Do you have PHP enabled for the same Apache?
Generally I discourage use of Anaconda Python distributions as they do things
which break embedding for Python.
One of the problems is that Anaconda Python ships its own versions of some
libraries which are usually installed system wide. The problem is that PHP
loads the system wide variants and when the Anaconda versions are incompatible,
the process trying to use the Anaconda version will crash.
So if you have PHP enabled, are you able to disable it so it isn't loaded by
Apache?
Not that it will help, but since you are using mod_wsgi daemon mode, also add
outside of VirtualHost definitions (good spot is after the LoadModule), the
directive:
WSGIRestrictEmbedded On
That will mean Python isn't initialised in Apache child worker processes where
it isn't needed.
Graham
> On 16 Oct 2024, at 6:30 AM, Molly Foley <molly.k.fo...@gmail.com> wrote:
>
> I'm struggling to get multiple conda environments working and I'm hoping to
> get some insight here.
>
> I have installed python with the miniforge3 distribution (conda, basically).
> In the base environment, I have installed mod_wsgi 5.0.0 which appears to
> compile again python 3.12. The base python environment has python 3.12.6
> installed (I left it as default because messing with the base environment is
> usually a no-no). Additionally, I have created two conda virtual
> environments, one for each virtual host I have in Apache. Each virtual
> environment has python 3.12.7 installed.
>
> sys.prefix is /opt/miniforge3
>
> As root user, echo $PATH results in:
> /root/.nvm/versions/node/v20.5.0/bin:/root/.local/bin:/root/bin:/opt/miniforge3/bin/:/sbin:/bin:/usr/sbin:/usr/bin:/var/cfengine/bin
>
>
>
> LoadModule config looks like this:
>
> # NOTE: mod_wsgi_python3 can not coexist in the same apache process as
>
> # mod_wsgi (python2). Only load if mod_wsgi is not already loaded.
>
> <IfModule !wsgi_module>
>
> LoadModule wsgi_module
> /opt/miniforge3/lib/python3.12/site-packages/mod_wsgi/server/mod_wsgi-py312.cpython-312-x86_64-linux-gnu.so
>
>
> </IfModule>
>
>
>
> In Apache, I have set the apache LogLevel to info. I have also set the
> virtual hosts' specific logs to LogLevel to info.
>
> Here is the relevant config for the virtual hosts:
> <VirtualHost *:443>
>
> ServerName myServerName.com
>
> ## Vhost docroot
>
> DocumentRoot "/var/www/vhosts/hydrosource_chap"
>
> ## Logging
>
> ErrorLog "/var/log/httpd/chap-error.log"
>
> LogLevel info
>
> ServerSignature Off
>
> CustomLog "/var/log/httpd/chap-access.log" combined
>
> ## WSGI configuration
>
> WSGIApplicationGroup %{GLOBAL}
>
> WSGIDaemonProcess hydrosource_chap display-name=%{GROUP}
> home=/var/www/vhosts/hydrosource_chap python-home=/opt/miniforge3/envs/chap
> threads=1 user=hydro
>
> WSGIProcessGroup hydrosource_chap
>
> WSGIScriptAlias / "/var/www/vhosts/hydrosource_chap/wsgi.py"
>
> ## Anything start with dot
>
> <DirectoryMatch "^\.|\/\.">
>
> Require all denied
>
> </DirectoryMatch>
>
>
>
> <LocationMatch "\/\.">
>
> Require all denied
>
> </LocationMatch>
>
>
>
> <Location />
>
> Require all granted
>
> </Location>
>
> </VirtualHost>
>
> <VirtualHost *:443>
>
> ServerName mySecondName.com
>
> ## Vhost docroot
>
> DocumentRoot "/var/www/vhosts/hydrosource-2"
>
> ## Logging
>
> ErrorLog "/var/log/httpd/dataexplorer-error.log"
>
> LogLevel info
>
> ServerSignature Off
>
> CustomLog "/var/log/httpd/dataexplorer-access.log" combined
>
> ## WSGI configuration
>
> WSGIApplicationGroup %{GLOBAL}
>
> WSGIDaemonProcess dataexplorer display-name=%{GROUP}
> home=/var/www/vhosts/hydrosource-2
> python-home=/opt/miniforge3/envs/dataexplorer threads=1 user=hydro
>
> WSGIProcessGroup dataexplorer
>
> WSGIScriptAlias / "/var/www/vhosts/hydrosource-2/wsgi.py"
>
> ## Anything start with dot
>
> <DirectoryMatch "^\.|\/\.">
>
> Require all denied
>
> </DirectoryMatch>
>
>
>
> <LocationMatch "\/\.">
>
> Require all denied
>
> </LocationMatch>
>
>
>
> <Location />
>
> Require all granted
>
> </Location>
>
> </VirtualHost>
>
>
>
> When I systemctl restart httpd and try to load the dataexplorer application,
> for instance, I get segmentation fault errors in the apache error_log and
> issues with oversized headers in the virtual host specific log.
>
>
>
> Apache Log:
>
> [Tue Oct 15 15:10:34.242996 2024] [wsgi:info] [pid 568871:tid 568871]
> mod_wsgi (pid=568871): Starting process 'hydrosource_chap' with uid=36143,
> gid=48 and threads=1.
>
> [Tue Oct 15 15:10:34.243772 2024] [wsgi:info] [pid 568872:tid 568872]
> mod_wsgi (pid=568872): Starting process 'dataexplorer' with uid=36143, gid=48
> and threads=1.
>
> [Tue Oct 15 15:10:34.246679 2024] [mpm_event:notice] [pid 568866:tid 568866]
> AH00489: Apache/2.4.57 (Red Hat Enterprise Linux) OpenSSL/3.0.7
> mod_wsgi/5.0.0 Python/3.12 configured -- resuming normal operations
>
> [Tue Oct 15 15:10:34.246702 2024] [mpm_event:info] [pid 568866:tid 568866]
> AH00490: Server built: Aug 5 2024 00:00:00
>
> [Tue Oct 15 15:10:34.246719 2024] [core:notice] [pid 568866:tid 568866]
> AH00094: Command line: '/usr/sbin/httpd -D FOREGROUND'
>
> [Tue Oct 15 15:10:34.248317 2024] [wsgi:info] [pid 568871:tid 568871]
> mod_wsgi (pid=568871): Python home /opt/miniforge3/envs/chap.
>
> [Tue Oct 15 15:10:34.248321 2024] [wsgi:info] [pid 568872:tid 568872]
> mod_wsgi (pid=568872): Python home /opt/miniforge3/envs/dataexplorer.
>
> [Tue Oct 15 15:10:34.248377 2024] [wsgi:info] [pid 568871:tid 568871]
> mod_wsgi (pid=568871): Initializing Python.
>
> [Tue Oct 15 15:10:34.248387 2024] [wsgi:info] [pid 568872:tid 568872]
> mod_wsgi (pid=568872): Initializing Python.
>
> [Tue Oct 15 15:10:34.249092 2024] [http2:info] [pid 568874:tid 568874]
> h2_workers: created with min=25 max=37 idle_ms=600000
>
> [Tue Oct 15 15:10:34.250137 2024] [wsgi:info] [pid 568874:tid 568874]
> mod_wsgi (pid=568874): Initializing Python.
>
> [Tue Oct 15 15:10:34.256663 2024] [http2:info] [pid 568875:tid 568875]
> h2_workers: created with min=25 max=37 idle_ms=600000
>
> [Tue Oct 15 15:10:34.257760 2024] [wsgi:info] [pid 568875:tid 568875]
> mod_wsgi (pid=568875): Initializing Python.
>
> [Tue Oct 15 15:10:34.258652 2024] [http2:info] [pid 568873:tid 568873]
> h2_workers: created with min=25 max=37 idle_ms=600000
>
> [Tue Oct 15 15:10:34.259732 2024] [wsgi:info] [pid 568873:tid 568873]
> mod_wsgi (pid=568873): Initializing Python.
>
> [Tue Oct 15 15:10:34.262413 2024] [wsgi:info] [pid 568874:tid 568874]
> mod_wsgi (pid=568874): Attach interpreter ''.
>
> [Tue Oct 15 15:10:34.271322 2024] [wsgi:info] [pid 568873:tid 568873]
> mod_wsgi (pid=568873): Attach interpreter ''.
>
> [Tue Oct 15 15:10:34.277995 2024] [wsgi:info] [pid 568875:tid 568875]
> mod_wsgi (pid=568875): Attach interpreter ''.
>
> [Tue Oct 15 15:10:34.279542 2024] [wsgi:info] [pid 568874:tid 568874]
> mod_wsgi (pid=568874): Imported 'mod_wsgi'.
>
> [Tue Oct 15 15:10:34.288265 2024] [wsgi:info] [pid 568873:tid 568873]
> mod_wsgi (pid=568873): Imported 'mod_wsgi'.
>
> [Tue Oct 15 15:10:34.296894 2024] [wsgi:info] [pid 568875:tid 568875]
> mod_wsgi (pid=568875): Imported 'mod_wsgi'.
>
> [Tue Oct 15 15:10:49.266694 2024] [http2:info] [pid 569108:tid 569108]
> h2_workers: created with min=25 max=37 idle_ms=600000
>
> [Tue Oct 15 15:10:49.267916 2024] [wsgi:info] [pid 569108:tid 569108]
> mod_wsgi (pid=569108): Initializing Python.
>
> [Tue Oct 15 15:10:49.281851 2024] [wsgi:info] [pid 569108:tid 569108]
> mod_wsgi (pid=569108): Attach interpreter ''.
>
> [Tue Oct 15 15:10:49.298865 2024] [wsgi:info] [pid 569108:tid 569108]
> mod_wsgi (pid=569108): Imported 'mod_wsgi'.
>
> [Tue Oct 15 15:10:50.264356 2024] [core:notice] [pid 568866:tid 568866]
> AH00051: child pid 568872 exit signal Segmentation fault (11), possible
> coredump in /etc/httpd
>
> [Tue Oct 15 15:10:50.264458 2024] [wsgi:info] [pid 568866:tid 568866]
> mod_wsgi (pid=568872): Process 'dataexplorer' has died, deregister and
> restart it.
>
> [Tue Oct 15 15:10:50.264466 2024] [wsgi:info] [pid 568866:tid 568866]
> mod_wsgi (pid=568872): Process 'dataexplorer' terminated by signal 11
>
> [Tue Oct 15 15:10:50.264473 2024] [wsgi:info] [pid 568866:tid 568866]
> mod_wsgi (pid=568872): Process 'dataexplorer' has been deregistered and will
> no longer be monitored.
>
> [Tue Oct 15 15:10:50.265514 2024] [wsgi:info] [pid 569173:tid 569173]
> mod_wsgi (pid=569173): Starting process 'dataexplorer' with uid=36143, gid=48
> and threads=1.
>
> [Tue Oct 15 15:10:50.268450 2024] [wsgi:info] [pid 569173:tid 569173]
> mod_wsgi (pid=569173): Python home /opt/miniforge3/envs/dataexplorer.
>
> [Tue Oct 15 15:10:50.268513 2024] [wsgi:info] [pid 569173:tid 569173]
> mod_wsgi (pid=569173): Initializing Python.
>
> [Tue Oct 15 15:10:51.265981 2024] [core:notice] [pid 568866:tid 568866]
> AH00051: child pid 569173 exit signal Segmentation fault (11), possible
> coredump in /etc/httpd
>
> [Tue Oct 15 15:10:51.266037 2024] [wsgi:info] [pid 568866:tid 568866]
> mod_wsgi (pid=569173): Process 'dataexplorer' has died, deregister and
> restart it.
>
> [Tue Oct 15 15:10:51.266044 2024] [wsgi:info] [pid 568866:tid 568866]
> mod_wsgi (pid=569173): Process 'dataexplorer' terminated by signal 11
>
> [Tue Oct 15 15:10:51.266050 2024] [wsgi:info] [pid 568866:tid 568866]
> mod_wsgi (pid=569173): Process 'dataexplorer' has been deregistered and will
> no longer be monitored.
>
> [Tue Oct 15 15:10:51.267079 2024] [wsgi:info] [pid 569188:tid 569188]
> mod_wsgi (pid=569188): Starting process 'dataexplorer' with uid=36143, gid=48
> and threads=1.
>
> [Tue Oct 15 15:10:51.269694 2024] [wsgi:info] [pid 569188:tid 569188]
> mod_wsgi (pid=569188): Python home /opt/miniforge3/envs/dataexplorer.
>
>
> [Tue Oct 15 15:10:51.269761 2024] [wsgi:info] [pid 569188:tid 569188]
> mod_wsgi (pid=569188): Initializing Python.
>
>
>
> dataexplorer log:
>
> [Tue Oct 15 15:10:34.267712 2024] [wsgi:info] [pid 568872:tid 568872]
> mod_wsgi (pid=568872): Attach interpreter ''.
>
> [Tue Oct 15 15:10:48.949190 2024] [wsgi:info] [pid 568872:tid 568981] [remote
> 10.159.64.61:59510] mod_wsgi (pid=568872, process='dataexplorer',
> application=''): Loading Python script file
> '/var/www/vhosts/hydrosource-2/wsgi.py'.
>
> [Tue Oct 15 15:10:49.636199 2024] [wsgi:error] [pid 568875:tid 569031]
> [client 10.159.64.61:59510] Truncated or oversized response headers received
> from daemon process 'dataexplorer': /var/www/vhosts/hydrosource-2/wsgi.py
>
> [Tue Oct 15 15:10:50.282619 2024] [wsgi:info] [pid 569173:tid 569173]
> mod_wsgi (pid=569173): Attach interpreter ''.
>
> [Tue Oct 15 15:10:50.293954 2024] [wsgi:info] [pid 569173:tid 569176] [remote
> 10.159.64.61:59511] mod_wsgi (pid=569173, process='dataexplorer',
> application=''): Loading Python script file
> '/var/www/vhosts/hydrosource-2/wsgi.py'.
>
> [Tue Oct 15 15:10:50.956465 2024] [wsgi:error] [pid 568874:tid 568980]
> [client 10.159.64.61:59511] Truncated or oversized response headers received
> from daemon process 'dataexplorer': /var/www/vhosts/hydrosource-2/wsgi.py,
> referer: https://dataexplorer.hydroclimate-dev.ornl.gov/
>
>
> [Tue Oct 15 15:10:51.281032 2024] [wsgi:info] [pid 569188:tid 569188]
> mod_wsgi (pid=569188): Attach interpreter ''.
>
>
>
> Given the segmentation faults, I do a core dump and then use gdb to look at
> the problem. To be honest, I don't really know what I'm looking at here. If I
> do "bt", it prints out a lot more stuff, but I can't make heads or tails of
> it. This is the output without backtracing with "bt".
>
> GNU gdb (GDB) Red Hat Enterprise Linux 10.2-13.el9
>
> Copyright (C) 2021 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".
>
> Type "show configuration" for configuration details.
>
> For bug reporting instructions, please see:
>
> <https://www.gnu.org/software/gdb/bugs/>.
>
> Find the GDB manual and other documentation resources online at:
>
> <http://www.gnu.org/software/gdb/documentation/>.
>
>
>
> For help, type "help".
>
> Type "apropos word" to search for commands related to "word"...
>
> Reading symbols from /usr/sbin/httpd...
>
> Reading symbols from .gnu_debugdata for /usr/sbin/httpd...
>
> (No debugging symbols found in .gnu_debugdata for /usr/sbin/httpd)
>
>
>
> warning: Can't open file /dev/zero (deleted) during file-backed mapping note
> processing
>
> [New LWP 568981]
>
> [New LWP 568872]
>
> [New LWP 568979]
>
> [New LWP 568977]
>
> [Thread debugging using libthread_db enabled]
>
> Using host libthread_db library "/lib64/libthread_db.so.1".
>
> Core was generated by `(wsgi:dataexplo -DFOREGROUND'.
>
> Program terminated with signal SIGSEGV, Segmentation fault.
>
> #0 PyObject_GetAttr (v=0x7fa2e8a44130, name=0x7fa2eae33c20
> <_PyRuntime+45280>) at /usr/local/src/conda/python-3.12.6/Include/object.h:968
>
> 968 /usr/local/src/conda/python-3.12.6/Include/object.h: No such file or
> directory.
>
> [Current thread is 1 (Thread 0x7fa2e9425640 (LWP 568981))]
>
>
> Missing separate debuginfos, use: dnf debuginfo-install
> httpd-core-2.4.57-11.el9_4.1.x86_64
>
>
>
> It seems like it's routing to an incorrect python install somehow.
> /usr/local/src/conda is not a path that exists on this machine, so the error
> makes sense, but I don't know what it's trying to do on this line.
>
> I have attempted to set header-buffer-size on my WSGIProcessDaemon directives
> but haven't had any luck with that. If I remove the offending packages
> (things that have to do with SQL like flask-sqlalchemy, psycopg2,
> geoalchemy2, etc) then the apps will run without crashing, but will obviously
> give me errors about being unable to import the packages I removed since
> they're needed in my app. I'm really not sure how to move forward on this. Is
> there something obviously wrong in my configuration? Do I need to install
> mod_wsgi in each virtual environment instead of the base environment (and if
> so, then how would LoadModule work in Apache?).
>
>
>
> Lastly, here's my wsgi.py script file (each app has the same one). I am using
> blueprints in my Flask app, so I import the create_app function to generate
> the application.
>
> import sys
> from api import create_app
> from os import getcwd
>
> sys.path.insert(0, getcwd() + "/api")
> sys.path.append(getcwd() + "/api/models")
>
> application = create_app()
>
> Any insight on how to debug this would be very helpful. I have reviewed the
> debugging technique docs, but I really feel lost with the gnu debugger.
>
> Thanks for your time!
>
> --
> You received this message because you are subscribed to the Google Groups
> "modwsgi" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to modwsgi+unsubscr...@googlegroups.com
> <mailto:modwsgi+unsubscr...@googlegroups.com>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/modwsgi/b6af7e32-21b7-4f04-9e5b-ab1e8cfaa7dan%40googlegroups.com
>
> <https://groups.google.com/d/msgid/modwsgi/b6af7e32-21b7-4f04-9e5b-ab1e8cfaa7dan%40googlegroups.com?utm_medium=email&utm_source=footer>.
--
You received this message because you are subscribed to the Google Groups
"modwsgi" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to modwsgi+unsubscr...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/modwsgi/C74A2968-18E4-4982-9D3F-8C5253AB18C2%40gmail.com.
