-- 

Hi Don,

Hm, very sorry for the trouble.  In fact, I'm hoping to get a new release out by the end of this week in anticipation of upcoming workshops and schools, so I'd like to track this down soon.

I don't exactly know what that problem is coming from, but my first suggestion would be to try to force reinstalling

pymatgen with conda:

    ~/xraylarch/bin/conda install -c conda-forge pymatgen

I think that ought to work but I'm not sure why the other version failed.  But it might be that taking pymatgen (with several binaries) is better done from conda anyway.

I'm going to try that on a couple of Linuxes...

--Matt

On Mon, Jun 28, 2021 at 12:42 PM Don Baker, Dr. <don.baker@mcgill.ca> wrote:

Hi Folks,

I think I am missing something obvious and am hoping that you can quickly tell me my mistake, so let me begin my story:

I downloaded xraylarch-2021-060Linux-x86_64.sh into downloads on a Asus Zenbook using ubuntu 20.04.2 LTS

I ran the command bash ./xraylarch-2021-060Linux-x86_64.sh

Larch appears to have been correctly installed, but because I am using a gnome desktop no shortcuts appeared on my desktop (as promised) and there were no files that       I could identify as shortcuts in my Downloads directory (which was set to display hidden files)

I then moved to the /xraylarch/bin and tried to launch larch using python and this is what happened:

python larch

Traceback (most recent call last):

  File "larch", line 5, in <module>

    from larch.apps import run_larch

  File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/__init__.py", line 52, in <module>

    from . import builtins

  File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/builtins.py", line 27, in <module>

    from . import xrd

  File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/xrd/__init__.py", line 25, in <module>

    from .amscifdb import CifStructure, get_amscifdb, get_cif, find_cifs

  File "/home/donb/xraylarch/lib/python3.8/site-packages/larch/xrd/amscifdb.py", line 40, in <module>

    from pymatgen.io.cif import CifParser

  File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/io/cif.py", line 25, in <module>

    from pymatgen.core.composition import Composition

  File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/core/__init__.py", line 21, in <module>

    from .lattice import Lattice  # noqa

  File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/core/lattice.py", line 23, in <module>

    from pymatgen.util.coord import pbc_shortest_vectors

  File "/home/donb/xraylarch/lib/python3.8/site-packages/pymatgen/util/coord.py", line 17, in <module>

    from . import coord_cython as cuc

  File "pymatgen/util/coord_cython.pyx", line 1, in init pymatgen.util.coord_cython

ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

I also tried to use python to start larch_server and xas_viewer and had the same results.  I also have the same results if I try to launch larch using ./larch

This is the information on the version of Python that I am running:

Python 3.8.10 (default, Jun  4 2021, 15:09:15) 

[GCC 7.5.0] :: Anaconda, Inc. on linux

Type "help", "copyright", "credits" or "license" for more information.

Any suggestions anyone has to offer will be appreciated.

Wishing you all the best,

Don

-- 

Melting rocks today for a better tomorrow . . .

Don R. Baker, Professor of Geochemistry, McGill University

_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

_______________________________________________

Ifeffit mailing list

Ifeffit@millenia.cars.aps.anl.gov

http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Unsubscribe: 

http://millenia.cars.aps.anl.gov/mailman/options/ifeffit