Discussion:
Segmentation Fault using gdal with Python 3
Clifford Snow
2021-05-28 02:36:25 UTC
Permalink
I'm getting a segmentation fault (core dump) when using the osgeo gdal
modules. Otherwise no problem.

I'm looking for some suggestions on how to troubleshoot this. I can't even
seem to find the core dump file.
from osgeo import gdal
quit()
Segmentation fault (core dumped)

I've reinstalled python3-gdal and gdal-python-tools with no help.

Thanks in advance,
Clifford
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Michael Hennebry
2021-05-28 05:44:11 UTC
Permalink
Post by Clifford Snow
I'm looking for some suggestions on how to troubleshoot this. I can't even
seem to find the core dump file.
My guess is that there is not one.
ulimit -c
will probably tell you the your cose size limit is zero.

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Clifford Snow
2021-05-28 05:46:59 UTC
Permalink
Michael,

On Thu, May 27, 2021 at 10:44 PM Michael Hennebry <
Post by Michael Hennebry
Post by Clifford Snow
I'm looking for some suggestions on how to troubleshoot this. I can't
even
Post by Clifford Snow
seem to find the core dump file.
My guess is that there is not one.
ulimit -c
will probably tell you the your cose size limit is zero.
ulimit -c reports unlimited
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www.snowandsnow.us
OpenStreetMap: Maps with a human touch
Ed Greshko
2021-05-28 06:07:08 UTC
Permalink
Post by Clifford Snow
Michael,
Post by Clifford Snow
I'm looking for some suggestions on how to troubleshoot this. I can't even
seem to find the core dump file.
My guess is that there is not one.
ulimit -c
will probably tell you the your cose size limit is zero.
ulimit -c reports unlimited
does the output of coredumpctl show that a core dump exists?

If so, check /usr/lib/systemd/systemd-coredump for the corresponding dump file.

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Ed Greshko
2021-05-28 06:10:23 UTC
Permalink
Post by Ed Greshko
Post by Clifford Snow
Michael,
    > I'm looking for some suggestions on how to troubleshoot this. I can't even
    > seem to find the core dump file.
    My guess is that there is not one.
    ulimit -c
    will probably tell you the your cose size limit is zero.
ulimit -c reports unlimited
does the output of coredumpctl show that a core dump exists?
If so, check /usr/lib/systemd/systemd-coredump for the corresponding dump file.
Sorry, I meant check

/usr/lib/systemd/

For the file named what is called out in coredumpctl

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Ed Greshko
2021-05-28 06:12:08 UTC
Permalink
Post by Ed Greshko
Post by Ed Greshko
Post by Clifford Snow
Michael,
    > I'm looking for some suggestions on how to troubleshoot this. I can't even
    > seem to find the core dump file.
    My guess is that there is not one.
    ulimit -c
    will probably tell you the your cose size limit is zero.
ulimit -c reports unlimited
does the output of coredumpctl show that a core dump exists?
If so, check /usr/lib/systemd/systemd-coredump for the corresponding dump file.
Sorry, I meant check
/usr/lib/systemd/
For the file named what is called out in coredumpctl
Oh CRAP.....  It is a *bad* afternoon.

The location would be....

/var/lib/systemd/coredump/

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George N. White III
2021-05-28 11:17:52 UTC
Permalink
Post by Clifford Snow
I'm getting a segmentation fault (core dump) when using the osgeo gdal
modules. Otherwise no problem.
I'm looking for some suggestions on how to troubleshoot this. I can't even
seem to find the core dump file.
from osgeo import gdal
quit()
Segmentation fault (core dumped)
You should show the complete output as in:
~% python3 ; echo $?
Python 3.9.5 (default, May 14 2021, 00:00:00)
[GCC 11.1.1 20210428 (Red Hat 11.1.1-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
Post by Clifford Snow
from osgeo import gdal
quit()
0

I can't reproduce your problem on Fedora 33 or 34. More details (Fedora
version,
python version) might help. Is it possible you have old python packages
installed
in /usr/local or ~/.local? Are you using a 3rd party python (Anaconda,
etc.)? Have
you tried "python3 -d -E -c 'from osgeo import gdal'? Have you set
"PYTHONPATH"?

https://pythondev.readthedocs.io/debug_tools.html
--
George N. White III
Clifford Snow
2021-05-28 20:21:04 UTC
Permalink
Thanks everyone for their suggestions. I believe my problem is that I've
installed postgis from the postgresql PGDG repository and it's conflicting
with the Fedora python gdal files. Not sure If I need to just use Fedora's
postgresql version or if there is another workaround.
Post by George N. White III
Post by Clifford Snow
I'm getting a segmentation fault (core dump) when using the osgeo gdal
modules. Otherwise no problem.
I'm looking for some suggestions on how to troubleshoot this. I can't
even seem to find the core dump file.
from osgeo import gdal
quit()
Segmentation fault (core dumped)
~% python3 ; echo $?
Python 3.9.5 (default, May 14 2021, 00:00:00)
[GCC 11.1.1 20210428 (Red Hat 11.1.1-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
Post by Clifford Snow
from osgeo import gdal
quit()
0
I can't reproduce your problem on Fedora 33 or 34. More details (Fedora
version,
python version) might help. Is it possible you have old python packages
installed
in /usr/local or ~/.local? Are you using a 3rd party python (Anaconda,
etc.)? Have
you tried "python3 -d -E -c 'from osgeo import gdal'? Have you set
"PYTHONPATH"?
https://pythondev.readthedocs.io/debug_tools.html
--
George N. White III
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OpenStreetMap: Maps with a human touch
George N. White III
2021-05-29 11:30:42 UTC
Permalink
Post by Clifford Snow
Thanks everyone for their suggestions. I believe my problem is that I've
installed postgis from the postgresql PGDG repository and it's conflicting
with the Fedora python gdal files. Not sure If I need to just use Fedora's
postgresql version or if there is another workaround.
You should report the problem to PGDG. You may need to use python
environments or even
a separate Python install (Anaconda?) if fedora's gdal configuration
doesn't work for your use case.
In my field there is a "mission critical" application that hasn't moved
past Python 3.6 (due to testing
resource constraints, only 3.6 has been properly tested and is available to
the developers when
they need to duplicate a problem) so it is routine to have a Python 3.6
install just for that application.

Anaconda has activate/deactivate scripts, but you can also use
environment-modules or Lmod to
"enable" a specific python version.

environment-modules.x86_64 : Provides dynamic modification of a user's
environment
Lmod.x86_64 : Environmental Modules System in Lua
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George N. White III
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