[Ifeffit] Cannon start larch on ubuntu 20.04.2 LTS
Don Baker, Dr.
don.baker at mcgill.ca
Tue Jun 29 07:49:04 CDT 2021
Hi Matt,
Thanks for looking into this problem. No need to apologize at all!
So, I tried you suggestion and I get the same ValueError message. Just in case I made a mistak I tried to do the re-install again and this time I kept all of the output in case it would help you. You can see it below.
Thanks so much again for all your help and even more for all of the software you have provided to the community.
Take care and stay cool!
Don
.....................
~/xraylarch/bin$ conda install -c conda-forge pymatgen
Collecting package metadata (current_repodata.json): done
Solving environment: -
Warning: >10 possible package resolutions (only showing differing packages):
- https://repo.continuum.io/pkgs/main/linux-64/linux-64::intel-openmp-2021.2.0-h06a4308_610, https://repo.continuum.io/pkgs/main/linux-64/linux-64::libgfortran4-7.5.0-ha8ba4b0_17, https://repo.continuum.io/pkgs/main/noarch/noarch::olefile-0.46-py_0, https://repo.continuum.io/pkgs/main/noarch/noarch::pyparsing-2.4.7-pyhd3eb1b0_0
- defaults/linux-64::intel-openmp-2021.2.0-h06a4308_610, https://repo.continuum.io/pkgs/main/linux-64/linux-64::libgfortran4-7.5.0-ha8ba4b0_17, https://repo.continuum.io/pkgs/main/noarch/noarch::olefile-0.46-py_0, https://repo.continuum.io/pkgs/main/noarch/noarch::pyparsing-2.4.7-pyhd3eb1b0_0
- defaults/linux-64::libgfortran4-7.5.0-ha8ba4b0_17, https://repo.continuum.io/pkgs/main/linux-64/linux-64::intel-openmp-2021.2.0-h06a4308_610, https://repo.continuum.io/pkgs/main/noarch/noarch::olefile-0.46-py_0, https://repo.continuum.io/pkgs/main/noarch/noarch::pyparsing-2.4.7-pyhd3eb1b0_0
- defaults/linux-64::intel-openmp-2021.2.0-h06a4308_610, defaults/linux-64::libgfortran4-7.5.0-ha8ba4b0_17, https://repo.continuum.io/pkgs/main/noarch/noarch::olefile-0.46-py_0, https://repo.continuum.io/pkgs/main/noarch/noarch::pyparsing-2.4.7-pyhd3eb1b0_0
- defaults/linux-64::libgfortran4-7.5.0-ha8ba4b0_17, defaults/noarch::olefile-0.46-py_0, https://repo.continuum.io/pkgs/main/linux-64/linux-64::intel-openmp-2021.2.0-h06a4308_610, https://repo.continuum.io/pkgs/main/noarch/noarch::pyparsing-2.4.7-pyhd3eb1b0_0
- defaults/linux-64::intel-openmp-2021.2.0-h06a4308_610, defaults/linux-64::libgfortran4-7.5.0-ha8ba4b0_17, defaults/noarch::olefile-0.46-py_0, https://repo.continuum.io/pkgs/main/noarch/noarch::pyparsing-2.4.7-pyhd3eb1b0_0
- defaults/noarch::olefile-0.46-py_0, https://repo.continuum.io/pkgs/main/linux-64/linux-64::intel-openmp-2021.2.0-h06a4308_610, https://repo.continuum.io/pkgs/main/linux-64/linux-64::libgfortran4-7.5.0-ha8ba4b0_17, https://repo.continuum.io/pkgs/main/noarch/noarch::pyparsing-2.4.7-pyhd3eb1b0_0
- defaults/linux-64::intel-openmp-2021.2.0-h06a4308_610, defaults/noarch::olefile-0.46-py_0, https://repo.continuum.io/pkgs/main/linux-64/linux-64::libgfortran4-7.5.0-ha8ba4b0_17, https://repo.continuum.io/pkgs/main/noarch/noarch::pyparsing-2.4.7-pyhd3eb1b0_0
- defaults/noarch::olefile-0.46-py_0, defaults/noarch::pyparsing-2.4.7-pyhd3eb1b0_0, https://repo.continuum.io/pkgs/main/linux-64/linux-64::intel-openmp-2021.2.0-h06a4308_610, https://repo.continuum.io/pkgs/main/linux-64/linux-64::libgfortran4-7.5.0-ha8ba4b0_17
- defaults/noarch::pyparsing-2.4.7-pyhd3eb1b0_0, https://repo.continuum.io/pkgs/main/linux-64/linux-64::intel-openmp-2021.2.0-h06a4308_610, https://repo.continuum.io/pkgs/main/linux-64/linux-64::libgfortran4-7.5.0-ha8ba4b0_17, https://repo.continuum.io/pkgs/main/noarch/noarch::olefile-0.46-py_0
... and othedone
# All requested packages already installed.
~/xraylarch/bin$ ./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
~/xraylarch/bin$ ./xas_viewer
Traceback (most recent call last):
File "./xas_viewer", line 5, in <module>
from larch.apps import run_xas_viewer
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
.......................
--
Melting rocks today for a better tomorrow . . .
Don R. Baker, Professor of Geochemistry, McGill University
On Mon, 2021-06-28 at 17:55 -0500, Matt Newville wrote:
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<mailto: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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