GSAS-II wouldn't start even after fresh installation

[Hmmmmmmmmmm]

Dear dev,

I'm pretty new to MacOS, but here's the log of me installing GSAS-II.

Last login: Thu Apr  3 13:40:10 on ttys000
tianrao@Tians-MacBook-Air Downloads % bash gsas2full-Latest-MacOSX-arm64.sh


Welcome to gsas2full 5786

In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>> 
====================================================
This is a single-download installer for GSAS-II. It includes other
software such as Git, used to install and update GSAS-II, a Python 
interpreter and a number of Python packages required by GSAS-II. The
installer you are running will install Python, etc. and then will install
the packaged version of GSAS-II, as listed above. Once that has been
completed, the software will invoke the gitstrap.py script, which will
use git to update to the latest version of GSAS-II (this requires an
internet connection). Then it will create shortcuts to simplify
GSAS-II use. Note that the gitstrap.py script can be rerun manually to
obtain updates. 

*** Note that while this installer can be used again to install
GSAS-II in a new location, once these files are installed, they should 
not be moved. ***

If you use GSAS-II in your research, please show your support by citing:
B.H. Toby & R.B. Von Dreele, J. Appl. Cryst. 46, 544-549 (2013)  
(also see Help/About)

See the LICENSE file in the GSAS-II source code
(https://github.com/AdvancedPhotonSource/GSAS-II) for software license
information. In addition, this installer uses the BSD-3-Clause license
and additional tools associated with it have their own licensing
terms, which are licensed under BSD-3-Clause, MIT and OpenSSL
licenses. By installing this  you agree to the licensing terms of individual
packages as well. Licenses and copyright notices of these
projects can be found at the following URL:
https://github.com/conda-forge/micromamba-feedstock/tree/master/recipe. 

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL CONTINUUM ANALYTICS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
THE POSSIBILITY OF SUCH DAMAGE.



Do you accept the license terms? [yes|no]
>>> yes

gsas2full will now be installed into this location:
/Users/tianrao/gsas2full

  - Press ENTER to confirm the location
  - Press CTRL-C to abort the installation
  - Or specify a different location below

[/Users/tianrao/gsas2full] >>> 
PREFIX=/Users/tianrao/gsas2full
Unpacking payload ...
                                                                                
Installing base environment...


Downloading and Extracting Packages:


Downloading and Extracting Packages:

Preparing transaction: done
Executing transaction: | 
done
Finish up GSAS-II installation, version 5786
launching bootstrap process
GSAS-II installer, version 5786 completed
installation finished.
Do you wish to update your shell profile to automatically initialize conda?
This will activate conda on startup and change the command prompt when activated.
If you'd prefer that conda's base environment not be activated on startup,
   run the following command when conda is activated:

conda config --set auto_activate_base false

You can undo this by running `conda init --reverse $SHELL`? [yes|no]
[no] >>> yes
no change     /Users/tianrao/gsas2full/condabin/conda
no change     /Users/tianrao/gsas2full/bin/conda
no change     /Users/tianrao/gsas2full/bin/conda-env
no change     /Users/tianrao/gsas2full/bin/activate
no change     /Users/tianrao/gsas2full/bin/deactivate
no change     /Users/tianrao/gsas2full/etc/profile.d/conda.sh
no change     /Users/tianrao/gsas2full/etc/fish/conf.d/conda.fish
no change     /Users/tianrao/gsas2full/shell/condabin/Conda.psm1
no change     /Users/tianrao/gsas2full/shell/condabin/conda-hook.ps1
no change     /Users/tianrao/gsas2full/lib/python3.11/site-packages/xontrib/conda.xsh
no change     /Users/tianrao/gsas2full/etc/profile.d/conda.csh
modified      /Users/tianrao/.zshrc

==> For changes to take effect, close and re-open your current shell. <==

Thank you for installing gsas2full!
tianrao@Tians-MacBook-Air Downloads % 

After this above installation, double-click on GSAS-II executable would only bring up this error message.

Last login: Thu Apr  3 21:56:55 on ttys000
'/Users/tianrao/gsas2full/GSAS-II/GSAS-II.app/Contents/MacOS/GSAS-II' '/Users/tianrao/gsas2full/GSAS-II/GSAS-II.py'; exit
(base) tianrao@Tians-MacBook-Air ~ % '/Users/tianrao/gsas2full/GSAS-II/GSAS-II.app/Contents/MacOS/GSAS-II' '/Users/tianrao/gsas2full/GSAS-II/GSAS-II.py'; exit
Traceback (most recent call last):
  File "/Users/tianrao/gsas2full/lib/python3.11/site-packages/numpy/core/__init__.py", line 24, in <module>
    from . import multiarray
  File "/Users/tianrao/gsas2full/lib/python3.11/site-packages/numpy/core/multiarray.py", line 10, in <module>
    from . import overrides
  File "/Users/tianrao/gsas2full/lib/python3.11/site-packages/numpy/core/overrides.py", line 8, in <module>
    from numpy.core._multiarray_umath import (
ImportError: dlopen(/Users/tianrao/gsas2full/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-darwin.so, 0x0002): Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <0BF6A426-9C50-3B1B-AD10-346F538CD16E> /Users/tianrao/gsas2full/lib/libopenblas.0.dylib
  Reason: tried: '/Users/tianrao/gsas2full/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/tianrao/gsas2full/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/tianrao/gsas2full/lib/python3.11/site-packages/numpy/core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/tianrao/gsas2full/lib/python3.11/site-packages/numpy/core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/tianrao/gsas2full/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/tianrao/gsas2full/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/tianrao/gsas2full/lib/python3.11/site-packages/numpy/__init__.py", line 130, in <module>
    from numpy.__config__ import show as show_config
  File "/Users/tianrao/gsas2full/lib/python3.11/site-packages/numpy/__config__.py", line 4, in <module>
    from numpy.core._multiarray_umath import (
  File "/Users/tianrao/gsas2full/lib/python3.11/site-packages/numpy/core/__init__.py", line 50, in <module>
    raise ImportError(msg)
ImportError: 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.11 from "/Users/tianrao/gsas2full/GSAS-II/GSAS-II.app/Contents/MacOS/GSAS-II"
  * The NumPy version is: "1.26.4"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: dlopen(/Users/tianrao/gsas2full/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-darwin.so, 0x0002): Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <0BF6A426-9C50-3B1B-AD10-346F538CD16E> /Users/tianrao/gsas2full/lib/libopenblas.0.dylib
  Reason: tried: '/Users/tianrao/gsas2full/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/tianrao/gsas2full/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/tianrao/gsas2full/lib/python3.11/site-packages/numpy/core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/tianrao/gsas2full/lib/python3.11/site-packages/numpy/core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/tianrao/gsas2full/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/tianrao/gsas2full/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)


The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/tianrao/gsas2full/GSAS-II/GSAS-II.py", line 12, in <module>
    import scipy.optimize # loading here addresses problem with build for wx on Pi
    ^^^^^^^^^^^^^^^^^^^^^
  File "/Users/tianrao/gsas2full/lib/python3.11/site-packages/scipy/__init__.py", line 47, in <module>
    from numpy import __version__ as __numpy_version__
  File "/Users/tianrao/gsas2full/lib/python3.11/site-packages/numpy/__init__.py", line 135, in <module>
    raise ImportError(msg) from e
ImportError: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.

Saving session...
...copying shared history...
...saving history...truncating history files...
...completed.

[Process completed]

THINGS I'VE TRIED

1. (deleted the whole folder to trash and) Fresh re-install, no luck, same error message.
2. Tried suggested bash command here "https://advancedphotonsource.github.io/GSAS-II-tutorials/install-g2f-mac.html", no luck, same.
   g2="https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/gsas2full-Latest-MacOSX-arm64.sh" curl -L "$g2" > /tmp/g2.sh; bash /tmp/g2.sh -b -p ~/g2full
3. Tried the reset bash commnad here "https://advancedphotonsource.github.io/GSAS-II-tutorials/help.html#on-macos-and-linux" (modified as instructed in the help manual), the following error was returned. To check if those packages are installed, pip list was excucted with all the required packages installed.

(base) tianrao@Tians-MacBook-Air bin % bash reset-gsasII.sh

Bootstrapping GSAS-II into /Users/tianrao/gsas2full/GSAS-II
at 2025-04-03 22:17:42.515737
from https://github.com/AdvancedPhotonSource/GSAS-II.git

script:     gitstrap.py from March 26, 2024
Python:     3.11.9
log in /Users/tianrao/gsas2full/gitstrap.log
**********************************************************************
Checking python packages... failed

Error during bootstrap: 
   Sorry, this version of Python cannot be used to run GSAS-II.
   It is missing the following package(s):
   	numpy scipy matplotlib
   Please install these package(s) and try running gitstrap.py again.

Rerun this script using command:
     /Users/tianrao/gsas2full/bin/python /Users/tianrao/gsas2full/gitstrap.py --reset
(base) tianrao@Tians-MacBook-Air bin % python -m pip list  
Package                 Version
----------------------- -----------
archspec                0.2.3
boltons                 24.0.0
Brotli                  1.1.0
cached-property         1.5.2
certifi                 2024.2.2
cffi                    1.16.0
charset-normalizer      3.3.2
colorama                0.4.6
conda                   24.5.0
conda-libmamba-solver   24.1.0
conda-package-handling  2.2.0
conda_package_streaming 0.9.0
contourpy               1.2.1
cycler                  0.12.1
distro                  1.9.0
fonttools               4.51.0
frozendict              2.4.4
gitdb                   4.0.11
GitPython               3.1.43
h5py                    3.11.0
idna                    3.7
imageio                 2.34.1
jsonpatch               1.33
jsonpointer             2.4
kiwisolver              1.4.5
libmambapy              1.5.8
**matplotlib              3.8.4**
menuinst                2.0.2
munkres                 1.1.4
**numpy                   1.26.4**
packaging               24.0
pathlib2                2.3.7.post1
pillow                  10.3.0
pip                     24.0
platformdirs            4.2.2
pluggy                  1.5.0
pycosat                 0.6.6
pycparser               2.22
PyOpenGL                3.1.6
pyparsing               3.1.2
Pypubsub                4.0.3
PySocks                 1.7.1
python-dateutil         2.9.0
requests                2.31.0
ruamel.yaml             0.18.6
ruamel.yaml.clib        0.2.8
**scipy                   1.13.0**
setuptools              69.5.1
six                     1.16.0
smmap                   5.0.0
tornado                 6.4
tqdm                    4.66.4
truststore              0.8.0
typing_extensions       4.11.0
urllib3                 2.2.1
wheel                   0.43.0
wxPython                4.2.1
zstandard               0.22.0
(base) tianrao@Tians-MacBook-Air bin % 

[briantoby]

Thanks for showing all this carefully compiled information. Alas, the problem here is not really with GSAS-II but with the numpy software that GSAS-II requires, though it could be related to the installer that I use. From the error messages, it seems that numpy is either not finding a library file that it needs (libgfortran) or the libgfortran file is not loading properly because it is not compatible with with how your computer is set up.

First of all, what version of MacOS are you using? (Find that by clicking on the Apple in the upper left and then "About this Mac".) If you have a really old version of MacOS, we might need to find an older version of Python to be compatible with that.

If that is not the case, there are a couple of different things we could try. One would be to install Python and packages directly from conda and see if that works. If not, another alternative is to install via homebrew. There is also a newer version of the self-installer, gsas2new. I'll wait to hear back from you.

[Hmmmmmmmmmm]

I'm using MacOS Sequoia 15.4, which I belive should be the latest version of OS.
Also, for your information, I believe that I was able to start GSAS-ii on the first installation, but after I acidentally move the g2full folder and did a delete & re-install, the above error appears.

Could you please give me more details on how to install Python and packages through gsas2new? I'm still at the very beginning of using Python / conda now. Thank you for your help!

[Hmmmmmmmmmm]

Also, if I search for the missing lib file as indicated by the error message, it's right there at
/Users/tianrao/gsas2full/lib/libgfortran.5.dylib

Also, should we worry about the duplicate LC_RPATH '@loader_path' thing? It seems like instead of missing, there are multiple entries somehow linked to the software. Could it be the result of multiple re-installation process?

[briantoby]

Sorry for the slow response. I was on vacation all of last week and did not spend a whole lot of time on my computer.

I have only done a bit of work on MacOS 15.x so far, but I do have a 15.3 VM that I could update to 15.4, so if needed I could try testing on that.

In general, I recommend that people do not install conda into their shell (say no rather than yes here:

Do you wish to update your shell profile to automatically initialize conda?
This will activate conda on startup and change the command prompt when activated.
If you'd prefer that conda's base environment not be activated on startup,
   run the following command when conda is activated:

conda config --set auto_activate_base false

You can undo this by running `conda init --reverse $SHELL`? [yes|no]
[no] >>> yes

but I don't think this causes any problems.

I'm having trouble making sense of your error message, it is looking for the libgfortran.5.dylib library in multiple places, but if I collapse out the /../ entries they all seem to be /Users/tianrao/gsas2full/lib/libgfortran.5.dylib so I'm not sure why that causes a problem. There is probably another copy elsewhere, since I stick that file into the directory with the GSAS-II binaries. You could move that elsewhere and see if that fixes anything.

Here are some choices to continue:

1. We could try to meet over Zoom and I could look to see if there is anything obvious that I could find that is wrong. What time zone are you in? Please contact me by e-mail, toby at ANL dot gov if you want to do this.

2. Alternately, you could install Python directly and if that works, have you run GSAS-II in that. To do this, install miniforge from here: https://github.com/conda-forge/miniforge/releases/latest and then after activating that you can use this conda command to configure a new Python environment:

conda install python=3.13 numpy=2.2 wxpython scipy matplotlib pyopengl pillow h5py imageio requests git gitpython PyCifRW zarr xmltodict pybaselines seekpath -c conda-forge

Once that is done see if this command works ok:

(py311) conda311 ~ % python
Python 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:34:54) [Clang 16.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> 

then finally

python /Users/tianrao/gsas2full/GSAS-II/GSASII/GSASII.py 

3. you can delete or rename the /Users/tianrao/gsas2full area and try the newer installer, gsas2new from https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/tag/v1.0.1

[Hmmmmmmmmmm]

Thank you so much for the detailed analysis. I'm currently at GMT+8 but first let me try the easier methods later today and get back to you if I have further questions. Again, thank you for the detailed response and help!

[Hmmmmmmmmmm]

Dear Mr. Toby,

For your information,

1. conda config --set auto_activate_base false + restart didn't help.
2. Moving out the problematic libgfortran.5.dylib to other folder didn't change the error message as well.
3. I didn't try manually installing python to avoid duplicate in Python environments on machine.
4. The total removal of installed g2full folder and reinstall the gsas2new worked. Now GSAS-II can start. I guess I'll stick using gsas2new to save me from dealing with software issues for now.

Thank you so much for your time and help. Hopefully these info can help anyone who might encounter this in the future / with the dev of GSAS-II. This software really helped me a lot when doing material research. I'd be happy to help if you want to investigate more on this issue.
All the best to you and your future work!

[briantoby]

This is very helpful to hear. I'm planning to have the gsas2new installer replace the gsas2full installer, most likely this month (there are a few things I need to do to facilitate people updating from the old gsas2full branch (called master) to the new gsas2new (called main), so I don't think I want to investigate what went wrong for you, since that version will be retired soon.

Just so you know, you will see a message when GSAS-II starts saying you are on a development branch:

...
  GSAS-II:    11291f81, 27-Mar-2025 14:57 (11.9 days old). Tag: #5805, v5.2.0
	Using development branch "main"
...

That is technically true for now and that branch may not always have the latest bug fixes in the standard (master) branch, but is at most a week or two behind and that message should disappear when the switch is made.