Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

xgboost==1.3.0 fails at import: Segmentation Fault #6480

Closed
hamzamohdzubair opened this issue Dec 9, 2020 · 13 comments
Closed

xgboost==1.3.0 fails at import: Segmentation Fault #6480

hamzamohdzubair opened this issue Dec 9, 2020 · 13 comments

Comments

@hamzamohdzubair
Copy link

hamzamohdzubair commented Dec 9, 2020 •
edited

I just downloaded the latest xgboost==1.3.0

import xgboost throws Segmentation Fault

I tried in

  1. Python 3.8.5
  2. Python 3.6.5

image

I had to downgrade to xgboost==1.2.1 for it to work
@hcho3
Copy link
Collaborator

hcho3 commented Dec 9, 2020

Thanks for reporting the issue. Can you try it within a GDB session and obtain a stack trace?

$ gdb python
(gdb) run -c 'import xgboost'

@hcho3
Copy link
Collaborator

hcho3 commented Dec 9, 2020

Also please share the OS. Is it RHEL or CentOS? XGBoost has been compiled using CentOS 6 Docker image.

@hcho3
Copy link
Collaborator

hcho3 commented Dec 9, 2020 •
edited

@hamzamohdzubair For now, you can install XGBoost from the source package:

python -m pip install --no-binary xgboost xgboost==1.3.0

@hamzamohdzubair
Copy link
Author

Thanks for the quick response.

OS: CentOS Linux 7 (Core)

Output from gdb:

Starting program: /home/hamza/sarajevo/solusgcore/.venv/bin/python -c 'import xgboost'
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/usr/lib64/libthread_db.so.1".
Missing separate debuginfo for /home/hamza/sarajevo/solusgcore/.venv/lib/python3.8/site-packages/numpy/core/../../numpy.libs/libgfortran-2e0d59d6.so.5.0.0
Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/5e/f8275331f3c7aea4d0b59f2fa7ae783457a91a.debug
Missing separate debuginfo for /home/hamza/sarajevo/solusgcore/.venv/lib/python3.8/site-packages/numpy/core/../../numpy.libs/libquadmath-2d0c479f.so.0.0.0
Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/e9/e2b7af3158e70f8af44f54f17ca0d14d95ed2d.debug
Missing separate debuginfo for /home/hamza/sarajevo/solusgcore/.venv/lib/python3.8/site-packages/numpy/core/../../numpy.libs/libz-eb09ad1d.so.1.2.3
Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/5f/a8e5038ec04a774af72a9bb62dc86e1049c4d6.debug
[New Thread 0x7fffece1e700 (LWP 180610)]
[New Thread 0x7fffec61d700 (LWP 180611)]
[New Thread 0x7fffe9e1c700 (LWP 180612)]
[New Thread 0x7fffe761b700 (LWP 180613)]
[New Thread 0x7fffe4e1a700 (LWP 180614)]
[New Thread 0x7fffe2619700 (LWP 180615)]
[New Thread 0x7fffdfe18700 (LWP 180616)]
[New Thread 0x7fffdd617700 (LWP 180617)]
[New Thread 0x7fffdae16700 (LWP 180618)]
[New Thread 0x7fffd8615700 (LWP 180619)]
[New Thread 0x7fffd5e14700 (LWP 180620)]
[New Thread 0x7fffd3613700 (LWP 180621)]
[New Thread 0x7fffd0e12700 (LWP 180622)]
[New Thread 0x7fffce611700 (LWP 180623)]
[New Thread 0x7fffcbe10700 (LWP 180624)]
[New Thread 0x7fffc960f700 (LWP 180625)]
[New Thread 0x7fffc6e0e700 (LWP 180626)]
[New Thread 0x7fffc460d700 (LWP 180627)]
[New Thread 0x7fffc1e0c700 (LWP 180628)]
[New Thread 0x7fffbf60b700 (LWP 180629)]
[New Thread 0x7fffbce0a700 (LWP 180630)]
[New Thread 0x7fffba609700 (LWP 180631)]
[New Thread 0x7fffb7e08700 (LWP 180632)]
[New Thread 0x7fffb5607700 (LWP 180633)]
[New Thread 0x7fffb2e06700 (LWP 180634)]
[New Thread 0x7fffb0605700 (LWP 180635)]
[New Thread 0x7fffade04700 (LWP 180636)]
[New Thread 0x7fffab603700 (LWP 180637)]
[New Thread 0x7fffa8e02700 (LWP 180638)]
[New Thread 0x7fffa6601700 (LWP 180639)]
[New Thread 0x7fffa3e00700 (LWP 180640)]
[New Thread 0x7fffa15ff700 (LWP 180641)]
[New Thread 0x7fff9edfe700 (LWP 180642)]
[New Thread 0x7fff9c5fd700 (LWP 180643)]
[New Thread 0x7fff99dfc700 (LWP 180644)]
[New Thread 0x7fff975fb700 (LWP 180645)]
[New Thread 0x7fff94dfa700 (LWP 180646)]
[New Thread 0x7fff925f9700 (LWP 180647)]
[New Thread 0x7fff8fdf8700 (LWP 180648)]
[New Thread 0x7fff8d5f7700 (LWP 180649)]
[New Thread 0x7fff8adf6700 (LWP 180650)]
[New Thread 0x7fff885f5700 (LWP 180651)]
[New Thread 0x7fff85df4700 (LWP 180652)]
[New Thread 0x7fff835f3700 (LWP 180653)]
[New Thread 0x7fff80df2700 (LWP 180654)]
[New Thread 0x7fff7e5f1700 (LWP 180655)]
[New Thread 0x7fff7bdf0700 (LWP 180657)]
[New Thread 0x7fff795ef700 (LWP 180658)]
[New Thread 0x7fff76dee700 (LWP 180659)]
[New Thread 0x7fff745ed700 (LWP 180660)]
[New Thread 0x7fff71dec700 (LWP 180661)]
[New Thread 0x7fff6f5eb700 (LWP 180662)]
[New Thread 0x7fff6cdea700 (LWP 180663)]
[New Thread 0x7fff6a5e9700 (LWP 180664)]
[New Thread 0x7fff67de8700 (LWP 180665)]
Missing separate debuginfo for /usr/local/lib/python3.8/lib-dynload/_bz2.cpython-38-x86_64-linux-gnu.so
Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/78/f760537b5c9f133db2ae0eccf66f1b30481cba.debug
Missing separate debuginfo for /home/hamza/sarajevo/solusgcore/.venv/lib/python3.8/site-packages/scikit_learn-0.24.0rc1-py3.8-linux-x86_64.egg/sklearn/__check_build/../../scikit_learn.libs/libgomp-f7e03b3e.so.1.0.0
Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/19/d77342ce207498ea675700ba73c584e30e0f27.debug
[Thread 0x7fff835f3700 (LWP 180653) exited]
[Thread 0x7fff67de8700 (LWP 180665) exited]
[Thread 0x7fffb7e08700 (LWP 180632) exited]
[Thread 0x7fff6a5e9700 (LWP 180664) exited]
[Thread 0x7fff80df2700 (LWP 180654) exited]
[Thread 0x7fff6f5eb700 (LWP 180662) exited]
[Thread 0x7fffc1e0c700 (LWP 180628) exited]
[Thread 0x7fff6cdea700 (LWP 180663) exited]
[Thread 0x7fffe2619700 (LWP 180615) exited]
[Thread 0x7fffc960f700 (LWP 180625) exited]
[Thread 0x7fff9edfe700 (LWP 180642) exited]
[Thread 0x7fff745ed700 (LWP 180660) exited]
[Thread 0x7fffece1e700 (LWP 180610) exited]
[Thread 0x7fff76dee700 (LWP 180659) exited]
[Thread 0x7fffba609700 (LWP 180631) exited]
[Thread 0x7fff71dec700 (LWP 180661) exited]
[Thread 0x7fff8d5f7700 (LWP 180649) exited]
[Thread 0x7fff795ef700 (LWP 180658) exited]
[Thread 0x7fffa6601700 (LWP 180639) exited]
[Thread 0x7fff7bdf0700 (LWP 180657) exited]
[Thread 0x7fffdae16700 (LWP 180618) exited]
[Thread 0x7fff7e5f1700 (LWP 180655) exited]
[Thread 0x7fff8adf6700 (LWP 180650) exited]
[Thread 0x7fff85df4700 (LWP 180652) exited]
[Thread 0x7fff885f5700 (LWP 180651) exited]
[Thread 0x7fffb5607700 (LWP 180633) exited]
[Thread 0x7fff8fdf8700 (LWP 180648) exited]
[Thread 0x7fffab603700 (LWP 180637) exited]
[Thread 0x7fff99dfc700 (LWP 180644) exited]
[Thread 0x7fff925f9700 (LWP 180647) exited]
[Thread 0x7fffdd617700 (LWP 180617) exited]
[Thread 0x7fff94dfa700 (LWP 180646) exited]
[Thread 0x7fffc460d700 (LWP 180627) exited]
[Thread 0x7fff975fb700 (LWP 180645) exited]
[Thread 0x7fffbf60b700 (LWP 180629) exited]
[Thread 0x7fff9c5fd700 (LWP 180643) exited]
[Thread 0x7fffa15ff700 (LWP 180641) exited]
[Thread 0x7fffa3e00700 (LWP 180640) exited]
[Thread 0x7fffe761b700 (LWP 180613) exited]
[Thread 0x7fffa8e02700 (LWP 180638) exited]
[Thread 0x7fffdfe18700 (LWP 180616) exited]
[Thread 0x7fffade04700 (LWP 180636) exited]
[Thread 0x7fffd3613700 (LWP 180621) exited]
[Thread 0x7fffb2e06700 (LWP 180634) exited]
[Thread 0x7fffbce0a700 (LWP 180630) exited]
[Thread 0x7fffb0605700 (LWP 180635) exited]
[Thread 0x7fffc6e0e700 (LWP 180626) exited]
[Thread 0x7fffe9e1c700 (LWP 180612) exited]
[Thread 0x7fffd5e14700 (LWP 180620) exited]
[Thread 0x7fffcbe10700 (LWP 180624) exited]
[Thread 0x7fffd0e12700 (LWP 180622) exited]
[Thread 0x7fffd8615700 (LWP 180619) exited]
[Thread 0x7fffce611700 (LWP 180623) exited]
[Thread 0x7fffe4e1a700 (LWP 180614) exited]
[Thread 0x7fffec61d700 (LWP 180611) exited]
[Detaching after fork from child process 180667]
Missing separate debuginfo for /home/hamza/sarajevo/solusgcore/.venv/lib/python3.8/site-packages/scipy/spatial/../../scipy.libs/libgfortran-ed201abd.so.3.0.0
[New Thread 0x7fff67de8700 (LWP 180668)]
[New Thread 0x7fff6a5e9700 (LWP 180669)]
[New Thread 0x7fff6cdea700 (LWP 180670)]
[New Thread 0x7fff6f5eb700 (LWP 180671)]
[New Thread 0x7fffe761b700 (LWP 180672)]
[New Thread 0x7fffe4e1a700 (LWP 180673)]
[New Thread 0x7fffe2619700 (LWP 180674)]
[New Thread 0x7fffdfe18700 (LWP 180675)]
[New Thread 0x7fffdd617700 (LWP 180676)]
[New Thread 0x7fffdae16700 (LWP 180677)]
[New Thread 0x7fffd8615700 (LWP 180678)]
[New Thread 0x7fffd5e14700 (LWP 180679)]
[New Thread 0x7fffd3613700 (LWP 180680)]
[New Thread 0x7fffd0e12700 (LWP 180681)]
[New Thread 0x7fffce611700 (LWP 180682)]
[New Thread 0x7fffcbe10700 (LWP 180683)]
[New Thread 0x7fffc960f700 (LWP 180684)]
[New Thread 0x7fffc6e0e700 (LWP 180685)]
[New Thread 0x7fffc460d700 (LWP 180686)]
[New Thread 0x7fffc1e0c700 (LWP 180688)]
[New Thread 0x7fffbf60b700 (LWP 180689)]
[New Thread 0x7fffbce0a700 (LWP 180690)]
[New Thread 0x7fffba609700 (LWP 180691)]
[New Thread 0x7fffb7e08700 (LWP 180692)]
[New Thread 0x7fffb5607700 (LWP 180693)]
[New Thread 0x7fffb2e06700 (LWP 180694)]
[New Thread 0x7fffb0605700 (LWP 180695)]
[New Thread 0x7fffade04700 (LWP 180696)]
[New Thread 0x7fffab603700 (LWP 180697)]
[New Thread 0x7fffa8e02700 (LWP 180699)]
[New Thread 0x7fffa6601700 (LWP 180700)]
[New Thread 0x7fffa3e00700 (LWP 180701)]
[New Thread 0x7fffa15ff700 (LWP 180702)]
[New Thread 0x7fff9edfe700 (LWP 180703)]
[New Thread 0x7fff9c5fd700 (LWP 180704)]
[New Thread 0x7fff99dfc700 (LWP 180705)]
[New Thread 0x7fff975fb700 (LWP 180706)]
[New Thread 0x7fff94dfa700 (LWP 180707)]
[New Thread 0x7fff925f9700 (LWP 180708)]
[New Thread 0x7fff8fdf8700 (LWP 180709)]
[New Thread 0x7fff8d5f7700 (LWP 180710)]
[New Thread 0x7fff8adf6700 (LWP 180711)]
[New Thread 0x7fff885f5700 (LWP 180712)]
[New Thread 0x7fff85df4700 (LWP 180713)]
[New Thread 0x7fff835f3700 (LWP 180714)]
[New Thread 0x7fff80df2700 (LWP 180715)]
[New Thread 0x7fff7e5f1700 (LWP 180716)]
[New Thread 0x7fff7bdf0700 (LWP 180717)]
[New Thread 0x7fff795ef700 (LWP 180718)]
[New Thread 0x7fff76dee700 (LWP 180719)]
[New Thread 0x7fff745ed700 (LWP 180720)]
[New Thread 0x7fff71dec700 (LWP 180721)]
[New Thread 0x7ffeea8d3700 (LWP 180722)]
[New Thread 0x7ffee80d2700 (LWP 180723)]
[New Thread 0x7ffee58d1700 (LWP 180725)]
[Thread 0x7fffe4e1a700 (LWP 180673) exited]
[Thread 0x7ffee58d1700 (LWP 180725) exited]
[Thread 0x7fff8d5f7700 (LWP 180710) exited]
[Thread 0x7fffb7e08700 (LWP 180692) exited]
[Thread 0x7fffe761b700 (LWP 180672) exited]
[Thread 0x7ffee80d2700 (LWP 180723) exited]
[Thread 0x7fff6a5e9700 (LWP 180669) exited]
[Thread 0x7ffeea8d3700 (LWP 180722) exited]
[Thread 0x7fffa6601700 (LWP 180700) exited]
[Thread 0x7fff71dec700 (LWP 180721) exited]
[Thread 0x7fff745ed700 (LWP 180720) exited]
[Thread 0x7fffc1e0c700 (LWP 180688) exited]
[Thread 0x7fff8fdf8700 (LWP 180709) exited]
[Thread 0x7fff76dee700 (LWP 180719) exited]
[Thread 0x7fff8adf6700 (LWP 180711) exited]
[Thread 0x7fff795ef700 (LWP 180718) exited]
[Thread 0x7fffdfe18700 (LWP 180675) exited]
[Thread 0x7fff7bdf0700 (LWP 180717) exited]
[Thread 0x7fffc960f700 (LWP 180684) exited]
[Thread 0x7fff7e5f1700 (LWP 180716) exited]
[Thread 0x7fffb2e06700 (LWP 180694) exited]
[Thread 0x7fff80df2700 (LWP 180715) exited]
[Thread 0x7fffc460d700 (LWP 180686) exited]
[Thread 0x7fff835f3700 (LWP 180714) exited]
[Thread 0x7fffab603700 (LWP 180697) exited]
[Thread 0x7fff85df4700 (LWP 180713) exited]
[Thread 0x7fff6cdea700 (LWP 180670) exited]
[Thread 0x7fff885f5700 (LWP 180712) exited]
[Thread 0x7fff925f9700 (LWP 180708) exited]
[Thread 0x7fff67de8700 (LWP 180668) exited]
[Thread 0x7fff94dfa700 (LWP 180707) exited]
[Thread 0x7fff99dfc700 (LWP 180705) exited]
[Thread 0x7fff6f5eb700 (LWP 180671) exited]
[Thread 0x7fff975fb700 (LWP 180706) exited]
[Thread 0x7fffce611700 (LWP 180682) exited]
[Thread 0x7fff9c5fd700 (LWP 180704) exited]
[Thread 0x7fff9edfe700 (LWP 180703) exited]
[Thread 0x7fffe2619700 (LWP 180674) exited]
[Thread 0x7fffa15ff700 (LWP 180702) exited]
[Thread 0x7fffdd617700 (LWP 180676) exited]
[Thread 0x7fffbce0a700 (LWP 180690) exited]
[Thread 0x7fffa3e00700 (LWP 180701) exited]
[Thread 0x7fffade04700 (LWP 180696) exited]
[Thread 0x7fffa8e02700 (LWP 180699) exited]
[Thread 0x7fffba609700 (LWP 180691) exited]
[Thread 0x7fffb0605700 (LWP 180695) exited]
[Thread 0x7fffd8615700 (LWP 180678) exited]
[Thread 0x7fffb5607700 (LWP 180693) exited]
[Thread 0x7fffc6e0e700 (LWP 180685) exited]
[Thread 0x7fffcbe10700 (LWP 180683) exited]
[Thread 0x7fffbf60b700 (LWP 180689) exited]
[Thread 0x7fffd5e14700 (LWP 180679) exited]
[Thread 0x7fffd0e12700 (LWP 180681) exited]
[Thread 0x7fffd3613700 (LWP 180680) exited]
[Thread 0x7fffdae16700 (LWP 180677) exited]
[Inferior 1 (process 180606) exited normally]
Missing separate debuginfos, use: debuginfo-install bzip2-libs-1.0.6-13.el7.x86_64 glibc-2.17-307.el7.1.x86_64 keyutils-libs-1.5.8-3.el7.x86_64 krb5-libs-1.15.1-46.el7.x86_64 libcom_err-1.42.9-17.el7.x86_64 libffi-3.0.13-19.el7.x86_64 libgcc-4.8.5-39.el7.x86_64 libgomp-4.8.5-39.el7.x86_64 libselinux-2.5-15.el7.x86_64 libstdc++-4.8.5-39.el7.x86_64 libuuid-2.23.2-63.el7.x86_64 nss-softokn-freebl-3.44.0-8.el7_7.x86_64 openssl-libs-1.0.2k-19.el7.x86_64 pcre-8.32-17.el7.x86_64 xz-libs-5.2.2-1.el7.x86_64 zlib-1.2.7-18.el7.x86_64

@hcho3
Copy link
Collaborator

hcho3 commented Dec 9, 2020 •
edited

@hamzamohdzubair Thanks, I'll try to create a CentOS 7 Docker container and reproduce the issue there.

As for the GDB log, the log suggests that the process exited normally without any stack trace. Did XGBoost not crash when inside the GDB session?

@hamzamohdzubair
Copy link
Author

hamzamohdzubair commented Dec 9, 2020 •
edited

@hcho3 Sorry my bad, I was running xgboost==1.2.1

I reinstalled xgboost==1.3.0

Output of gdb:

(.venv) [hamza@lserver010-mum solusgcore]$ gdb python
GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-119.el7
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /usr/local/bin/python3.8...done.
(gdb) run -c 'import xgboost'
Starting program: /home/hamza/sarajevo/solusgcore/.venv/bin/python -c 'import xgboost'
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/usr/lib64/libthread_db.so.1".
Missing separate debuginfo for /home/hamza/sarajevo/solusgcore/.venv/lib/python3.8/site-packages/numpy/core/../../numpy.libs/libgfortran-2e0d59d6.so.5.0.0
Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/5e/f8275331f3c7aea4d0b59f2fa7ae783457a91a.debug
Missing separate debuginfo for /home/hamza/sarajevo/solusgcore/.venv/lib/python3.8/site-packages/numpy/core/../../numpy.libs/libquadmath-2d0c479f.so.0.0.0
Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/e9/e2b7af3158e70f8af44f54f17ca0d14d95ed2d.debug
Missing separate debuginfo for /home/hamza/sarajevo/solusgcore/.venv/lib/python3.8/site-packages/numpy/core/../../numpy.libs/libz-eb09ad1d.so.1.2.3
Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/5f/a8e5038ec04a774af72a9bb62dc86e1049c4d6.debug
[New Thread 0x7fffecb52700 (LWP 182196)]
[New Thread 0x7fffec351700 (LWP 182197)]
[New Thread 0x7fffe9b50700 (LWP 182198)]
[New Thread 0x7fffe734f700 (LWP 182199)]
[New Thread 0x7fffe2b4e700 (LWP 182200)]
[New Thread 0x7fffe234d700 (LWP 182201)]
[New Thread 0x7fffdfb4c700 (LWP 182202)]
[New Thread 0x7fffdd34b700 (LWP 182203)]
[New Thread 0x7fffdab4a700 (LWP 182204)]
[New Thread 0x7fffd8349700 (LWP 182205)]
[New Thread 0x7fffd5b48700 (LWP 182206)]
[New Thread 0x7fffd3347700 (LWP 182207)]
[New Thread 0x7fffd0b46700 (LWP 182208)]
[New Thread 0x7fffce345700 (LWP 182209)]
[New Thread 0x7fffcbb44700 (LWP 182210)]
[New Thread 0x7fffc9343700 (LWP 182211)]
[New Thread 0x7fffc6b42700 (LWP 182212)]
[New Thread 0x7fffc4341700 (LWP 182213)]
[New Thread 0x7fffc1b40700 (LWP 182214)]
[New Thread 0x7fffbf33f700 (LWP 182215)]
[New Thread 0x7fffbcb3e700 (LWP 182216)]
[New Thread 0x7fffba33d700 (LWP 182217)]
[New Thread 0x7fffb7b3c700 (LWP 182218)]
[New Thread 0x7fffb533b700 (LWP 182219)]
[New Thread 0x7fffb2b3a700 (LWP 182220)]
[New Thread 0x7fffb0339700 (LWP 182221)]
[New Thread 0x7fffadb38700 (LWP 182222)]
[New Thread 0x7fffab337700 (LWP 182223)]
[New Thread 0x7fffa8b36700 (LWP 182224)]
[New Thread 0x7fffa6335700 (LWP 182225)]
[New Thread 0x7fffa3b34700 (LWP 182226)]
[New Thread 0x7fffa1333700 (LWP 182227)]
[New Thread 0x7fff9eb32700 (LWP 182228)]
[New Thread 0x7fff9c331700 (LWP 182229)]
[New Thread 0x7fff99b30700 (LWP 182230)]
[New Thread 0x7fff9732f700 (LWP 182231)]
[New Thread 0x7fff94b2e700 (LWP 182232)]
[New Thread 0x7fff9232d700 (LWP 182233)]
[New Thread 0x7fff8fb2c700 (LWP 182234)]
[New Thread 0x7fff8d32b700 (LWP 182235)]
[New Thread 0x7fff8ab2a700 (LWP 182236)]
[New Thread 0x7fff88329700 (LWP 182237)]
[New Thread 0x7fff85b28700 (LWP 182238)]
[New Thread 0x7fff83327700 (LWP 182239)]
[New Thread 0x7fff80b26700 (LWP 182240)]
[New Thread 0x7fff7e325700 (LWP 182241)]
[New Thread 0x7fff7bb24700 (LWP 182242)]
[New Thread 0x7fff79323700 (LWP 182243)]
[New Thread 0x7fff76b22700 (LWP 182244)]
[New Thread 0x7fff74321700 (LWP 182245)]
[New Thread 0x7fff71b20700 (LWP 182246)]
[New Thread 0x7fff6f31f700 (LWP 182247)]
[New Thread 0x7fff6cb1e700 (LWP 182248)]
[New Thread 0x7fff6a31d700 (LWP 182249)]
[New Thread 0x7fff67b1c700 (LWP 182250)]
Missing separate debuginfo for /usr/local/lib/python3.8/lib-dynload/_bz2.cpython-38-x86_64-linux-gnu.so
Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/78/f760537b5c9f133db2ae0eccf66f1b30481cba.debug
Missing separate debuginfo for /home/hamza/sarajevo/solusgcore/.venv/lib/python3.8/site-packages/scikit_learn-0.24.0rc1-py3.8-linux-x86_64.egg/sklearn/__check_build/../../scikit_learn.libs/libgomp-f7e03b3e.so.1.0.0
Try: yum --enablerepo='*debug*' install /usr/lib/debug/.build-id/19/d77342ce207498ea675700ba73c584e30e0f27.debug
[Thread 0x7fffba33d700 (LWP 182217) exited]
[Thread 0x7fff6cb1e700 (LWP 182248) exited]
[Thread 0x7fffec351700 (LWP 182197) exited]
[Thread 0x7fff67b1c700 (LWP 182250) exited]
[Thread 0x7fff6a31d700 (LWP 182249) exited]
[Thread 0x7fff6f31f700 (LWP 182247) exited]
[Thread 0x7fff76b22700 (LWP 182244) exited]
[Thread 0x7fff71b20700 (LWP 182246) exited]
[Thread 0x7fff79323700 (LWP 182243) exited]
[Thread 0x7fffd3347700 (LWP 182207) exited]
[Thread 0x7fffdfb4c700 (LWP 182202) exited]
[Thread 0x7fff74321700 (LWP 182245) exited]
[Thread 0x7fff7bb24700 (LWP 182242) exited]
[Thread 0x7fffce345700 (LWP 182209) exited]
[Thread 0x7fff7e325700 (LWP 182241) exited]
[Thread 0x7fffbf33f700 (LWP 182215) exited]
[Thread 0x7fff80b26700 (LWP 182240) exited]
[Thread 0x7fffb7b3c700 (LWP 182218) exited]
[Thread 0x7fff94b2e700 (LWP 182232) exited]
[Thread 0x7fff83327700 (LWP 182239) exited]
[Thread 0x7fffc4341700 (LWP 182213) exited]
[Thread 0x7fff85b28700 (LWP 182238) exited]
[Thread 0x7fffd8349700 (LWP 182205) exited]
[Thread 0x7fff88329700 (LWP 182237) exited]
[Thread 0x7fff8ab2a700 (LWP 182236) exited]
[Thread 0x7fffa6335700 (LWP 182225) exited]
[Thread 0x7fffa8b36700 (LWP 182224) exited]
[Thread 0x7fff8d32b700 (LWP 182235) exited]
[Thread 0x7fffb533b700 (LWP 182219) exited]
[Thread 0x7fff8fb2c700 (LWP 182234) exited]
[Thread 0x7fffbcb3e700 (LWP 182216) exited]
[Thread 0x7fff9232d700 (LWP 182233) exited]
[Thread 0x7fff99b30700 (LWP 182230) exited]
[Thread 0x7fff9732f700 (LWP 182231) exited]
[Thread 0x7fffb0339700 (LWP 182221) exited]
[Thread 0x7fff9c331700 (LWP 182229) exited]
[Thread 0x7fffdd34b700 (LWP 182203) exited]
[Thread 0x7fff9eb32700 (LWP 182228) exited]
[Thread 0x7fffa1333700 (LWP 182227) exited]
[Thread 0x7fffb2b3a700 (LWP 182220) exited]
[Thread 0x7fffc9343700 (LWP 182211) exited]
[Thread 0x7fffa3b34700 (LWP 182226) exited]
[Thread 0x7fffdab4a700 (LWP 182204) exited]
[Thread 0x7fffab337700 (LWP 182223) exited]
[Thread 0x7fffd5b48700 (LWP 182206) exited]
[Thread 0x7fffadb38700 (LWP 182222) exited]
[Thread 0x7fffecb52700 (LWP 182196) exited]
[Thread 0x7fffc1b40700 (LWP 182214) exited]
[Thread 0x7fffe9b50700 (LWP 182198) exited]
[Thread 0x7fffc6b42700 (LWP 182212) exited]
[Thread 0x7fffd0b46700 (LWP 182208) exited]
[Thread 0x7fffcbb44700 (LWP 182210) exited]
[Thread 0x7fffe734f700 (LWP 182199) exited]
[Thread 0x7fffe234d700 (LWP 182201) exited]
[Thread 0x7fffe2b4e700 (LWP 182200) exited]
[Detaching after fork from child process 182253]
Missing separate debuginfo for /home/hamza/sarajevo/solusgcore/.venv/lib/python3.8/site-packages/scipy/spatial/../../scipy.libs/libgfortran-ed201abd.so.3.0.0
[New Thread 0x7fff67b1c700 (LWP 182254)]
[New Thread 0x7fff6a31d700 (LWP 182255)]
[New Thread 0x7fff6cb1e700 (LWP 182256)]
[New Thread 0x7fff6f31f700 (LWP 182257)]
[New Thread 0x7fffe734f700 (LWP 182258)]
[New Thread 0x7fffe2b4e700 (LWP 182259)]
[New Thread 0x7fffe234d700 (LWP 182260)]
[New Thread 0x7fffdfb4c700 (LWP 182261)]
[New Thread 0x7fffdd34b700 (LWP 182262)]
[New Thread 0x7fffdab4a700 (LWP 182263)]
[New Thread 0x7fffd8349700 (LWP 182264)]
[New Thread 0x7fffd5b48700 (LWP 182265)]
[New Thread 0x7fffd3347700 (LWP 182266)]
[New Thread 0x7fffd0b46700 (LWP 182267)]
[New Thread 0x7fffce345700 (LWP 182268)]
[New Thread 0x7fffcbb44700 (LWP 182269)]
[New Thread 0x7fffc9343700 (LWP 182270)]
[New Thread 0x7fffc6b42700 (LWP 182271)]
[New Thread 0x7fffc4341700 (LWP 182272)]
[New Thread 0x7fffc1b40700 (LWP 182273)]
[New Thread 0x7fffbf33f700 (LWP 182274)]
[New Thread 0x7fffbcb3e700 (LWP 182275)]
[New Thread 0x7fffba33d700 (LWP 182276)]
[New Thread 0x7fffb7b3c700 (LWP 182277)]
[New Thread 0x7fffb533b700 (LWP 182278)]
[New Thread 0x7fffb2b3a700 (LWP 182279)]
[New Thread 0x7fffb0339700 (LWP 182280)]
[New Thread 0x7fffadb38700 (LWP 182281)]
[New Thread 0x7fffab337700 (LWP 182282)]
[New Thread 0x7fffa8b36700 (LWP 182283)]
[New Thread 0x7fffa6335700 (LWP 182284)]
[New Thread 0x7fffa3b34700 (LWP 182285)]
[New Thread 0x7fffa1333700 (LWP 182286)]
[New Thread 0x7fff9eb32700 (LWP 182287)]
[New Thread 0x7fff9c331700 (LWP 182288)]
[New Thread 0x7fff99b30700 (LWP 182289)]
[New Thread 0x7fff9732f700 (LWP 182290)]
[New Thread 0x7fff94b2e700 (LWP 182291)]
[New Thread 0x7fff9232d700 (LWP 182292)]
[New Thread 0x7fff8fb2c700 (LWP 182293)]
[New Thread 0x7fff8d32b700 (LWP 182294)]
[New Thread 0x7fff8ab2a700 (LWP 182295)]
[New Thread 0x7fff88329700 (LWP 182296)]
[New Thread 0x7fff85b28700 (LWP 182297)]
[New Thread 0x7fff83327700 (LWP 182298)]
[New Thread 0x7fff80b26700 (LWP 182299)]
[New Thread 0x7fff7e325700 (LWP 182300)]
[New Thread 0x7fff7bb24700 (LWP 182301)]
[New Thread 0x7fff79323700 (LWP 182302)]
[New Thread 0x7fff76b22700 (LWP 182303)]
[New Thread 0x7fff74321700 (LWP 182304)]
[New Thread 0x7fff71b20700 (LWP 182305)]
[New Thread 0x7ffeea8dd700 (LWP 182306)]
[New Thread 0x7ffee80dc700 (LWP 182307)]
[New Thread 0x7ffee58db700 (LWP 182308)]

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff7dec028 in _dl_check_map_versions () from /lib64/ld-linux-x86-64.so.2
Missing separate debuginfos, use: debuginfo-install bzip2-libs-1.0.6-13.el7.x86_64 glibc-2.17-307.el7.1.x86_64 keyutils-libs-1.5.8-3.el7.x86_64 krb5-libs-1.15.1-46.el7.x86_64 libcom_err-1.42.9-17.el7.x86_64 libffi-3.0.13-19.el7.x86_64 libgcc-4.8.5-39.el7.x86_64 libselinux-2.5-15.el7.x86_64 libstdc++-4.8.5-39.el7.x86_64 libuuid-2.23.2-63.el7.x86_64 nss-softokn-freebl-3.44.0-8.el7_7.x86_64 openssl-libs-1.0.2k-19.el7.x86_64 pcre-8.32-17.el7.x86_64 xz-libs-5.2.2-1.el7.x86_64 zlib-1.2.7-18.el7.x86_64

Sorry for the extremely long outputs, i am not sure what all is irrelevant. Thanks

@hcho3
Copy link
Collaborator

hcho3 commented Dec 9, 2020

@hamzamohdzubair Please run backtrace command to obtain the stack trace of the segfault error.

@hamzamohdzubair
Copy link
Author

@hcho3

(gdb) backtrace
#0  0x00007ffff7dec028 in _dl_check_map_versions () from /lib64/ld-linux-x86-64.so.2
#1  0x00007ffff7def5d1 in dl_open_worker () from /lib64/ld-linux-x86-64.so.2
#2  0x00007ffff7dea7c4 in _dl_catch_error () from /lib64/ld-linux-x86-64.so.2
#3  0x00007ffff7deeb7b in _dl_open () from /lib64/ld-linux-x86-64.so.2
#4  0x00007ffff7784fab in dlopen_doit () from /usr/lib64/libdl.so.2
#5  0x00007ffff7dea7c4 in _dl_catch_error () from /lib64/ld-linux-x86-64.so.2
#6  0x00007ffff77855ad in _dlerror_run () from /usr/lib64/libdl.so.2
#7  0x00007ffff7785041 in dlopen@@GLIBC_2.2.5 () from /usr/lib64/libdl.so.2
#8  0x00007ffff0317300 in py_dl_open (self=<optimized out>, args=<optimized out>) at /root/Python-3.8.5/Modules/_ctypes/callproc.c:1427
#9  0x000000000043bc30 in cfunction_call_varargs (kwargs=<optimized out>, args=<optimized out>, func=0x7ffff7e43bd0) at Objects/call.c:757
#10 PyCFunction_Call (func=0x7ffff7e43bd0, args=<optimized out>, kwargs=<optimized out>) at Objects/call.c:772
#11 0x0000000000438cc6 in _PyObject_MakeTpCall (callable=callable@entry=0x7ffff7e43bd0, args=args@entry=0x7ffff052b608, nargs=<optimized out>, 
    keywords=keywords@entry=0x0) at Objects/call.c:159
#12 0x0000000000428b56 in _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=<optimized out>, callable=<optimized out>)
    at ./Include/cpython/abstract.h:125
#13 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x96cc10) at Python/ceval.c:4963
#14 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3500
#15 0x00000000004ec04d in PyEval_EvalFrameEx (throwflag=0, f=0x7ffff052b440) at Python/ceval.c:741
#16 _PyEval_EvalCodeWithName (_co=0x7ffff7e2f500, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=2, 
    kwnames=0x0, kwargs=kwargs@entry=0x7fffffffb960, kwcount=0, kwstep=kwstep@entry=1, defs=defs@entry=0x7ffff0531968, defcount=defcount@entry=5, 
    kwdefs=kwdefs@entry=0x0, closure=closure@entry=0x0, name=<optimized out>, qualname=0x7ffff0527270) at Python/ceval.c:4298
#17 0x0000000000439702 in _PyFunction_Vectorcall (func=<optimized out>, stack=<optimized out>, nargsf=<optimized out>, kwnames=<optimized out>)
    at Objects/call.c:435
#18 0x000000000043b757 in _PyObject_FastCallDict (callable=0x7ffff0529790, args=<optimized out>, nargsf=<optimized out>, kwargs=<optimized out>)
    at Objects/call.c:96
#19 0x000000000043b86b in _PyObject_Call_Prepend (callable=callable@entry=0x7ffff0529790, obj=obj@entry=0x7ffed84efd00, 
    args=args@entry=0x7fff5a33b1c0, kwargs=kwargs@entry=0x0) at Objects/call.c:887
#20 0x00000000004929e1 in slot_tp_init (self=0x7ffed84efd00, args=0x7fff5a33b1c0, kwds=0x0) at Objects/typeobject.c:6787
#21 0x000000000048c142 in type_call (type=<optimized out>, type@entry=0x9fdeb0, args=args@entry=0x7fff5a33b1c0, kwds=kwds@entry=0x0)
    at Objects/typeobject.c:994
#22 0x0000000000438cc6 in _PyObject_MakeTpCall (callable=callable@entry=0x9fdeb0, args=args@entry=0x7ffed940a9c8, nargs=<optimized out>, 
    keywords=keywords@entry=0x0) at Objects/call.c:159
#23 0x0000000000429732 in _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=<optimized out>, callable=<optimized out>)
    at ./Include/cpython/abstract.h:125
#24 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x96cc10) at Python/ceval.c:4963
#25 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3469
#26 0x0000000000421528 in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=2, globals=<optimized out>)
    at Objects/call.c:283
---Type <return> to continue, or q <return> to quit---
#27 0x00000000005d6f61 in _PyObject_Vectorcall (kwnames=0x0, nargsf=2, args=0x19262a8, callable=0x7ffff0529b80)
    at ./Include/cpython/abstract.h:127
#28 method_vectorcall (method=<optimized out>, args=0x19262b0, nargsf=<optimized out>, kwnames=0x0) at Objects/classobject.c:60
#29 0x0000000000429696 in _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=<optimized out>, callable=<optimized out>)
    at ./Include/cpython/abstract.h:127
#30 trace_call_function (kwnames=<optimized out>, nargs=<optimized out>, args=<optimized out>, func=<optimized out>, tstate=<optimized out>)
    at Python/ceval.c:4944
#31 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x96cc10) at Python/ceval.c:4960
#32 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3469
#33 0x0000000000421528 in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=0, globals=<optimized out>)
    at Objects/call.c:283
#34 0x000000000042581f in _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=<optimized out>, callable=<optimized out>)
    at ./Include/cpython/abstract.h:127
#35 trace_call_function (kwnames=<optimized out>, nargs=<optimized out>, args=<optimized out>, func=<optimized out>, tstate=<optimized out>)
    at Python/ceval.c:4944
#36 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x96cc10) at Python/ceval.c:4960
#37 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3500
#38 0x00000000004eb788 in PyEval_EvalFrameEx (throwflag=0, f=0x7ffff7e663e0) at Python/ceval.c:741
#39 _PyEval_EvalCodeWithName (qualname=0x0, name=<optimized out>, closure=0x0, kwdefs=0x0, defcount=0, defs=0x0, kwstep=2, kwcount=0, kwargs=0x0, 
    kwnames=0x0, argcount=0, args=0x0, locals=locals@entry=0x7ffff7e663e0, globals=globals@entry=0x7ffff7e83920, _co=0x7ffff7e83920, 
    _co@entry=0x96cc10) at Python/ceval.c:4298
#40 PyEval_EvalCodeEx (closure=0x0, kwdefs=0x0, defcount=0, defs=0x0, kwcount=0, kws=0x0, argcount=0, args=0x0, 
    locals=locals@entry=0x7ffff7e663e0, globals=globals@entry=0x7ffff7e83920, _co=0x7ffff7e83920, _co@entry=0x96cc10) at Python/ceval.c:4327
#41 PyEval_EvalCode (co=co@entry=0x7ffff7e83920, globals=globals@entry=0x7ffff7e6a080, locals=locals@entry=0x7ffff7e6a080) at Python/ceval.c:718
#42 0x000000000061d1ed in builtin_exec_impl (module=<optimized out>, locals=0x7ffff7e6a080, globals=0x7ffff7e6a080, source=0x7ffff7e83920)
    at Python/bltinmodule.c:1033
#43 builtin_exec (module=<optimized out>, args=0x7ffff7e09718, nargs=<optimized out>) at Python/clinic/bltinmodule.c.h:396
#44 0x0000000000472110 in cfunction_vectorcall_FASTCALL (func=func@entry=0x7ffff7f7b590, args=<optimized out>, nargsf=nargsf@entry=2, 
    kwnames=<optimized out>) at Objects/methodobject.c:422
#45 0x000000000043b8ec in PyVectorcall_Call (callable=0x7ffff7f7b590, tuple=<optimized out>, kwargs=<optimized out>) at Objects/call.c:199
#46 0x000000000042bcff in do_call_core (kwdict=0x7ffff7e6a100, callargs=0x7ffff7e09700, func=0x7ffff7f7b590, tstate=0x96cc10)
    at Python/ceval.c:4983
#47 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3559
#48 0x00000000004ec04d in PyEval_EvalFrameEx (throwflag=0, f=0x7ffff7e4cc10) at Python/ceval.c:741
#49 _PyEval_EvalCodeWithName (_co=0x7ffff7f839d0, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=3, 
    kwnames=0x0, kwargs=kwargs@entry=0x7ffff7f6b3a8, kwcount=0, kwstep=kwstep@entry=1, defs=defs@entry=0x0, defcount=defcount@entry=0, 
    kwdefs=kwdefs@entry=0x0, closure=closure@entry=0x0, name=<optimized out>, qualname=0x7ffff7f84440) at Python/ceval.c:4298
#50 0x0000000000439702 in _PyFunction_Vectorcall (func=<optimized out>, stack=<optimized out>, nargsf=<optimized out>, kwnames=<optimized out>)
---Type <return> to continue, or q <return> to quit---
    at Objects/call.c:435
#51 0x0000000000429696 in _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=<optimized out>, callable=<optimized out>)
    at ./Include/cpython/abstract.h:127
#52 trace_call_function (kwnames=<optimized out>, nargs=<optimized out>, args=<optimized out>, func=<optimized out>, tstate=<optimized out>)
    at Python/ceval.c:4944
#53 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x96cc10) at Python/ceval.c:4960
#54 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3469
#55 0x0000000000421528 in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=2, globals=<optimized out>)
    at Objects/call.c:283
#56 0x00000000004242a3 in _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=<optimized out>, callable=<optimized out>)
    at ./Include/cpython/abstract.h:127
#57 trace_call_function (kwnames=<optimized out>, nargs=<optimized out>, args=<optimized out>, func=<optimized out>, tstate=<optimized out>)
    at Python/ceval.c:4944
#58 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x96cc10) at Python/ceval.c:4960
#59 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3486
#60 0x0000000000421528 in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=1, globals=<optimized out>)
    at Objects/call.c:283
#61 0x000000000042581f in _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=<optimized out>, callable=<optimized out>)
    at ./Include/cpython/abstract.h:127
#62 trace_call_function (kwnames=<optimized out>, nargs=<optimized out>, args=<optimized out>, func=<optimized out>, tstate=<optimized out>)
    at Python/ceval.c:4944
#63 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x96cc10) at Python/ceval.c:4960
#64 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3500
#65 0x0000000000421528 in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=2, globals=<optimized out>)
    at Objects/call.c:283
#66 0x000000000042581f in _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=<optimized out>, callable=<optimized out>)
    at ./Include/cpython/abstract.h:127
#67 trace_call_function (kwnames=<optimized out>, nargs=<optimized out>, args=<optimized out>, func=<optimized out>, tstate=<optimized out>)
    at Python/ceval.c:4944
#68 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x96cc10) at Python/ceval.c:4960
#69 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3500
#70 0x0000000000421528 in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=2, globals=<optimized out>)
    at Objects/call.c:283
#71 0x0000000000438fb8 in _PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x7fffffffc9a0, callable=0x7ffff7f9a3a0)
    at ./Include/cpython/abstract.h:127
#72 _PyObject_FastCall (nargs=2, args=0x7fffffffc9a0, func=0x7ffff7f9a3a0) at ./Include/cpython/abstract.h:147
#73 object_vacall (base=base@entry=0x0, callable=0x7ffff7f9a3a0, vargs=vargs@entry=0x7fffffffca28) at Objects/call.c:1186
#74 0x000000000043b305 in _PyObject_CallMethodIdObjArgs (obj=0x0, name=name@entry=0x925160 <PyId__find_and_load.13976>) at Objects/call.c:1244
---Type <return> to continue, or q <return> to quit---
#75 0x000000000050f37d in import_find_and_load (abs_name=0x7ffff7e699b0) at Python/import.c:1698
#76 PyImport_ImportModuleLevelObject (name=name@entry=0x7ffff7e69830, globals=<optimized out>, locals=<optimized out>, 
    fromlist=fromlist@entry=0x7ffff7eb55c0, level=1) at Python/import.c:1798
#77 0x0000000000429dcf in import_name (level=0x949300 <small_ints+192>, fromlist=0x7ffff7eb55c0, name=0x7ffff7e69830, f=0x7ffff7ef9440, 
    tstate=0x96cc10) at Python/ceval.c:5139
#78 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2993
#79 0x00000000004eb788 in PyEval_EvalFrameEx (throwflag=0, f=0x7ffff7ef9440) at Python/ceval.c:741
#80 _PyEval_EvalCodeWithName (qualname=0x0, name=<optimized out>, closure=0x0, kwdefs=0x0, defcount=0, defs=0x0, kwstep=2, kwcount=0, kwargs=0x0, 
    kwnames=0x0, argcount=0, args=0x0, locals=locals@entry=0x7ffff7ef9440, globals=globals@entry=0x7ffff7e62870, _co=0x7ffff7e62870, 
    _co@entry=0x96cc10) at Python/ceval.c:4298
#81 PyEval_EvalCodeEx (closure=0x0, kwdefs=0x0, defcount=0, defs=0x0, kwcount=0, kws=0x0, argcount=0, args=0x0, 
    locals=locals@entry=0x7ffff7ef9440, globals=globals@entry=0x7ffff7e62870, _co=0x7ffff7e62870, _co@entry=0x96cc10) at Python/ceval.c:4327
#82 PyEval_EvalCode (co=co@entry=0x7ffff7e62870, globals=globals@entry=0x7ffff7f2b300, locals=locals@entry=0x7ffff7f2b300) at Python/ceval.c:718
#83 0x000000000061d1ed in builtin_exec_impl (module=<optimized out>, locals=0x7ffff7f2b300, globals=0x7ffff7f2b300, source=0x7ffff7e62870)
    at Python/bltinmodule.c:1033
#84 builtin_exec (module=<optimized out>, args=0x7ffff7e69198, nargs=<optimized out>) at Python/clinic/bltinmodule.c.h:396
#85 0x0000000000472110 in cfunction_vectorcall_FASTCALL (func=func@entry=0x7ffff7f7b590, args=<optimized out>, nargsf=nargsf@entry=2, 
    kwnames=<optimized out>) at Objects/methodobject.c:422
#86 0x000000000043b8ec in PyVectorcall_Call (callable=0x7ffff7f7b590, tuple=<optimized out>, kwargs=<optimized out>) at Objects/call.c:199
#87 0x000000000042bcff in do_call_core (kwdict=0x7ffff7e692c0, callargs=0x7ffff7e69180, func=0x7ffff7f7b590, tstate=0x96cc10)
    at Python/ceval.c:4983
#88 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3559
#89 0x00000000004ec04d in PyEval_EvalFrameEx (throwflag=0, f=0x7ffff7f1ea60) at Python/ceval.c:741
#90 _PyEval_EvalCodeWithName (_co=0x7ffff7f839d0, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=3, 
    kwnames=0x0, kwargs=kwargs@entry=0x7ffff7ed3568, kwcount=0, kwstep=kwstep@entry=1, defs=defs@entry=0x0, defcount=defcount@entry=0, 
    kwdefs=kwdefs@entry=0x0, closure=closure@entry=0x0, name=<optimized out>, qualname=0x7ffff7f84440) at Python/ceval.c:4298
#91 0x0000000000439702 in _PyFunction_Vectorcall (func=<optimized out>, stack=<optimized out>, nargsf=<optimized out>, kwnames=<optimized out>)
    at Objects/call.c:435
#92 0x0000000000429696 in _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=<optimized out>, callable=<optimized out>)
    at ./Include/cpython/abstract.h:127
#93 trace_call_function (kwnames=<optimized out>, nargs=<optimized out>, args=<optimized out>, func=<optimized out>, tstate=<optimized out>)
    at Python/ceval.c:4944
#94 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x96cc10) at Python/ceval.c:4960
#95 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3469
#96 0x0000000000421528 in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=2, globals=<optimized out>)
    at Objects/call.c:283
#97 0x00000000004242a3 in _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=<optimized out>, callable=<optimized out>)
    at ./Include/cpython/abstract.h:127
---Type <return> to continue, or q <return> to quit---
#98 trace_call_function (kwnames=<optimized out>, nargs=<optimized out>, args=<optimized out>, func=<optimized out>, tstate=<optimized out>)
    at Python/ceval.c:4944
#99 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x96cc10) at Python/ceval.c:4960
#100 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3486
#101 0x0000000000421528 in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=1, globals=<optimized out>)
    at Objects/call.c:283
#102 0x000000000042581f in _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=<optimized out>, callable=<optimized out>)
    at ./Include/cpython/abstract.h:127
#103 trace_call_function (kwnames=<optimized out>, nargs=<optimized out>, args=<optimized out>, func=<optimized out>, tstate=<optimized out>)
    at Python/ceval.c:4944
#104 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x96cc10) at Python/ceval.c:4960
#105 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3500
#106 0x0000000000421528 in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=2, globals=<optimized out>)
    at Objects/call.c:283
#107 0x000000000042581f in _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=<optimized out>, callable=<optimized out>)
    at ./Include/cpython/abstract.h:127
#108 trace_call_function (kwnames=<optimized out>, nargs=<optimized out>, args=<optimized out>, func=<optimized out>, tstate=<optimized out>)
    at Python/ceval.c:4944
#109 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x96cc10) at Python/ceval.c:4960
#110 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3500
#111 0x0000000000421528 in function_code_fastcall (co=<optimized out>, args=<optimized out>, nargs=2, globals=<optimized out>)
    at Objects/call.c:283
#112 0x0000000000438fb8 in _PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x7fffffffd700, callable=0x7ffff7f9a3a0)
    at ./Include/cpython/abstract.h:127
#113 _PyObject_FastCall (nargs=2, args=0x7fffffffd700, func=0x7ffff7f9a3a0) at ./Include/cpython/abstract.h:147
#114 object_vacall (base=base@entry=0x0, callable=0x7ffff7f9a3a0, vargs=vargs@entry=0x7fffffffd788) at Objects/call.c:1186
#115 0x000000000043b305 in _PyObject_CallMethodIdObjArgs (obj=0x0, name=name@entry=0x925160 <PyId__find_and_load.13976>) at Objects/call.c:1244
#116 0x000000000050f37d in import_find_and_load (abs_name=0x7ffff7e69270) at Python/import.c:1698
#117 PyImport_ImportModuleLevelObject (name=name@entry=0x7ffff7e69270, globals=<optimized out>, locals=<optimized out>, 
    fromlist=fromlist@entry=0x91d3e0 <_Py_NoneStruct>, level=0) at Python/import.c:1798
#118 0x0000000000429dcf in import_name (level=0x9492e0 <small_ints+160>, fromlist=0x91d3e0 <_Py_NoneStruct>, name=0x7ffff7e69270, 
    f=0x7ffff7eef800, tstate=0x96cc10) at Python/ceval.c:5139
#119 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2993
#120 0x00000000004eb788 in PyEval_EvalFrameEx (throwflag=0, f=0x7ffff7eef800) at Python/ceval.c:741
#121 _PyEval_EvalCodeWithName (qualname=0x0, name=<optimized out>, closure=0x0, kwdefs=0x0, defcount=0, defs=0x0, kwstep=2, kwcount=0, 
    kwargs=0x0, kwnames=0x0, argcount=0, args=0x0, locals=locals@entry=0x7ffff7eef968, globals=globals@entry=0x7ffff7eef800, 
    _co=_co@entry=0x7ffff7f26710) at Python/ceval.c:4298
#122 PyEval_EvalCodeEx (closure=0x0, kwdefs=0x0, defcount=0, defs=0x0, kwcount=0, kws=0x0, argcount=0, args=0x0, 
---Type <return> to continue, or q <return> to quit---
    locals=locals@entry=0x7ffff7eef968, globals=globals@entry=0x7ffff7eef800, _co=_co@entry=0x7ffff7f26710) at Python/ceval.c:4327
#123 PyEval_EvalCode (co=co@entry=0x7ffff7f26710, globals=globals@entry=0x7ffff7f5aec0, locals=locals@entry=0x7ffff7f5aec0) at Python/ceval.c:718
#124 0x00000000005310d1 in run_eval_code_obj (locals=0x7ffff7f5aec0, globals=0x7ffff7f5aec0, co=0x7ffff7f26710) at Python/pythonrun.c:1125
#125 run_mod (mod=<optimized out>, filename=<optimized out>, globals=0x7ffff7f5aec0, locals=0x7ffff7f5aec0, flags=<optimized out>, 
    arena=<optimized out>) at Python/pythonrun.c:1147
#126 0x0000000000533fd5 in PyRun_StringFlags (flags=0x7fffffffdb40, locals=0x7ffff7f5aec0, globals=0x7ffff7f5aec0, start=257, 
    str=0x7ffff7f503e0 "import xgboost\n") at Python/pythonrun.c:1034
#127 PyRun_SimpleStringFlags (command=0x7ffff7f503e0 "import xgboost\n", flags=flags@entry=0x7fffffffdb40) at Python/pythonrun.c:460
#128 0x000000000042c76c in pymain_run_command (cf=0x7fffffffdb40, command=<optimized out>) at Modules/main.c:258
#129 pymain_run_python (exitcode=0x7fffffffdb20) at Modules/main.c:597
#130 Py_RunMain () at Modules/main.c:685
#131 0x000000000042d1af in pymain_main (args=0x7fffffffdc30) at Modules/main.c:715
#132 Py_BytesMain (argc=<optimized out>, argv=<optimized out>) at Modules/main.c:739
#133 0x00007ffff6ed3555 in __libc_start_main () from /usr/lib64/libc.so.6
#134 0x000000000042bff4 in _start ()
(gdb)

@hcho3
Copy link
Collaborator

hcho3 commented Dec 9, 2020

@hamzamohdzubair I managed to reproduce the segmentation fault on my end, using the container centos:centos7 from this page. Will investigate. Thanks!

@hcho3 hcho3 mentioned this issue Dec 9, 2020
Closed
@trivialfis
Copy link
Member

Is there any change in toolchain?

@hcho3
Copy link
Collaborator

hcho3 commented Dec 9, 2020 •
edited

@hamzamohdzubair @harupy I managed to find a quick fix for the segfault. Can you please try this new wheel? https://xgboost-examples.s3-us-west-2.amazonaws.com/xgboost-1.3.0-py3-none-manylinux2010_x86_64.whl I tried it using both centos:centos6 and python:3.7 containers and I was able to run import xgboost. Let me know if it works on your machine, so that I can apply this fix globally.

@trivialfis No, it had to do with #6461. I was using an incorrect container to perform auditwheel repair command, which involves patching .so file. Patching a binary file is a delicate task, and it has to be done using the official manylinux Docker image to ensure that it doesn't break anything.

@hcho3 hcho3 mentioned this issue Dec 9, 2020
Merged
@trivialfis
Copy link
Member

Awesome that you can root the issue.

@hcho3
Copy link
Collaborator

hcho3 commented Dec 9, 2020

The 1.3.0.post0 version is now available on PyPI: https://pypi.org/project/xgboost/1.3.0.post0/#files. It contains the hot fix (#6482) and should not crash upon import.

@hcho3 hcho3 closed this as completed Dec 9, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@hcho3 @hamzamohdzubair @trivialfis