Solving common installation issues

[nikolasibalic]

Place for all common installation issues encountered by users. Hopefully collective intelligence can resolve them all.

[nikolasibalic]

If numpy reports error after installation when you try to use ARC, and you are using conda installation/Anaconda Python distribution, the cause is most probably that curent conda installation is using older version of the Numpy, while the ARC has been compiled with the latest version of the Numpy. Problem is resolved by installing new Numpy version directly from pip. See issues #25, #63, and #100 .

UPDATE: As of ver. 3.1.9. This should be resolved with no extra action needed by the user (see discussion in #100 if you are interested in details of this resolution).

[Neo-Niu-XG]

It reports error when I installing ARC. I insure that my numpy is the latest version. I'm using Anaconda in macOS. Can you help me?
The error is just like this:
`Building wheel for ARC-Alkali-Rydberg-Calculator (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Users/apple/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/1t/vjkw9s6n56b84fq1gy5n287r0000gn/T/pip-install-p_fp92wc/arc-alkali-rydberg-calculator/setup.py'"'"'; file='"'"'/private/var/folders/1t/vjkw9s6n56b84fq1gy5n287r0000gn/T/pip-install-p_fp92wc/arc-alkali-rydberg-calculator/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/1t/vjkw9s6n56b84fq1gy5n287r0000gn/T/pip-wheel-beeivddq
cwd: /private/var/folders/1t/vjkw9s6n56b84fq1gy5n287r0000gn/T/pip-install-p_fp92wc/arc-alkali-rydberg-calculator/
Complete output (107 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.8
creating build/lib.macosx-10.9-x86_64-3.8/arc
copying arc/alkali_atom_functions.py -> build/lib.macosx-10.9-x86_64-3.8/arc
copying arc/wigner.py -> build/lib.macosx-10.9-x86_64-3.8/arc
copying arc/web_functionality.py -> build/lib.macosx-10.9-x86_64-3.8/arc
copying arc/calculations_atom_single.py -> build/lib.macosx-10.9-x86_64-3.8/arc
copying arc/beta.py -> build/lib.macosx-10.9-x86_64-3.8/arc
copying arc/divalent_atom_data.py -> build/lib.macosx-10.9-x86_64-3.8/arc
copying arc/materials.py -> build/lib.macosx-10.9-x86_64-3.8/arc
copying arc/calculations_atom_pairstate.py -> build/lib.macosx-10.9-x86_64-3.8/arc
copying arc/init.py -> build/lib.macosx-10.9-x86_64-3.8/arc
copying arc/setupc.py -> build/lib.macosx-10.9-x86_64-3.8/arc
copying arc/arc_c_extensions.py -> build/lib.macosx-10.9-x86_64-3.8/arc
copying arc/alkali_atom_data.py -> build/lib.macosx-10.9-x86_64-3.8/arc
copying arc/divalent_atom_functions.py -> build/lib.macosx-10.9-x86_64-3.8/arc
creating build/lib.macosx-10.9-x86_64-3.8/arc/advanced
copying arc/advanced/init.py -> build/lib.macosx-10.9-x86_64-3.8/arc/advanced
copying arc/advanced/population_lifetime.py -> build/lib.macosx-10.9-x86_64-3.8/arc/advanced
creating build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/h_NIST_level_data.ascii -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/NIST_cs_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/sodium_literature_dme.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/h_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/na23_hfs_data.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/li7_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/potassium_literature_dme.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/li7_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/ca_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/NIST_li6_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/na_NIST_level_data.ascii -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/yb_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/cs_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/precalculated_stark.db -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/li6_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/precalculated6j.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/rb85_hfs_data.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/k41_hfs_data.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/k_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/caesium_literature_dme.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/li_NIST_level_data.ascii -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/angularMatrix_meta.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/li6_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/NIST_k_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/precalculated_pair.db -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/rb_NIST_level_data.ascii -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/k40_hfs_data.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/rb_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/na23_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/NIST_rb_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/NIST_li7_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/sr_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/h_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/na23_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/yb_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/NIST_na23_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/NIST_li6_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/li7_hfs_data.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/cs_NIST_level_data.ascii -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/NIST_na23_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/ca_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/k_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/ytterbium_literature_dme.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/ca_level_data.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/strontium_literature_dme.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/cs_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/li6_hfs_data.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/sr_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/rb87_hfs_data.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/sr_level_data.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/k_NIST_level_data.ascii -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/NIST_cs_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/NIST_rb_quadrupole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/NIST_k_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/cs_hfs_data.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/angularMatrix.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/rubidium_literature_dme.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/calcium_literature_dme.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/NIST_li7_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/rb_dipole_matrix_elements.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/precalculated3j.npy -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/k39_hfs_data.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
copying arc/data/yb_level_data.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data
creating build/lib.macosx-10.9-x86_64-3.8/arc/data/refractive_index_data
copying arc/data/refractive_index_data/Querry-o.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data/refractive_index_data
copying arc/data/refractive_index_data/Mathar-2.8.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data/refractive_index_data
copying arc/data/refractive_index_data/Mathar-4.35.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data/refractive_index_data
copying arc/data/refractive_index_data/Mathar-1.3.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data/refractive_index_data
copying arc/data/refractive_index_data/Mathar-7.5.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data/refractive_index_data
copying arc/data/refractive_index_data/Querry-e.csv -> build/lib.macosx-10.9-x86_64-3.8/arc/data/refractive_index_data
copying arc/arc_c_extensions.c -> build/lib.macosx-10.9-x86_64-3.8/arc
running build_ext
building 'arc.arc_c_extensions' extension
Warning: Can't read registry to find the necessary compiler setting
Make sure that Python modules winreg, win32api or win32con are installed.
INFO: C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/apple/opt/anaconda3/include -arch x86_64 -I/Users/apple/opt/anaconda3/include -arch x86_64

creating build/temp.macosx-10.9-x86_64-3.8
creating build/temp.macosx-10.9-x86_64-3.8/arc
INFO: compile options: '-I/Users/apple/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/apple/opt/anaconda3/include/python3.8 -c'
extra options: '-Wall -O3'
INFO: gcc: arc/arc_c_extensions.c
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: Command "gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/apple/opt/anaconda3/include -arch x86_64 -I/Users/apple/opt/anaconda3/include -arch x86_64 -I/Users/apple/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/apple/opt/anaconda3/include/python3.8 -c arc/arc_c_extensions.c -o build/temp.macosx-10.9-x86_64-3.8/arc/arc_c_extensions.o -Wall -O3" failed with exit status 1
ERROR: Failed building wheel for ARC-Alkali-Rydberg-Calculator`

[nikolaqm]

@Neo-Niu-XG

Hi, the problem is not with numpy. Problem is that pip doesn't pick wheel (precompiled version) for MacOS python 3.8, maybe because wheel is build with newer OS version than what you have.
However since you are on Mac this should be relatively easily solvable by installing appropriate developer tools on Mac (so that you can build wheel on your computer, as the pip is trying to do, but currently fails). Can you try running from command line:

xcode-select --install

This should install command line tools. And try running pip install... after (you might need to close terminal window and open a fresh one before running pip install). That should solve the immediate error that you have now.

Please let me know if installation works then or you get a new error now.

[Neo-Niu-XG]

The new error is:
`NameError Traceback (most recent call last)
in
----> 1 xcode-select --install

NameError: name 'xcode' is not defined
`
I'm using anaconda jupyter

[nikolaqm]

@Neo-Niu-XG Just to clarify, you should just use terminal to install Xcode Command Line Tools.
That tools don't have to do anything with Jupyter or Anaconda, it just installs necessary commands on Mac Command line that enables compilation etc.

1. Go to Terminal in /Applications/Utilities/.
2. Input the following command string in Terminal: xcode-select —install
3. Follow prompts to finish installation

Let me know if it works

[Neo-Niu-XG]

It works! That's very kind of you to help me patiently! Thank you! Wish you happy!