ImportError: No module named '_nmtlib' about namaster HOT 8 CLOSED

Hi @brandonshensley,

I would say (but not 100% sure) that the C Healpix library shipped with MacPorts is not the same version that healpy is internally using (if you did pip install healpy I think that it pulls and installs a copy of libchealpix if it doesn't locate one) and when you try to import healpy it conflicts with the newly-loaded healpix library. If this is the case, you can set the environment variable export DYLD_LIBRARY_PATH='/opt/local/lib' and then reinstall healpy pip install --upgrade --force-reinstall healpy. If this doesn't work we'll need to check out the installing code.

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Hi @fjaviersanchez, Thanks so much for the reply! I tried your suggestion, but the healpy installation fails (with a similar message as when I try to import it):

bhensley$ pip install --upgrade --force-reinstall healpy
Traceback (most recent call last):
File "/anaconda3/bin/pip", line 7, in
from pip._internal import main
File "/anaconda3/lib/python3.6/site-packages/pip/_internal/init.py", line 42, in
from pip._internal import cmdoptions
File "/anaconda3/lib/python3.6/site-packages/pip/_internal/cmdoptions.py", line 16, in
from pip._internal.index import (
File "/anaconda3/lib/python3.6/site-packages/pip/_internal/index.py", line 14, in
from pip._vendor import html5lib, requests, six
File "/anaconda3/lib/python3.6/site-packages/pip/_vendor/html5lib/init.py", line 28, in
from .serializer import serialize
File "/anaconda3/lib/python3.6/site-packages/pip/_vendor/html5lib/serializer.py", line 11, in
from xml.sax.saxutils import escape
File "/anaconda3/lib/python3.6/xml/sax/saxutils.py", line 6, in
import os, urllib.parse, urllib.request
File "/anaconda3/lib/python3.6/urllib/request.py", line 2585, in
from _scproxy import _get_proxy_settings, _get_proxies
ImportError: dlopen(/anaconda3/lib/python3.6/lib-dynload/_scproxy.cpython-36m-darwin.so, 2): Symbol not found: _iconv
Referenced from: /usr/lib/libcups.2.dylib
Expected in: /opt/local/lib/libiconv.2.dylib
in /usr/lib/libcups.2.dylib

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:( I think it's getting kind of confused between the system and the macports libraries, what if you try with export DYLD_LIBRARY_PATH='/opt/local/lib:/usr/lib:/usr/local/lib'? Does it still die?

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Amazingly, that broke both pymaster and healpy! Just export DYLD_LIBRARY_PATH='/opt/local/lib:/usr/local/lib' returned pymaster to functionality but with healpy still unable to be imported. I am also kind of confused...

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Progress! Setting instead export DYLD_FALLBACK_LIBRARY_PATH='/opt/local/lib' lets me import both. (I confess I don't really understand why) However, I am still failing three unit tests, unsure if it is related to the issues I've been having:

FAIL: test_mask_c1 (test.test_nmt_utils.TestUtilsMaskSph)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/bhensley/Software/NaMaster/test/test_nmt_utils.py", line 215, in test_mask_c1
    self.assertTrue((np.fabs(msk_apo[self.th<self.th0-np.radians(self.aposize)]-1.)<1E-10).all())
AssertionError: False is not true

======================================================================
FAIL: test_mask_c2 (test.test_nmt_utils.TestUtilsMaskSph)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/bhensley/Software/NaMaster/test/test_nmt_utils.py", line 227, in test_mask_c2
    self.assertTrue((np.fabs(msk_apo[self.th<self.th0-np.radians(self.aposize)]-1.)<1E-10).all())
AssertionError: False is not true

======================================================================
FAIL: test_synfast_flat_stats (test.test_nmt_utils.TestUtilsSynfastFsk)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/bhensley/Software/NaMaster/test/test_nmt_utils.py", line 114, in test_synfast_flat_stats
    self.assertTrue(get_diff(ctt1,self.cltt,self.cltt,self.cltt,self.cltt,nk).all())
AssertionError: False is not true

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🎉 glad to hear! I think that it might be related.

I would try to reinstall healpy using the ports version of libchealpix (which I am not sure how to do because it seems that it can't find the _icov library... An option can be maybe creating a link in /usr/local/lib to /opt/local/lib/libcheakpix.dylib but I am not convinced that will work) or download HEALPix and compile from source:

wget https://sourceforge.net/projects/healpix/files/Healpix_3.11/autotools_packages/chealpix-3.11.4.tar.gz && tar xzf chealpix-3.11.4.tar.gz && cd chealpix-3.11.4 && ./configure --enable-shared && make && sudo make install && cd ..

And then: pip install --upgrade --force-reinstall healpy

Also, thanks a lot for your patience and for pointing out these issues!

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Success! What finally worked was uninstalling my conda installation of healpy and reinstalling with the "--no-deps" flag. I was never able to get healpy to install properly via pip, but it seems like others are also having trouble on macOS 10.13. One lingering thing is a warning during the tests:

test_workspace_compute_coupled_cell (test.test_nmt_master.TestWorkspaceSph) ... /anaconda3/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
  return f(*args, **kwds)
/anaconda3/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
  return f(*args, **kwds)

but since all tests pass now I'll close the issue and report back if I experience any problems running the code. Thanks so much for all of the help!

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I am glad it worked. Please, feel free to open this again if you experience any other related problems and thanks for reporting your solution.

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