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shiralkarprashant / knowledgestream

Code to reproduce results in "Finding Streams in Knowledge Graphs to Support Fact Checking"
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Error to repeat the example #6

Open sirius-aerostar opened 5 years ago

sirius-aerostar commented 5 years ago

[10:58:10] Computing KS for 104 triples..

  1. Working on (392035, 599, 2115741) .. Segmentation fault (core dumped)

Not sure the problem.

shiralkarprashant commented 5 years ago

Could you please share the configuration of your machine and the python version? Does it satisfy the system requirements: https://github.com/shiralkarprashant/knowledgestream#system-requirements?

sirius-aerostar commented 5 years ago

Yes. 8GB Ram. Ubuntu 18.10, Python 2.7. No problem to compile but cannot run.
Not sure the reason.

sirius-aerostar commented 5 years ago

I install everything again in virtual machine. But didn't work out. To be specific, here is my environment.

Name Version Build Channel

_ipyw_jlab_nb_ext_conf 0.1.0 py27_0
_libgcc_mutex 0.1 main
alabaster 0.7.12 py27_0
anaconda 2019.07 py27_0
anaconda-client 1.7.2 py27_0
anaconda-navigator 1.9.7 py27_0
anaconda-project 0.8.3 py_0
asn1crypto 0.24.0 py27_0
astroid 1.6.5 py27_0
astropy 2.0.9 py27hdd07704_0
atomicwrites 1.3.0 py27_1
attrs 19.1.0 py27_1
babel 2.7.0 py_0
backports 1.0 py_2
backports.functools_lru_cache 1.5 py_2
backports.os 0.1.1 py27_0
backports.shutil_get_terminal_size 1.0.0 py27_2
backports.tempfile 1.0 py_1
backports.weakref 1.0.post1 py_1
backports_abc 0.5 py27_0
beautifulsoup4 4.7.1 py27_1
bitarray 0.9.3 py27h7b6447c_0
bkcharts 0.2 py27_0
blas 1.0 mkl
bleach 3.1.0 py27_0
blosc 1.16.3 hd408876_0
bokeh 1.2.0 py27_0
boto 2.49.0 py27_0
bottleneck 1.2.1 py27h035aef0_1
bzip2 1.0.8 h7b6447c_0
ca-certificates 2019.5.15 0
cairo 1.14.12 h8948797_3
cdecimal 2.3 py27h14c3975_3
certifi 2019.6.16 py27_0
cffi 1.12.3 py27h2e261b9_0
chardet 3.0.4 py27_1
click 7.0 py27_0
cloudpickle 1.2.1 py_0
clyent 1.2.2 py27_1
colorama 0.4.1 py27_0
conda 4.7.10 py27_0
conda-build 3.18.8 py27_0
conda-env 2.6.0 1
conda-package-handling 1.3.11 py27_0
conda-verify 3.4.2 py_1
configparser 3.7.4 py27_0
contextlib2 0.5.5 py27_0
cryptography 2.7 py27h1ba5d50_0
curl 7.65.2 hbc83047_0
cycler 0.10.0 py27_0
cython 0.29.12 py27he6710b0_0
cytoolz 0.10.0 py27h7b6447c_0
dask 1.2.2 py_0
dask-core 1.2.2 py_0
dbus 1.13.6 h746ee38_0
decorator 4.4.0 py27_1
defusedxml 0.6.0 py_0
distributed 1.28.1 py27_0
docutils 0.14 py27_0
entrypoints 0.3 py27_0
enum34 1.1.6 py27_1
et_xmlfile 1.0.1 py27_0
expat 2.2.6 he6710b0_0
fastcache 1.1.0 py27h7b6447c_0
filelock 3.0.12 py_0
flask 1.1.1 py_0
fontconfig 2.13.0 h9420a91_0
freetype 2.9.1 h8a8886c_1
fribidi 1.0.5 h7b6447c_0
funcsigs 1.0.2 py27_0
functools32 3.2.3.2 py27_1
future 0.17.1 py27_0
futures 3.3.0 py27_0
get_terminal_size 1.0.0 haa9412d_0
gevent 1.4.0 py27h7b6447c_0
glib 2.56.2 hd408876_0
glob2 0.7 py_0
gmp 6.1.2 h6c8ec71_1
gmpy2 2.0.8 py27h10f8cd9_2
graphite2 1.3.13 h23475e2_0
greenlet 0.4.15 py27h7b6447c_0
grin 1.2.1 py27_4
gst-plugins-base 1.14.0 hbbd80ab_1
gstreamer 1.14.0 hb453b48_1
h5py 2.9.0 py27h7918eee_0
harfbuzz 1.8.8 hffaf4a1_0
hdf5 1.10.4 hb1b8bf9_0
heapdict 1.0.0 py27_2
html5lib 1.0.1 py27_0
icu 58.2 h9c2bf20_1
idna 2.8 py27_0
imageio 2.5.0 py27_0
imagesize 1.1.0 py27_0
importlib_metadata 0.17 py27_1
intel-openmp 2019.4 243
ipaddress 1.0.22 py27_0
ipykernel 4.10.0 py27_0
ipython 5.8.0 py27_0
ipython_genutils 0.2.0 py27_0
ipywidgets 7.5.0 py_0
isort 4.3.21 py27_0
itsdangerous 1.1.0 py27_0
jbig 2.1 hdba287a_0
jdcal 1.4.1 py_0
jedi 0.13.3 py27_0
jinja2 2.10.1 py27_0
jpeg 9b h024ee3a_2
jsonschema 3.0.1 py27_0
jupyter 1.0.0 py27_7
jupyter_client 5.3.1 py_0
jupyter_console 5.2.0 py27_1
jupyter_core 4.5.0 py_0
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jupyterlab_launcher 0.11.2 py27h28b3542_0
kiwisolver 1.1.0 py27he6710b0_0
krb5 1.16.1 h173b8e3_7
lazy-object-proxy 1.4.1 py27h7b6447c_0
libarchive 3.3.3 h5d8350f_5
libcurl 7.65.2 h20c2e04_0
libedit 3.1.20181209 hc058e9b_0
libffi 3.2.1 hd88cf55_4
libgcc-ng 9.1.0 hdf63c60_0
libgfortran-ng 7.3.0 hdf63c60_0
liblief 0.9.0 h7725739_2
libpng 1.6.37 hbc83047_0
libsodium 1.0.16 h1bed415_0
libssh2 1.8.2 h1ba5d50_0
libstdcxx-ng 9.1.0 hdf63c60_0
libtiff 4.0.10 h2733197_2
libtool 2.4.6 h7b6447c_5
libuuid 1.0.3 h1bed415_2
libxcb 1.13 h1bed415_1
libxml2 2.9.9 hea5a465_1
libxslt 1.1.33 h7d1a2b0_0
linecache2 1.0.0 py27_0
llvmlite 0.29.0 py27hd408876_0
locket 0.2.0 py27_1
lxml 4.3.4 py27hefd8a0e_0
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matplotlib 2.2.3 py27hb69df0a_0
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mistune 0.8.4 py27h7b6447c_0
mkl 2019.4 243
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networkx 2.2 py27_1
nltk 3.4.4 py27_0
nose 1.3.7 py27_2
notebook 5.7.8 py27_0
numba 0.44.1 py27h962f231_0
numexpr 2.6.9 py27h9e4a6bb_0
numpy 1.16.4 py27h7e9f1db_0
numpy-base 1.16.4 py27hde5b4d6_0
numpydoc 0.9.1 py_0
olefile 0.46 py27_0
openpyxl 2.6.2 py_0
openssl 1.1.1c h7b6447c_1
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pandas 0.24.2 py27he6710b0_0
pandoc 2.2.3.2 0
pandocfilters 1.4.2 py27_1
pango 1.42.4 h049681c_0
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partd 1.0.0 py_0
patchelf 0.9 he6710b0_3
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pathlib2 2.3.4 py27_0
patsy 0.5.1 py27_0
pcre 8.43 he6710b0_0
pep8 1.7.1 py27_0
pexpect 4.7.0 py27_0
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pip 19.1.1 py27_0
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ply 3.11 py27_0
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py 1.8.0 py27_0
py-lief 0.9.0 py27h7725739_2
pycairo 1.18.1 py27h2a1e443_0
pycodestyle 2.5.0 py27_0
pycosat 0.6.3 py27h14c3975_0
pycparser 2.19 py27_0
pycrypto 2.6.1 py27h14c3975_9
pycurl 7.43.0.3 py27h1ba5d50_0
pyflakes 2.1.1 py27_0
pygments 2.4.2 py_0
pylint 1.9.2 py27_0
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pyopenssl 19.0.0 py27_0
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pytables 3.5.2 py27h71ec239_1
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python 2.7.16 h9bab390_0
python-dateutil 2.8.0 py27_0
python-libarchive-c 2.8 py27_11
pytz 2019.1 py_0
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qt 5.9.7 h5867ecd_1
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scipy 1.2.1 py27h7c811a0_0
seaborn 0.9.0 py27_0
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sip 4.19.8 py27hf484d3e_0
six 1.12.0 py27_0
snappy 1.1.7 hbae5bb6_3
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sqlalchemy 1.3.5 py27h7b6447c_0
sqlite 3.29.0 h7b6447c_0
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statsmodels 0.10.0 py27hdd07704_0
subprocess32 3.5.4 py27h7b6447c_0
sympy 1.4 py27_0
tblib 1.4.0 py_0
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testpath 0.4.2 py27_0
tk 8.6.8 hbc83047_0
toolz 0.10.0 py_0
tornado 5.1.1 py27h7b6447c_0
tqdm 4.32.1 py_0
traceback2 1.4.0 py27_0
traitlets 4.3.2 py27_0
typing 3.7.4 py27_0
ujson 1.35 pypi_0 pypi unicodecsv 0.14.1 py27_0
unittest2 1.1.0 py27_0
unixodbc 2.3.7 h14c3975_0
urllib3 1.24.2 py27_0
wcwidth 0.1.7 py27_0
webencodings 0.5.1 py27_1
werkzeug 0.15.4 py_0
wheel 0.33.4 py27_0
widgetsnbextension 3.5.0 py27_0
wrapt 1.11.2 py27h7b6447c_0
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xlrd 1.2.0 py27_0
xlsxwriter 1.1.8 py_0
xlwt 1.3.0 py27_0
xz 5.2.4 h14c3975_4
yaml 0.1.7 had09818_2
zeromq 4.3.1 he6710b0_3
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zlib 1.2.11 h7b6447c_3
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shiralkarprashant commented 5 years ago

Hi, sorry for my delayed response. Were you able to figure out a solution?

If not, could you please try to isolate the line causing the exception? I don't see any apparent problem with your installed libraries, and unfortunately, I don't have a Ubuntu machine to try to reproduce your error. Please feel free to share any debugging output so that I can help you identify the root cause and eventually run it successfully.

If it helps, I have created a video today (Sep 03, 2019) demonstrating the use of the code on a Linux machine, right from cloning the code repository, downloading the data to launching the Knowledge Stream algorithm on the sample file containing 104 triples. The video however shows the computation for only the first 20 triples for demonstration purposes. The Cython version on this machine is 0.28.5.

Video: https://www.dropbox.com/s/xlhyna1oiqtn86j/knowledge-stream-linux-demo-09032019.mov?dl=0

lihuiliullh commented 5 years ago

Hi @shiralkarprashant

I also face the same problem. I try to add some try catch to the code. But it seems like doesn't work. I am not familiar with kstream, can you tell us how to modify the code?

shiralkarprashant commented 5 years ago

Hi, thanks for bringing this to our notice again. We are looking into it and will update you.

zaimahid commented 5 years ago

hi @shiralkarprashant

I encountered the same error "Segmentation fault (core dumped) ", but not sure the cause of this problem. FYI, my Cython version is 0.29.13. Could it be because of the installed Cython? Please advise on how to solve this problem. Thank you

zaimahid commented 4 years ago

HI @shiralkarprashant

Just to update that i managed to run the code. I decided to uninstall Cython version 0.29.13 and installed the 0.28.5 version... the code worked :)

zai@zai-OptiPlex-7010:~/Projects/knowledgestream$ kstream -m stream -d datasets/sample.csv -o output/ [10:37:01] Launching stream.. [10:37:01] Dataset: sample.csv [10:37:01] Output dir: /home/zai/Projects/knowledgestream/output [10:37:01] Read data: (104, 7) sample.csv [10:37:01] Note: Found non-NA records: (104, 7) Reconstructing graph from /home/zai/Projects/knowledgestream/data/kg/_undir => Loaded: undir_data.npy => Loaded: undir_indptr.npy => Loaded: undir_indices.npy => Loaded: undir_indeg_vec.npy => Graph loaded: 0.30 secs.

[10:37:02] Computing KS for 104 triples..

  1. Working on (392035, 599, 2115741) .. mincostflow: 0.08771, #paths: 5, time: 12.88s.
  2. Working on (392035, 599, 4119746) .. mincostflow: 0.02783, #paths: 5, time: 8.92s.
  3. Working on (392035, 599, 917821) .. mincostflow: 0.02691, #paths: 5, time: 9.37s.
  4. Working on (392035, 599, 3218267) .. mincostflow: 0.02697, #paths: 5, time: 10.33s.
  5. Working on (482030, 599, 2364618) .. mincostflow: 0.17561, #paths: 5, time: 3.78s.
  6. Working on (482030, 599, 1487110) .. mincostflow: 0.03159, #paths: 5, time: 4.67s. ....
  7. Working on (3391697, 599, 2115741) .. mincostflow: 0.02909, #paths: 5, time: 7.68s.
  8. Working on (3391697, 599, 685564) .. mincostflow: 0.03057, #paths: 5, time: 6.28s. [10:50:04] * Saved results: /home/zai/Projects/knowledgestream/output/out_kstream_sample_2020-01-02.csv [10:50:04] Mincostflow computation complete. Time taken: 782.68 secs.

List of Installed libraries: asn1crypto==0.24.0 astroid==1.6.6 backports.functools-lru-cache==1.6.1 configparser==4.0.2 cryptography==2.1.4 Cython==0.28.5 enum34==1.1.6 futures==3.3.0 idna==2.6 ipaddress==1.0.17 isort==4.3.21 keyring==10.6.0 keyrings.alt==3.0 knowledgestream==0.1.0 lazy-object-proxy==1.4.3 mccabe==0.6.1 numpy==1.16.6 pandas==0.24.2 pycrypto==2.6.1 pygobject==3.26.1 pylint==1.9.5 python-dateutil==2.8.1 pytz==2019.3 pyxdg==0.25 scikit-learn==0.20.4 scipy==1.2.2 SecretStorage==2.3.1 singledispatch==3.4.0.3 six==1.13.0 sklearn==0.0 ujson==1.35 wrapt==1.11.2

Best regards,

glciampaglia commented 4 years ago

Hi, we can confirm that downgrading to Cython 0.28.5 solves the issue. Perhaps we could pass install_requires=["Cython <= 0.28.5"] to setuptools script?

mayanksingh2298 commented 4 years ago

Perhaps you may want to add this constraint in the readme.