Segmentation Fault
ewu20 opened this issue · 5 comments
Hi,
I am new to fragmenter and I am trying to learn how to use it. I have installed fragmenter through conda. I am trying to run the example code, fragment_molecules.py, in the terminal but it gives me the following error:
Fatal Python error: Segmentation fault
Current thread 0x0000000119aa0dc0 (most recent call first):
File "", line 219 in _call_with_frames_removed
File "", line 922 in create_module
File "", line 571 in module_from_spec
File "", line 658 in _load_unlocked
File "", line 955 in _find_and_load_unlocked
File "", line 971 in _find_and_load
File "/Users/emmawu/opt/anaconda3/lib/python3.6/site-packages/rdkit/init.py", line 2 in
File "", line 219 in _call_with_frames_removed
File "", line 678 in exec_module
File "", line 665 in _load_unlocked
File "", line 955 in _find_and_load_unlocked
File "", line 971 in _find_and_load
File "/Users/emmawu/opt/anaconda3/lib/python3.6/site-packages/cmiles/utils.py", line 10 in
File "", line 219 in _call_with_frames_removed
File "", line 678 in exec_module
File "", line 665 in _load_unlocked
File "", line 955 in _find_and_load_unlocked
File "", line 971 in _find_and_load
File "/Users/emmawu/opt/anaconda3/lib/python3.6/site-packages/cmiles/generator.py", line 8 in
File "", line 219 in _call_with_frames_removed
File "", line 678 in exec_module
File "", line 665 in _load_unlocked
File "", line 955 in _find_and_load_unlocked
File "", line 971 in _find_and_load
File "/Users/emmawu/opt/anaconda3/lib/python3.6/site-packages/cmiles/init.py", line 11 in
File "", line 219 in _call_with_frames_removed
File "", line 678 in exec_module
File "", line 665 in _load_unlocked
File "", line 955 in _find_and_load_unlocked
File "", line 971 in _find_and_load
File "", line 219 in _call_with_frames_removed
File "", line 941 in _find_and_load_unlocked
File "", line 971 in _find_and_load
File "/Users/emmawu/opt/anaconda3/lib/python3.6/site-packages/fragmenter/fragment.py", line 2 in
File "", line 219 in _call_with_frames_removed
File "", line 678 in exec_module
File "", line 665 in _load_unlocked
File "", line 955 in _find_and_load_unlocked
File "", line 971 in _find_and_load
File "", line 219 in _call_with_frames_removed
File "", line 1023 in _handle_fromlist
File "/Users/emmawu/opt/anaconda3/lib/python3.6/site-packages/fragmenter/init.py", line 12 in
File "", line 219 in _call_with_frames_removed
File "", line 678 in exec_module
File "", line 665 in _load_unlocked
File "", line 955 in _find_and_load_unlocked
File "", line 971 in _find_and_load
File "frag_test.py", line 8 in
zsh: segmentation fault python -q -X faulthandler frag_test.py
I am using the following python: Python 3.6.10 :: Anaconda, Inc.
The command I use to run the script is python frag_test.py
(I just copied and pasted the code from fragment_molecules.py to frag_test.py)
I am not sure how to fix this error. Any input is appreciated! Thanks!
Hi @ewu20,
Hm, I've never seen this before. A segmentation fault usually means that something in the installation is misconfigured. Three pieces of information could help debug this:
Could you...
- Paste the command you used to install fragmenter (if you still have it)
- Paste the output of running
conda list - Paste the output of running
conda info
Thanks!
Hi @j-wags
I installed fragmenter using conda install -c omnia fragmenter.
Here is the output of conda list:
# packages in environment at /Users/emmawu/opt/anaconda3:
#
# Name Version Build Channel
_ipyw_jlab_nb_ext_conf 0.1.0 py36_0
alabaster 0.7.12 py36_0
anaconda 2020.07 py36_0
anaconda-client 1.7.2 py36_0
anaconda-navigator 1.9.12 py36_0
anaconda-project 0.8.4 py_0
applaunchservices 0.2.1 py_0
appnope 0.1.0 py36hf537a9a_0
appscript 1.1.1 py36haf1e3a3_0
argh 0.26.2 py36_0
asn1crypto 1.3.0 py36_0
astroid 2.4.2 py36_0
astropy 4.0.1.post1 py36h01d97ff_1
atomicwrites 1.4.0 py_0
attrs 19.3.0 py_0
autopep8 1.5.3 py_0
babel 2.8.0 py_0
backcall 0.2.0 py_0
backports 1.0 py_2
backports.functools_lru_cache 1.6.1 py_0
backports.shutil_get_terminal_size 1.0.0 py36_2
backports.tempfile 1.0 py_1
backports.weakref 1.0.post1 py_1
beautifulsoup4 4.9.1 py36_0
bitarray 1.4.0 py36haf1e3a3_0
bkcharts 0.2 py36_0
blas 1.0 mkl
bleach 3.1.5 py_0
blosc 1.19.0 hab81aa3_0
bokeh 2.1.1 py36_0
boost 1.63.0 py36_1 rdkit
boto 2.49.0 py36_0
bottleneck 1.3.2 py36hf1fa96c_1
brotlipy 0.7.0 py36haf1e3a3_1000
bzip2 1.0.8 h1de35cc_0
ca-certificates 2020.6.24 0
cairo 1.14.12 hc4e6be7_4
certifi 2020.6.20 py36_0
cffi 1.14.0 py36hc512035_1
chardet 3.0.4 py36_1003
click 7.1.2 py_0
cloudpickle 1.5.0 py_0
clyent 1.2.2 py36_1
cmiles 0.1.5 py36_2 omnia
colorama 0.4.3 py_0
conda 4.7.5 py36_0
conda-build 3.20.2 py36_0
conda-env 2.6.0 1
conda-package-handling 1.6.1 py36h1de35cc_0
conda-verify 3.4.2 py_1
contextlib2 0.6.0.post1 py_0
contextvars 2.4 py_0
cryptography 2.9.2 py36ha12b0ac_0
curl 7.71.1 hb0a8c7a_1
cycler 0.10.0 py36hfc81398_0
cython 0.29.21 py36hb1e8313_0
cytoolz 0.10.1 py36h1de35cc_0
dask 2.20.0 py_0
dask-core 2.20.0 py_0
dbus 1.13.16 h18a8e69_0
decorator 4.4.2 py_0
defusedxml 0.6.0 py_0
diff-match-patch 20200713 py_0
distributed 2.20.0 py36_0
docutils 0.16 py36_1
entrypoints 0.3 py36_0
et_xmlfile 1.0.1 py_1001
expat 2.2.9 hb1e8313_2
fastcache 1.1.0 py36h1de35cc_0
filelock 3.0.12 py_0
flake8 3.8.3 py_0
flask 1.1.2 py_0
fontconfig 2.13.0 h5d5b041_1
fragmenter 0.0.4 py36_0 omnia
freetype 2.10.2 ha233b18_0
fsspec 0.7.4 py_0
future 0.18.2 py36_1
get_terminal_size 1.0.0 h7520d66_0
gettext 0.19.8.1 hb0f4f8b_2
gevent 20.6.2 py36haf1e3a3_0
glib 2.65.0 hc5f4afa_0
glob2 0.7 py_0
gmp 6.1.2 hb37e062_1
gmpy2 2.0.8 py36h6ef4df4_2
greenlet 0.4.16 py36haf1e3a3_0
h5py 2.10.0 py36h3134771_0
hdf5 1.10.4 hfa1e0ec_0
heapdict 1.0.1 py_0
html5lib 1.1 py_0
icu 58.2 h0a44026_3
idna 2.10 py_0
imageio 2.9.0 py_0
imagesize 1.2.0 py_0
immutables 0.14 py36haf1e3a3_0
importlib-metadata 1.7.0 py36_0
importlib_metadata 1.7.0 0
intel-openmp 2019.4 233
intervaltree 3.0.2 py_1
ipykernel 5.3.2 py36h5ca1d4c_0
ipython 7.16.1 py36h5ca1d4c_0
ipython_genutils 0.2.0 py36_0
ipywidgets 7.5.1 py_0
isort 4.3.21 py36_0
itsdangerous 1.1.0 py36_0
jbig 2.1 h4d881f8_0
jdcal 1.4.1 py_0
jedi 0.17.1 py36_0
jinja2 2.11.2 py_0
joblib 0.16.0 py_0
jpeg 9b he5867d9_2
json5 0.9.5 py_0
jsonschema 3.2.0 py36_0
jupyter 1.0.0 py36_7
jupyter_client 6.1.6 py_0
jupyter_console 6.1.0 py_0
jupyter_core 4.6.3 py36_0
jupyterlab 2.1.5 py_0
jupyterlab_server 1.2.0 py_0
keyring 21.2.1 py36_0
kiwisolver 1.2.0 py36h04f5b5a_0
krb5 1.18.2 h75d18d8_0
lazy-object-proxy 1.4.3 py36h1de35cc_0
lcms2 2.11 h92f6f08_0
libarchive 3.4.2 haa3ed63_0
libcurl 7.71.1 h8a08a2b_1
libcxx 10.0.0 1
libedit 3.1.20191231 h1de35cc_1
libffi 3.3 hb1e8313_2
libgfortran 3.0.1 h93005f0_2
libiconv 1.16 h1de35cc_0
liblief 0.10.1 h0a44026_0
libllvm9 9.0.1 h21ff451_1
libpng 1.6.37 ha441bb4_0
libsodium 1.0.18 h1de35cc_0
libspatialindex 1.9.3 h0a44026_0
libssh2 1.9.0 ha12b0ac_1
libtiff 4.1.0 hcb84e12_1
libxml2 2.9.10 h3b9e6c8_1
libxslt 1.1.34 h83b36ba_0
llvm-openmp 10.0.0 h28b9765_0
llvmlite 0.33.0 py36ha11be7d_1
locket 0.2.0 py36hca03003_1
lxml 4.5.2 py36h63b7cb6_0
lz4-c 1.9.2 h0a44026_0
lzo 2.10 h1de35cc_2
markupsafe 1.1.1 py36h1de35cc_0
matplotlib 3.2.2 0
matplotlib-base 3.2.2 py36h5670ca0_0
mccabe 0.6.1 py36_1
mistune 0.8.4 py36h1de35cc_0
mkl 2019.4 233
mkl-service 2.3.0 py36hfbe908c_0
mkl_fft 1.0.14 py36h27c97d8_0
mkl_random 1.0.4 py36h27c97d8_0
mock 4.0.2 py_0
more-itertools 8.4.0 py_0
mpc 1.1.0 h6ef4df4_1
mpfr 4.0.2 h9066e36_1
mpmath 1.1.0 py36_0
msgpack-python 1.0.0 py36h04f5b5a_1
multipledispatch 0.6.0 py36_0
navigator-updater 0.2.1 py36_0
nbconvert 5.6.1 py36_0
nbformat 5.0.7 py_0
ncurses 6.2 h0a44026_1
networkx 2.4 py_1
nltk 3.5 py_0
nose 1.3.7 py36_2
notebook 6.0.3 py36_0
numba 0.50.1 py36h959d312_1
numexpr 2.7.1 py36hce01a72_0
numpy 1.17.0 py36hacdab7b_0
numpy-base 1.17.0 py36h6575580_0
numpydoc 1.1.0 py_0
olefile 0.46 py36_0
openeye-toolkits 2020.1.0 py36_0 openeye
openpyxl 3.0.4 py_0
openssl 1.1.1g h1de35cc_0
packaging 20.4 py_0
pandas 1.0.5 py36h959d312_0
pandoc 2.10 0
pandocfilters 1.4.2 py36_1
parso 0.7.0 py_0
partd 1.1.0 py_0
path 13.1.0 py36_0
path.py 12.4.0 0
pathlib2 2.3.5 py36_0
pathtools 0.1.2 py_1
patsy 0.5.1 py36_0
pcre 8.44 hb1e8313_0
pep8 1.7.1 py36_0
pexpect 4.8.0 py36_0
pickleshare 0.7.5 py36_0
pillow 7.2.0 py36ha54b6ba_0
pip 20.1.1 py36_1
pixman 0.40.0 haf1e3a3_0
pkginfo 1.5.0.1 py36_0
pluggy 0.13.1 py36_0
ply 3.11 py36_0
prometheus_client 0.8.0 py_0
prompt-toolkit 3.0.5 py_0
prompt_toolkit 3.0.5 0
psutil 5.7.0 py36h1de35cc_0
ptyprocess 0.6.0 py36_0
py 1.9.0 py_0
py-lief 0.10.1 py36haf313ee_0
pycodestyle 2.6.0 py_0
pycosat 0.6.3 py36h1de35cc_0
pycparser 2.20 py_2
pycrypto 2.6.1 py36haf1e3a3_10
pycurl 7.43.0.5 py36ha12b0ac_0
pydocstyle 5.0.2 py_0
pyflakes 2.2.0 py_0
pygments 2.6.1 py_0
pylint 2.5.3 py36_0
pyodbc 4.0.30 py36h0a44026_0
pyopenssl 19.1.0 py_1
pyparsing 2.4.7 py_0
pyqt 5.9.2 py36h655552a_2
pyrsistent 0.16.0 py36h1de35cc_0
pysocks 1.7.1 py36_0
pytables 3.6.1 py36h5bccee9_0
pytest 5.4.3 py36_0
python 3.6.10 hf48f09d_2
python-dateutil 2.8.1 py_0
python-jsonrpc-server 0.3.4 py_1
python-language-server 0.34.1 py36_0
python-libarchive-c 2.9 py_0
python.app 2 py36_10
pytz 2020.1 py_0
pywavelets 1.1.1 py36h1de35cc_0
pyyaml 5.3.1 py36haf1e3a3_1
pyzmq 19.0.1 py36hb1e8313_1
qdarkstyle 2.8.1 py_0
qt 5.9.7 h468cd18_1
qtawesome 0.7.2 py_0
qtconsole 4.7.5 py_0
qtpy 1.9.0 py_0
rdkit 2017.09.3.0 py36_1 rdkit
readline 8.0 h1de35cc_0
regex 2020.6.8 py36haf1e3a3_0
requests 2.24.0 py_0
ripgrep 11.0.2 he32d670_0
rope 0.17.0 py_0
rtree 0.9.4 py36_1
ruamel_yaml 0.15.87 py36haf1e3a3_1
scikit-image 0.16.2 py36h6c726b0_0
scikit-learn 0.23.1 py36h603561c_0
scipy 1.5.0 py36h912ce22_0
seaborn 0.10.1 py_0
send2trash 1.5.0 py36_0
setuptools 49.2.0 py36_0
simplegeneric 0.8.1 py36_2
singledispatch 3.4.0.3 py36hf20db9d_0
sip 4.19.8 py36h0a44026_0
six 1.15.0 py_0
snappy 1.1.8 hb1e8313_0
snowballstemmer 2.0.0 py_0
sortedcollections 1.2.1 py_0
sortedcontainers 2.2.2 py_0
soupsieve 2.0.1 py_0
sphinx 3.1.2 py_0
sphinxcontrib 1.0 py36_1
sphinxcontrib-applehelp 1.0.2 py_0
sphinxcontrib-devhelp 1.0.2 py_0
sphinxcontrib-htmlhelp 1.0.3 py_0
sphinxcontrib-jsmath 1.0.1 py_0
sphinxcontrib-qthelp 1.0.3 py_0
sphinxcontrib-serializinghtml 1.1.4 py_0
sphinxcontrib-websupport 1.2.3 py_0
spyder 4.1.4 py36_0
spyder-kernels 1.9.2 py36_0
sqlalchemy 1.3.18 py36haf1e3a3_0
sqlite 3.32.3 hffcf06c_0
statsmodels 0.11.1 py36haf1e3a3_0
sympy 1.6.1 py36_0
tbb 2020.0 h04f5b5a_0
tblib 1.6.0 py_0
terminado 0.8.3 py36_0
testpath 0.4.4 py_0
threadpoolctl 2.1.0 pyh5ca1d4c_0
tk 8.6.10 hb0a8c7a_0
toml 0.10.1 py_0
toolz 0.10.0 py_0
tornado 6.0.4 py36h1de35cc_1
tqdm 4.47.0 py_0
traitlets 4.3.3 py36_0
typed-ast 1.4.1 py36h1de35cc_0
typing_extensions 3.7.4.2 py_0
ujson 1.35 py36h1de35cc_0
unicodecsv 0.14.1 py36he531d66_0
unixodbc 2.3.7 h1de35cc_0
urllib3 1.25.9 py_0
watchdog 0.10.3 py36haf1e3a3_0
wcwidth 0.2.5 py_0
webencodings 0.5.1 py36_1
werkzeug 1.0.1 py_0
wheel 0.34.2 py36_0
widgetsnbextension 3.5.1 py36_0
wrapt 1.11.2 py36h1de35cc_0
wurlitzer 2.0.1 py36_0
xlrd 1.2.0 py36_0
xlsxwriter 1.2.9 py_0
xlwings 0.19.5 py36_0
xlwt 1.2.0 py36h5ad1178_0
xmltodict 0.12.0 py_0
xz 5.2.5 h1de35cc_0
yaml 0.2.5 haf1e3a3_0
yapf 0.30.0 py_0
zeromq 4.3.2 hb1e8313_2
zict 2.0.0 py_0
zipp 3.1.0 py_0
zlib 1.2.11 h1de35cc_3
zope 1.0 py36_1
zope.event 4.4 py36_0
zope.interface 4.7.1 py36h1de35cc_0
zstd 1.4.5 h41d2c2f_0
Here is the output for conda info:
active environment : base
active env location : /Users/emmawu/opt/anaconda3
shell level : 1
user config file : /Users/emmawu/.condarc
populated config files : /Users/emmawu/.condarc
conda version : 4.7.5
conda-build version : 3.20.2
python version : 3.6.10.final.0
virtual packages :
base environment : /Users/emmawu/opt/anaconda3 (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /Users/emmawu/opt/anaconda3/pkgs
/Users/emmawu/.conda/pkgs
envs directories : /Users/emmawu/opt/anaconda3/envs
/Users/emmawu/.conda/envs
platform : osx-64
user-agent : conda/4.7.5 requests/2.24.0 CPython/3.6.10 Darwin/19.2.0 OSX/10.15.2
UID:GID : 501:20
netrc file : None
offline mode : False
Thank you so much in advance for helping!
Thanks. I'm not able to reproduce the segfault on my machine, but there are some general debugging steps we can follow:
- Verify that you have an active openeye license (or contact them to get an academic license) [1]
- Try creating a fresh environment, pulling dependencies from the
conda-forgechannel, and ensuring that it finds the 2019 OpenEye package (since the 2020 one has breaking API changes):
conda create -n fragmenter -c conda-forge -c omnia -c openeye fragmenter "openeye-toolkits<2020"
conda activate fragmenter
python fragment_molecules.py
[1] OpenEye offers free licenses for academics -- You can request one here. In the future, we're looking to refactor Fragmenter to use the free open-source RDKit and AmberTools packages (with no license file required), but until then we're reliant on OpenEye.
Thank you @j-wags for looking into it! I think the issue was that I did not have a valid license for Openeye. I am contacting them about it. Thanks! I'll let you know if I am still having issues after!
I was able to get fragmenter running without the segmentation fault after getting a valid OpenEye license! Thank you!