Unable to import

[swyatt7]

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?

[lpsinger]

How did you install ligo.skymap?

[lpsinger]

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

[swyatt7]

Thanks for getting back to me!

For installation I used:

sudo pip3 install ligo.skymap

The machine is an Amazon AWS machine running Ubuntu 18.04

Ubuntu 18.04.2 LTS (GNU/Linux 4.15.0-1044-aws x86_64)

Python distribution is 3.6.8

• SW

On Mon, Aug 26, 2019 at 11:27 AM Leo Singer notifications@github.com wrote:

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

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lpsinger/ligo.skymap/issues/3?email_source=notifications&email_token=AGE4DPDPBNJUJKQ3IVKZE4DQGQOAXA5CNFSM4IPQ6VVKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5FHJ7I#issuecomment-524973309, or mute the thread https://github.com/notifications/unsubscribe-auth/AGE4DPARINDAIFA3ZTNBAYDQGQOAXANCNFSM4IPQ6VVA .

[lpsinger]

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.

[swyatt7]

hey Leo,

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

[swyatt7]

I will close this issue

[Adiolph]

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.

[lpsinger]

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

[Adiolph]

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

[Adiolph]

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.

[lpsinger]

Would you please show me the output of pip freeze?

Also, I added commit addb83246263c956fecf022f90cc0cfbb4ffb3c3 which should catch a few possible uncaught exceptions in the ligo.skymap.core module initialization.

[Adiolph]

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

[lpsinger]

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

[Adiolph]

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

[lpsinger]

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?

[Adiolph]

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.

[lpsinger]

Hooray!

[Adiolph]

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

[lpsinger]

My pleasure. Happy mapmaking!

[choudharyharsh122]

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)

[lpsinger]

@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?

[choudharyharsh122]

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

[parsotat]

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) Requirement already satisfied: PyYAML>=3.13 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) (6.0) Requirement already satisfied: python-dateutil in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from lalsuite!=7.2,>=6.82->ligo.skymap) (2.8.2) Requirement already satisfied: lscsoft-glue in ./.local/lib/python3.9/site-packages (from lalsuite!=7.2,>=6.82->ligo.skymap) (3.0.1) Requirement already satisfied: requests>=2.6.0 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from ligo-gracedb>=2.0.1->ligo.skymap) (2.27.1) Requirement already satisfied: future>=0.15.0 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from ligo-gracedb>=2.0.1->ligo.skymap) (0.18.2) Requirement already satisfied: igwn-auth-utils>=0.3.1 in ./.local/lib/python3.9/site-packages (from ligo-gracedb>=2.0.1->ligo.skymap) (0.4.0) Requirement already satisfied: safe-netrc>=1.0.0 in ./.local/lib/python3.9/site-packages (from ligo-gracedb>=2.0.1->ligo.skymap) (1.0.1) Requirement already satisfied: cryptography>=1.7.2 in ./.local/lib/python3.9/site-packages (from ligo-gracedb>=2.0.1->ligo.skymap) (37.0.4) Requirement already satisfied: contourpy>=1.0.1 in ./.local/lib/python3.9/site-packages (from matplotlib>=3.5.0->ligo.skymap) (1.1.0) Requirement already satisfied: cycler>=0.10 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from matplotlib>=3.5.0->ligo.skymap) (0.11.0) Requirement already satisfied: importlib-resources>=3.2.0 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from matplotlib>=3.5.0->ligo.skymap) (5.7.1) Requirement already satisfied: fonttools>=4.22.0 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from matplotlib>=3.5.0->ligo.skymap) (4.33.3) Requirement already satisfied: kiwisolver>=1.0.1 in ./.local/lib/python3.9/site-packages (from matplotlib>=3.5.0->ligo.skymap) (1.3.1) Requirement already satisfied: pyparsing<3.1,>=2.3.1 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from matplotlib>=3.5.0->ligo.skymap) (3.0.9) Requirement already satisfied: dask[array]>=2020 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from reproject>=0.3.2->ligo.skymap) (2022.5.1) Requirement already satisfied: fsspec in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from reproject>=0.3.2->ligo.skymap) (2022.5.0) Requirement already satisfied: zarr in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from reproject>=0.3.2->ligo.skymap) (2.11.3) Requirement already satisfied: cloudpickle in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from reproject>=0.3.2->ligo.skymap) (2.1.0) Requirement already satisfied: cffi>=1.12 in ./.local/lib/python3.9/site-packages (from cryptography>=1.7.2->ligo-gracedb>=2.0.1->ligo.skymap) (1.15.1) Requirement already satisfied: toolz>=0.8.2 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from dask[array]>=2020->reproject>=0.3.2->ligo.skymap) (0.11.2) Requirement already satisfied: partd>=0.3.10 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from dask[array]>=2020->reproject>=0.3.2->ligo.skymap) (1.2.0) Requirement already satisfied: scitokens>=1.7.0 in ./.local/lib/python3.9/site-packages (from igwn-auth-utils>=0.3.1->ligo-gracedb>=2.0.1->ligo.skymap) (1.8.1) Requirement already satisfied: zipp>=3.1.0 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from importlib-resources>=3.2.0->matplotlib>=3.5.0->ligo.skymap) (3.8.0) Requirement already satisfied: charset-normalizer~=2.0.0 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from requests>=2.6.0->ligo-gracedb>=2.0.1->ligo.skymap) (2.0.12) Requirement already satisfied: idna<4,>=2.5 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from requests>=2.6.0->ligo-gracedb>=2.0.1->ligo.skymap) (3.3) Requirement already satisfied: certifi>=2017.4.17 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from requests>=2.6.0->ligo-gracedb>=2.0.1->ligo.skymap) (2022.6.15) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./.local/lib/python3.9/site-packages (from requests>=2.6.0->ligo-gracedb>=2.0.1->ligo.skymap) (1.26.12) Requirement already satisfied: pyRXP in ./.local/lib/python3.9/site-packages (from lscsoft-glue->lalsuite!=7.2,>=6.82->ligo.skymap) (3.0.1) Requirement already satisfied: pyOpenSSL in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from lscsoft-glue->lalsuite!=7.2,>=6.82->ligo.skymap) (22.0.0) Requirement already satisfied: fasteners in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from zarr->reproject>=0.3.2->ligo.skymap) (0.17.3) Requirement already satisfied: asciitree in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from zarr->reproject>=0.3.2->ligo.skymap) (0.3.3) Requirement already satisfied: numcodecs>=0.6.4 in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from zarr->reproject>=0.3.2->ligo.skymap) (0.9.1) Requirement already satisfied: pycparser in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from cffi>=1.12->cryptography>=1.7.2->ligo-gracedb>=2.0.1->ligo.skymap) (2.21) Requirement already satisfied: locket in /gpfsm/dulocal/sles12/other/python/JH.1/GEOSpyD/4.11.0_py3.9/2022-05-25/lib/python3.9/site-packages (from partd>=0.3.10->dask[array]>=2020->reproject>=0.3.2->ligo.skymap) (1.0.0) Requirement already satisfied: PyJWT>=1.6.1 in ./.local/lib/python3.9/site-packages (from scitokens>=1.7.0->igwn-auth-utils>=0.3.1->ligo-gracedb>=2.0.1->ligo.skymap) (2.8.0) 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)

[lpsinger]

@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?

[parsotat]

@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.

[lpsinger]

The operating system on NCCS is SLES. What version?

[parsotat]

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

[lpsinger]

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

[parsotat]

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

[lpsinger]

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.