Unable to import about ligo.skymap HOT 30 CLOSED

Hooray!

from ligo.skymap.

How did you install ligo.skymap?

from ligo.skymap.

What operating system are you using, and what Python distribution?

from ligo.skymap.

from ligo.skymap.

Do you know what version of pip you are using? There are prebuilt binary wheels, but they require pip 19.0.0 or newer (see the recently updated installation instructions for ligo.skymap). If you have an older version of pip, it will be trying to build ligo.skymap from source.

It's a bother that building from source is not working for you, but try updating to a sufficiently new version of pip.

from ligo.skymap.

hey Leo,

That's what fixed it. Updating pip3 and reinstalling ligo.skymap seemed to have worked. Thanks for walking me through this.

from ligo.skymap.

I will close this issue

from ligo.skymap.

Hi, I am facing the exactly same problem:

import ligo.skymap.plot

---------------------------------------------------------------------------
SystemError                               Traceback (most recent call last)
<ipython-input-2-b71ca8970227> in <module>
----> 1 import ligo.skymap.plot
~/anaconda3/lib/python3.7/site-packages/ligo/skymap/__init__.py in <module>
     28 if not _ASTROPY_SETUP_:   # noqa
     29     # For egg_info test builds to pass, put package imports here.
---> 30     from .core import omp   # noqa
     31     # Then you can be explicit to control what ends up in the namespace,
     32     __all__ += ['omp']   # noqa
SystemError: initialization of core raised unreported exception

Here is my pip information:

pip version: pip 20.1 from /Users/apple/anaconda3/lib/python3.7/site-packages/pip (python 3.7)
sys.version: 3.7.2 (default, Dec 29 2018, 00:00:04)
[Clang 4.0.1 (tags/RELEASE_401/final)]

I have updated my pip, uninstall and reinstall ligo.skymap. But it doesn't work.

from ligo.skymap.

This is a different error message. Was there any other output? What's the full output of python -c 'import ligo.skymap.plot'?

from ligo.skymap.

Thanks for replay. I type the command in the shell and get the output as follows:

$ python -c 'import ligo.skymap.plot'

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/apple/anaconda3/lib/python3.7/site-packages/ligo/skymap/__init__.py", line 30, in <module>
    from .core import omp   # noqa
SystemError: initialization of core raised unreported exception

from ligo.skymap.

An information that might help is that, I have changed the pip "channel" (I don't what the specific word is) to a mirror site in China by this simple application when I install ligo.skymap.

After I noticed that it might cause problem, I changed back to the original "channel" and reinstalled. But it still didn't work.

from ligo.skymap.

Would you please show me the output of pip freeze?

Also, I added commit addb832 which should catch a few possible uncaught exceptions in the ligo.skymap.core module initialization.

from ligo.skymap.

It's a long list:

$ pip freeze

aiohttp==3.6.2
alabaster==0.7.12
anaconda-client==1.7.2
anaconda-navigator==1.9.2
anaconda-project==0.8.3
appdirs==1.4.3
appnope==0.1.0
appscript==1.0.1
asn1crypto==1.3.0
astroid==2.3.3
astroplan==0.6
astropy==3.2.3
astropy-healpix==0.5
async-timeout==3.0.1
atomicwrites==1.3.0
attrs==19.3.0
autobahn==20.4.1
Automat==0.7.0
Babel==2.8.0
backcall==0.1.0
backports.os==0.1.1
backports.shutil-get-terminal-size==1.0.0
bcrypt==3.1.7
beautifulsoup4==4.8.2
bitarray==1.2.1
bkcharts==0.2
blaze==0.11.3
bleach==3.1.0
bokeh==1.4.0
boto==2.49.0
Bottleneck==1.3.2
certifi==2019.11.28
cffi==1.14.0
chardet==3.0.4
Click==7.0
cloudpickle==1.3.0
clyent==1.2.2
colorama==0.4.3
conda==4.8.2
conda-build==3.15.1
conda-package-handling==1.6.0
constantly==15.1.0
contextlib2==0.6.0.post1
coverage==5.1
cryptography==2.8
cycler==0.10.0
Cython==0.29.15
cytoolz==0.10.1
dask==2.11.0
datashape==0.5.4
decorator==4.4.1
defusedxml==0.6.0
distributed==2.11.0
doc8==0.8.0
docutils==0.16
entrypoints==0.3
et-xmlfile==1.0.1
fastcache==1.1.0
filelock==3.0.12
Flask==1.1.1
Flask-Cors==3.0.8
fsspec==0.6.2
future==0.18.2
gevent==1.4.0
glob2==0.7
gmpy2==2.0.8
greenlet==0.4.15
h5py==2.8.0
healpy==1.13.0
HeapDict==1.0.1
html5lib==1.0.1
hyperlink==18.0.0
hypothesis==5.5.4
idna==2.8
imageio==2.6.1
imagesize==1.2.0
importlib-metadata==1.5.0
incremental==17.5.0
ipykernel==5.1.4
ipython==7.12.0
ipython-genutils==0.2.0
ipywidgets==7.5.1
isort==4.3.21
itsdangerous==1.1.0
jdcal==1.4.1
jedi==0.16.0
Jinja2==2.11.1
json5==0.9.1
jsonschema==3.2.0
jupyter==1.0.0
jupyter-client==5.3.4
jupyter-console==6.1.0
jupyter-core==4.6.1
jupyter-server-proxy==1.3.2
jupyterlab==1.2.6
jupyterlab-launcher==0.13.1
jupyterlab-server==1.0.6
keyring==21.1.0
kiwisolver==1.1.0
lalsuite==6.70
lazy-object-proxy==1.4.3
libarchive-c==2.8
lief==0.9.0
ligo-gracedb==2.5.0
ligo-segments==1.2.0
ligo.skymap==0.2.2
llvmlite==0.31.0
locket==0.2.0
lscsoft-glue==2.0.0
lxml==4.5.0
MarkupSafe==1.1.1
matplotlib==3.1.3
mccabe==0.6.1
mistune==0.8.4
mkl-fft==1.0.6
mkl-random==1.0.1
more-itertools==8.2.0
mpmath==1.1.0
msgpack==0.6.1
multidict==4.7.5
multipledispatch==0.6.0
navigator-updater==0.2.1
nbconvert==5.6.1
nbformat==5.0.4
networkx==2.4
nltk==3.4.5
nose==1.3.7
notebook==6.0.3
numba==0.48.0
numexpr==2.6.8
numpy==1.15.4
numpydoc==0.9.2
odo==0.5.1
olefile==0.46
openpyxl==3.0.3
packaging==20.1
pandas==1.0.1
pandocfilters==1.4.2
parso==0.6.1
partd==1.1.0
path==13.1.0
pathlib2==2.3.5
patsy==0.5.0
pbr==5.4.4
pep8==1.7.1
pexpect==4.8.0
pickleshare==0.7.5
Pillow==7.0.0
pkginfo==1.5.0.1
pluggy==0.13.1
ply==3.11
prometheus-client==0.7.1
prompt-toolkit==3.0.3
psutil==5.6.7
ptemcee==1.0.0
ptyprocess==0.6.0
py==1.8.1
pyasn1==0.4.4
pyasn1-modules==0.2.2
pybind11==2.4.3
pycodestyle==2.5.0
pycosat==0.6.3
pycparser==2.19
pycrypto==2.6.1
pycurl==7.43.0.5
pyflakes==2.1.1
Pygments==2.5.2
PyHamcrest==1.9.0
pylint==2.4.4
pyodbc===4.0.0-unsupported
pyOpenSSL==19.1.0
pyparsing==2.4.6
PyQt5==5.12.3
PyQt5-sip==12.7.2
PyQtWebEngine==5.12.1
pyrsistent==0.15.7
PySocks==1.7.1
pytest==5.3.5
pytest-arraydiff==0.3
pytest-astropy==0.8.0
pytest-astropy-header==0.1.2
pytest-cov==2.8.1
pytest-doctestplus==0.5.0
pytest-filter-subpackage==0.1.1
pytest-openfiles==0.4.0
pytest-remotedata==0.3.2
python-dateutil==2.8.1
python-ligo-lw==1.6.0
pytz==2019.3
PyWavelets==1.1.1
PyYAML==5.3
pyzmq==18.1.1
QtAwesome==0.6.1
qtconsole==4.6.0
QtPy==1.9.0
reproject==0.7
requests==2.22.0
restructuredtext-lint==1.3.0
rope==0.16.0
ruamel-yaml==0.15.87
scikit-image==0.14.0
scikit-learn==0.19.2
scipy==1.1.0
seaborn==0.9.0
Send2Trash==1.5.0
service-identity==17.0.0
simpervisor==0.3
simplegeneric==0.8.1
singledispatch==3.4.0.3
six==1.14.0
snowballstemmer==2.0.0
sortedcollections==1.1.2
sortedcontainers==2.1.0
soupsieve==1.9.5
Sphinx==2.4.0
sphinx-rtd-theme==0.4.3
sphinxcontrib-applehelp==1.0.1
sphinxcontrib-devhelp==1.0.1
sphinxcontrib-htmlhelp==1.0.2
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.2
sphinxcontrib-serializinghtml==1.1.3
sphinxcontrib-websupport==1.2.0
spyder==3.3.6
spyder-kernels==0.5.2
SQLAlchemy==1.3.13
statsmodels==0.9.0
stevedore==1.31.0
sympy==1.5.1
tables==3.4.4
TBB==0.1
tblib==1.6.0
terminado==0.8.3
testpath==0.4.4
toolz==0.10.0
tornado==6.0.3
tqdm==4.42.1
traitlets==4.3.3
Twisted==19.2.0
txaio==20.4.1
typed-ast==1.4.1
unicodecsv==0.14.1
urllib3==1.25.8
vpython==7.6.1
wcwidth==0.1.8
webencodings==0.5.1
Werkzeug==1.0.0
widgetsnbextension==3.5.1
wrapt==1.11.2
wurlitzer==2.0.0
xlrd==1.2.0
XlsxWriter==1.2.7
xlwings==0.17.1
xlwt==1.3.0
yarl==1.4.2
zict==1.0.0
zipp==2.2.0
zope.interface==4.5.0

from ligo.skymap.

Do you know if when you installed ligo.skymap it was from a binary wheel or from source?

from ligo.skymap.

I didn't notice it when I first install ligo.skymap. When I reinstall it, the output is:

$ pip install ligo.skymap

Collecting ligo.skymap
  Using cached ligo.skymap-0.2.2-cp37-cp37m-macosx_10_12_x86_64.whl (2.4 MB)
Requirement already satisfied: lscsoft-glue>=2.0.0 in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (2.0.0)
Requirement already satisfied: numpy!=1.15.3,>=1.14 in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (1.15.4)
Requirement already satisfied: astropy!=4.0.1,>=3.1 in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (3.2.3)
Requirement already satisfied: astroplan>=0.5 in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (0.6)
Requirement already satisfied: ligo-gracedb>=2.0.1 in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (2.5.0)
Requirement already satisfied: astropy-healpix>=0.3 in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (0.5)
Requirement already satisfied: networkx in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (2.4)
Requirement already satisfied: ptemcee in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (1.0.0)
Requirement already satisfied: matplotlib>=3.0.2 in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (3.1.3)
Requirement already satisfied: ligo-segments>=1.2.0 in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (1.2.0)
Requirement already satisfied: pillow>=2.5.0 in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (7.0.0)
Requirement already satisfied: reproject>=0.3.2 in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (0.7)
Requirement already satisfied: lalsuite>=6.53 in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (6.70)
Requirement already satisfied: tqdm>=4.27.0 in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (4.42.1)
Requirement already satisfied: scipy>=0.14 in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (1.1.0)
Requirement already satisfied: h5py in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (2.8.0)
Requirement already satisfied: pytz in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (2019.3)
Requirement already satisfied: healpy in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (1.13.0)
Requirement already satisfied: python-ligo-lw in ./anaconda3/lib/python3.7/site-packages (from ligo.skymap) (1.6.0)
Requirement already satisfied: pyOpenSSL in ./anaconda3/lib/python3.7/site-packages (from lscsoft-glue>=2.0.0->ligo.skymap) (19.1.0)
Requirement already satisfied: six in ./anaconda3/lib/python3.7/site-packages (from lscsoft-glue>=2.0.0->ligo.skymap) (1.14.0)
Requirement already satisfied: future>=0.15.0 in ./anaconda3/lib/python3.7/site-packages (from ligo-gracedb>=2.0.1->ligo.skymap) (0.18.2)
Requirement already satisfied: cryptography>=1.7.2 in ./anaconda3/lib/python3.7/site-packages (from ligo-gracedb>=2.0.1->ligo.skymap) (2.8)
Requirement already satisfied: decorator>=4.3.0 in ./anaconda3/lib/python3.7/site-packages (from networkx->ligo.skymap) (4.4.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./anaconda3/lib/python3.7/site-packages (from matplotlib>=3.0.2->ligo.skymap) (2.4.6)
Requirement already satisfied: cycler>=0.10 in ./anaconda3/lib/python3.7/site-packages (from matplotlib>=3.0.2->ligo.skymap) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in ./anaconda3/lib/python3.7/site-packages (from matplotlib>=3.0.2->ligo.skymap) (1.1.0)
Requirement already satisfied: python-dateutil>=2.1 in ./anaconda3/lib/python3.7/site-packages (from matplotlib>=3.0.2->ligo.skymap) (2.8.1)
Requirement already satisfied: pyyaml in ./anaconda3/lib/python3.7/site-packages (from python-ligo-lw->ligo.skymap) (5.3)
Requirement already satisfied: cffi!=1.11.3,>=1.8 in ./anaconda3/lib/python3.7/site-packages (from cryptography>=1.7.2->ligo-gracedb>=2.0.1->ligo.skymap) (1.14.0)
Requirement already satisfied: setuptools in ./anaconda3/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib>=3.0.2->ligo.skymap) (45.2.0.post20200210)
Requirement already satisfied: pycparser in ./anaconda3/lib/python3.7/site-packages (from cffi!=1.11.3,>=1.8->cryptography>=1.7.2->ligo-gracedb>=2.0.1->ligo.skymap) (2.19)
Installing collected packages: ligo.skymap
Successfully installed ligo.skymap-0.2.2

from ligo.skymap.

Yes, that's a wheel: the filename ligo.skymap-0.2.2-cp37-cp37m-macosx_10_12_x86_64.whl ends in .whl. So that's a prebuilt binary.

I haven't been able to reproduce this yet on my own machine. Can you try updating to the latest version of Numpy and see if that fixes it?

from ligo.skymap.

Thank you. The problem seems to be fixed!

$ pip install numpy --upgrade

Collecting numpy
  Downloading numpy-1.18.4-cp37-cp37m-macosx_10_9_x86_64.whl (15.1 MB)
     |████████████████████████████████| 15.1 MB 12.4 MB/s
Installing collected packages: numpy
  Attempting uninstall: numpy
    Found existing installation: numpy 1.15.4
    Uninstalling numpy-1.15.4:
      Successfully uninstalled numpy-1.15.4
Successfully installed numpy-1.18.4

Then I type python -c 'import ligo.skymap.plot' and no error returned.

from ligo.skymap.

Now I can successfully make those wonderful plots in the example files. Thanks a lot!

from ligo.skymap.

My pleasure. Happy mapmaking!

from ligo.skymap.

Hi, I get the following error while importing :
from ligo.skymap.io.fits import read_sky_map

Error : libgsl.so.25: cannot open shared object file: No such file or directory (Done installing libgsl.so.0 but still non help)

from ligo.skymap.

@choudharyharsh122, how did you install ligo.skymap, on what operating system, and on what version and distribution of Python? Did you follow the installation instructions?

from ligo.skymap.

@lpsinger thanks for your response, i was able to resolve this. It was some installation issue with gsl library.
Thank you again

from ligo.skymap.

Similar to the original post that this issue was opened under I am finding that import ligo.skymap.io produces the problem.

(base) tparsota@discover11:/discover/nobackup/tparsota> python -c 'import ligo.skymap.io'
Traceback (most recent call last):
File "", line 1, in
File "/home/tparsota/.local/lib/python3.9/site-packages/ligo/skymap/io/init.py", line 9, in
exec('from . import {0};'
File "", line 1, in
File "/home/tparsota/.local/lib/python3.9/site-packages/ligo/skymap/io/fits.py", line 70, in
from .. import moc
File "/home/tparsota/.local/lib/python3.9/site-packages/ligo/skymap/moc.py", line 36, in
from .core import nest2uniq, uniq2nest, uniq2order, uniq2pixarea, uniq2ang
ImportError: /home/tparsota/.local/lib/python3.9/site-packages/ligo/skymap/core.abi3.so: undefined symbol: gsl_root_fdfsolver_steffenson
`

to install on the system that I am on, I specify where gsl is and do:

(base) tparsota@discover13:> CFLAGS='-I/usr/local/other/gsl/2.5/include/' LIBS='-L/usr/local/other/gsl/2.5/lib/libgsl.a -L/usr/local/other/gsl/2.5/lib/libgslcblas.a -lgsl' pip install ligo.skymap
Defaulting to user installation because normal site-packages is not writeable
Collecting ligo.skymap
Downloading ligo.skymap-1.1.1.tar.gz (2.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 31.6 MB/s eta 0:00:00
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: scipy!=1.10.0,>=0.14 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from ligo.skymap) (1.8.1)
Requirement already satisfied: python-ligo-lw>=1.8.0 in ./.local/lib/python3.9/site-packages (from ligo.skymap) (1.8.3)
Requirement already satisfied: astroplan>=0.7 in ./.local/lib/python3.9/site-packages (from ligo.skymap) (0.9)
Requirement already satisfied: numpy!=1.22.0,>=1.19.3 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from ligo.skymap) (1.21.6)
Requirement already satisfied: lalsuite!=7.2,>=6.82 in ./.local/lib/python3.9/site-packages (from ligo.skymap) (7.11)
Requirement already satisfied: matplotlib>=3.5.0 in ./.local/lib/python3.9/site-packages (from ligo.skymap) (3.7.2)
Requirement already satisfied: tqdm>=4.27.0 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from ligo.skymap) (4.64.0)
Requirement already satisfied: astropy-healpix>=0.3 in ./.local/lib/python3.9/site-packages (from ligo.skymap) (0.7)
Requirement already satisfied: ligo-gracedb>=2.0.1 in ./.local/lib/python3.9/site-packages (from ligo.skymap) (2.11.0)
Requirement already satisfied: healpy in ./.local/lib/python3.9/site-packages (from ligo.skymap) (1.15.1)
Requirement already satisfied: ptemcee in ./.local/lib/python3.9/site-packages (from ligo.skymap) (1.0.0)
Requirement already satisfied: networkx in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from ligo.skymap) (2.8.2)
Requirement already satisfied: h5py in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from ligo.skymap) (3.7.0)
Requirement already satisfied: pytz in ./.local/lib/python3.9/site-packages (from ligo.skymap) (2022.2.1)
Requirement already satisfied: astropy>=5.0 in ./.local/lib/python3.9/site-packages (from ligo.skymap) (5.3.1)
Requirement already satisfied: pillow>=2.5.0 in ./.local/lib/python3.9/site-packages (from ligo.skymap) (8.4.0)
Requirement already satisfied: ligo-segments>=1.2.0 in ./.local/lib/python3.9/site-packages (from ligo.skymap) (1.4.0)
Requirement already satisfied: reproject>=0.3.2 in ./.local/lib/python3.9/site-packages (from ligo.skymap) (0.11.0)
Requirement already satisfied: six in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from astroplan>=0.7->ligo.skymap) (1.16.0)
Requirement already satisfied: packaging>=19.0 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from astropy>=5.0->ligo.skymap) (21.3)
Requirement already satisfied: pyerfa>=2.0 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from astropy>=5.0->ligo.skymap) (2.0.0.1)
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Building wheels for collected packages: ligo.skymap
Building wheel for ligo.skymap (pyproject.toml) ... done
Created wheel for ligo.skymap: filename=ligo.skymap-1.1.1-cp39-abi3-linux_x86_64.whl size=1619223 sha256=9bf02981fbc27f59bbae29cbd2d6dddde69172ae759012f5c3490b5ca7a0c891
Stored in directory: /gpfsm/dhome/tparsota/.cache/pip/wheels/67/5c/8a/cd824baf7b0f48106b845f9b6fb317f411507c0b4afa95d104
Successfully built ligo.skymap
Installing collected packages: ligo.skymap
WARNING: The scripts bayestar-inject, bayestar-localize-coincs, bayestar-localize-lvalert, bayestar-mcmc, bayestar-realize-coincs, bayestar-sample-model-psd, ligo-skymap-combine, ligo-skymap-constellations, ligo-skymap-contour, ligo-skymap-contour-moc, ligo-skymap-flatten, ligo-skymap-from-samples, ligo-skymap-plot, ligo-skymap-plot-airmass, ligo-skymap-plot-coherence, ligo-skymap-plot-observability, ligo-skymap-plot-pp-samples, ligo-skymap-plot-stats, ligo-skymap-plot-volume, ligo-skymap-stats and ligo-skymap-unflatten are installed in '/home/tparsota/.local/bin' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed ligo.skymap-1.1.1

I have also verified that my pip is >v19.3:

(base) tparsota@discover13:~> pip --version
pip 22.1.1 from /usr/local/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages/pip (python 3.9)

from ligo.skymap.

@parsotat, it looks like pip is trying to build ligo.skymap from source rather than installing a binary wheel. What operating system and platform are you working on?

The Linux binaries are built using manylinux_2_28. They should support Linux distributions that are based on glibc 2.28 or newer. According to the manylinux project, that should include "ALT Linux 10+, RHEL 9+, Debian 11+, Fedora 34+, Mageia 8+, Photon OS 3.0 with updates, Ubuntu 21.04+". Are you on a very old Linux distribution?

from ligo.skymap.

@lpsinger I am on NCCS trying to install this library (and also the graceDB one). I actually found solution to this I have to preload the appropriate GSL shared libraries by doing:

LD_PRELOAD=/usr/local/other/gsl/2.5/lib/libgsl.so:/usr/local/other/gsl/2.5/lib/libgslcblas.so python -c "import ligo.skymap.io"

This gives no errors and it indicates that the compilation of the core.abi3.so was not properly linked to the GSL libraries on my system. These libraries are in a non-standard location and it seems as though appending CFLAGS and LIBS to my call for pip install ligo.skymap did not connect these libraries properly.

from ligo.skymap.

The operating system on NCCS is SLES. What version?

from ligo.skymap.

Operating System: SUSE Linux Enterprise Server 12 SP5
CPE OS Name: cpe:/o:suse:sles:12:sp5
Kernel: Linux 4.12.14-122.156-default
Architecture: x86-64

from ligo.skymap.

Yeah, that's a pretty old distro. Not really supported.

from ligo.skymap.

Ok, I think that there are plans to upgrade to SLES15 relatively soon. That should be supported if I understand the manylinux documentation, correct?

from ligo.skymap.

Hello all,

Not sure if this has anything to do on your end. But I am unable to successfully import the ligo.skymap module. I went through the pip installation procedures but when I try to import, I am left with this error:

>>> import ligo.skymap
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.6/dist-packages/ligo/skymap/__init__.py", line 30, in <module>
    from .core import omp   # noqa
ImportError: /usr/local/lib/python3.6/dist-packages/ligo/skymap/core.cpython-36m-x86_64-linux-gnu.so: undefined symbol: gsl_root_fdfsolver_steffenson

I tried updating the gnu_gsl library but still am getting the same error. Have you seen this error before?

I was eventually able to reproduce this when building from source. The problem was that I didn't have pkg-config installed; you need pkg-config when building from source. See https://git.ligo.org/lscsoft/ligo.skymap/-/merge_requests/351.

from ligo.skymap.