[Ifeffit] Cannon start larch on ubuntu 20.04.2 LTS

[Matt Newville]

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 at 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
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-- 
--Matt Newville <newville at cars.uchicago.edu> 630-327-7411
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