Anaconda site.

[jan-eberhardt]

When I try that I end up with this error:

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/Users/eberhardt/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 17, in __call__
        return func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^
      File "/Users/eberhardt/anaconda3/lib/python3.11/site-packages/conda/cli/main.py", line 64, in main_subshell
        exit_code = do_call(args, parser)
                    ^^^^^^^^^^^^^^^^^^^^^
      File "/Users/eberhardt/anaconda3/lib/python3.11/site-packages/conda/cli/conda_argparse.py", line 167, in do_call
        result = getattr(module, func_name)(args, parser)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/Users/eberhardt/anaconda3/lib/python3.11/site-packages/conda/cli/main_init.py", line 36, in execute
        return initialize(
               ^^^^^^^^^^^
      File "/Users/eberhardt/anaconda3/lib/python3.11/site-packages/conda/core/initialize.py", line 137, in initialize
        run_plan_elevated(plan2)
      File "/Users/eberhardt/anaconda3/lib/python3.11/site-packages/conda/core/initialize.py", line 853, in run_plan_elevated
        result = subprocess_call(
                 ^^^^^^^^^^^^^^^^
      File "/Users/eberhardt/anaconda3/lib/python3.11/site-packages/conda/gateways/subprocess.py", line 108, in subprocess_call
        stdout, stderr = process.communicate(input=stdin)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/Users/eberhardt/anaconda3/lib/python3.11/subprocess.py", line 1209, in communicate
        stdout, stderr = self._communicate(input, endtime, timeout)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/Users/eberhardt/anaconda3/lib/python3.11/subprocess.py", line 2088, in _communicate
        input_view = memoryview(self._input)
                     ^^^^^^^^^^^^^^^^^^^^^^^
    TypeError: memoryview: a bytes-like object is required, not 'str'

Which again leaves an incomplete installation. The directory and files are there but I get a -bash: conda: command not found error when I try to use Conda.

[jan-eberhardt]

I managed to install Anaconda / Conda correctly, by refusing the conda init command during installation, activating conda's base environment manually and updating my shell from bash to zsh. Now generally, Python / Conda works as intended but after a new installation of ExoStriker, and trying to run it, I get this:

Traceback (most recent call last):
  File "/Users/eberhardt/anaconda3/envs/exostriker/bin/exostriker", line 5, in <module>
    from exostriker.gui import main
  File "/Users/eberhardt/anaconda3/envs/exostriker/lib/python3.11/site-packages/exostriker/__init__.py", line 1, in <module>
    from exostriker import gui
  File "/Users/eberhardt/anaconda3/envs/exostriker/lib/python3.11/site-packages/exostriker/gui.py", line 13, in <module>
    from PyQt5 import QtCore, QtGui, QtWidgets, uic
ImportError: dlopen(/Users/eberhardt/anaconda3/envs/exostriker/lib/python3.11/site-packages/PyQt5/QtCore.abi3.so, 0x0002): Symbol not found: __ZTVNSt3__13pmr25monotonic_buffer_resourceE
  Referenced from: <645DDC2C-F655-324A-BE87-40804F3AC471> /Users/eberhardt/anaconda3/envs/exostriker/lib/python3.11/site-packages/PyQt5/Qt5/lib/QtCore.framework/Versions/5/QtCore
  Expected in:     <54E8FBE1-DF0D-33A2-B8FA-356565C12929> /usr/lib/libc++.1.dylib
(exostriker) eberhardt@mac-n-190 exostriker % 

[vvkrddy]

@jan-eberhardt Did you install gfortran in the conda env before running exostriker?

[3fon3fonov]

@vvkrddy, @jan-eberhardt, gfortran is not related to this error

    from PyQt5 import QtCore, QtGui, QtWidgets, uic
ImportError: dlopen(/Users/eberhardt/anaconda3/envs/exostriker/lib/python3.11/site-packages/PyQt5/QtCore.abi3.so, 0x0002): Symbol not found: __ZTVNSt3__13pmr25monotonic_buffer_resourceE
  Referenced from: <645DDC2C-F655-324A-BE87-40804F3AC471> /Users/eberhardt/anaconda3/envs/exostriker/lib/python3.11/site-packages/PyQt5/Qt5/lib/QtCore.framework/Versions/5/QtCore
  Expected in:     <54E8FBE1-DF0D-33A2-B8FA-356565C12929> /usr/lib/libc++.1.dylib

This seems to be a PyQt5 problem in MAC os, which should go to another thread. @jan-eberhardt if this is an MPIA laptop, I would suggest asking the IT people for help. Else, you need to seek solution for this issue on the internet, since this has nothing to do with the Exo-Striker installation. Of course, if you find a solution, one way or another, please let us know!

[3fon3fonov]

Since a fix to the initial problem was quickly provided, I will close this issue, but we still hope that @jan-eberhardt will share a solution in a separate tread.