Document Tips for Debugging C Extensions #35100

WillAyd · 2020-07-02T19:20:06Z

Quick notes in case they are helpful to others. Can move to the Wiki as well if we don't want in the standard docs

WillAyd · 2020-07-02T19:22:54Z

setup.py

@@ -435,8 +433,14 @@ def run(self):
 else:
    extra_compile_args = ["-Werror"]
    extra_link_args = []
-    if debugging_symbols_requested:
-        extra_compile_args.append("-g")
+    if not debugging_symbols_requested:


I guess Python by default (at least locally and looking at some of the CI builds) includes the -g flag as part of the CFLAGS that distutils uses to compile extensions, so in the current setup this does nothing.

According to SO we can override that by appending here, which might help reduce file size by removing those symbols:

https://stackoverflow.com/a/37952343/621736

I can also remove this from this PR if deemed too orthogonal. IIRC @xhochy or @TomAugspurger may have experience with stripping debug symbols from built distributions

Multibuild may do this by default now? I don't recall.

Yes, multibuild includes this nowadays.

WillAyd · 2020-07-02T19:24:00Z

setup.py

+        # Strip debugging symbols (included by default)
+        extra_compile_args.append("-g0")
+    else:
+        # TODO: these should override the defaults provided by Python


distutils adds NDEBUG and -O3 by default it seems without a feasible way to remove those compilation flags. Appending these at the end should override those according to the SO link shared above

I don't recommend building with -O0 actually as it hides a lot of problems. In case of -O0 memory is mored often zeroed and thus invalid memory access is not that fatal (in the higher -Ox cases you would get random data). This makes the detection of bugs a lot harder. It might be better to keep the optimization level here and add flags that make debugging easier. Personally I like -ggdb -fno-omit-frame-pointer. This gives better stacktraces and a bit more debugging information.

gdb suggests turning off optimizations:

https://sourceware.org/gdb/onlinedocs/gdb/Optimized-Code.html

There are certainly exceptions but I think as a general rule (especially for people that aren't super well versed in debugging the extensions yet) that no optimizations will be easier to follow

Yes, the debug information with -O0 is definitely better, I would like to leave -fno-omit-frame-pointer somewhere here in the document as this is the option that provides the most debug information for the smallest performance hit and is really useful if you have an memory-out-of-bounds issue that wouldn't occur easily in the unoptimized version.

Sounds good. I think this is off by default with -O0 per the docs but doesn't hurt to add again

https://gcc.gnu.org/onlinedocs/gcc-3.4.4/gcc/Optimize-Options.html

doc/source/development/debugging_extensions.rst

pep8speaks · 2020-07-06T23:41:15Z

Hello @WillAyd! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2020-12-09 00:49:35 UTC

jbrockmendel · 2020-07-07T01:49:33Z

doc/source/development/debugging_extensions.rst

+
+.. code-block:: sh
+
+   gdb --args python -m pytest


$ gdb --args python3 -m pytest [...] "~/.pyenv/shims/python3": not in executable format: File format not recognized (gdb) run Starting program: -m pytest No executable file specified. Use the "file" or "exec-file" command.

Can you try gdb -ex r --args python3 -m pytest? Taking that from this link:

https://wiki.python.org/moin/DebuggingWithGdb

Yea looks like gdb -ex r --args python3 -m pytest pandas/tests was working for me if you want to try on yours and confirm

$ gdb -ex r --args python3 -m pytest pandas/tests [...] "~/.pyenv/shims/python3": not in executable format: File format not recognized Starting program: -m pytest pandas/tests No executable file specified. Use the "file" or "exec-file" command. (gdb)

Are you using pyenv for development or Conda?

you've already gone above and beyond helping me debug this; ill spend some more time on this and ping you if i find anything new

All good - I think this is generally helpful to hash out together so thanks for the input.

It looks like this might be specific to pyenv and how it manages the python executable:

https://stackoverflow.com/questions/48141135/cannot-start-dbg-on-my-python-c-extension

gdb -ex r --args bash pytest pandas/tests --skip-slow --skip-db tentatively looks like a winner

is the command from my previous comment specific to my case, or relevant to the document?

I'm trying to avoid adding too much detail here since this issue is more of a pyenv thing than a debugger issue

WillAyd · 2020-09-10T18:59:57Z

Any other comments here? Otherwise plan on merging in a few days

jbrockmendel · 2020-09-11T01:09:42Z

One question, no objections.

jreback · 2020-09-13T23:22:55Z

doc/source/development/debugging_extensions.rst

+Using a debugger
+================
+
+You can create a script that hits the extension module you are looking to debug and place it in the project root. Thereafter launch a Python process under lldb:


is there a reference on lldb (link / how to install?)

I have only used on macOS where it comes bundled with the Xcode tools. Not sure about other systems

On my ubuntu machine it's not available (while gdb is). So I would at least link to some web page about it if we want to recommend it over gdb, I suppose most readers won't know what lldb is (I also didn't).
it seems you can install it from conda-forge.

To be clear I don't recommend one over the other - should just use whatever comes with your build system.

I'll try to reword

Did you settle on a wording here?

jbrockmendel · 2020-10-09T15:39:35Z

any movement here?

WillAyd · 2020-10-19T21:14:15Z

Been tight on time lately so closing this temporarily to clean the queue - will come back to this at a later date

WillAyd · 2020-12-09T00:50:56Z

Getting back around to this. Since there was some confusion around gdb vs lldb I added a blurb about which one to choose when. I also made it so all of the steps are shown for both debuggers

jbrockmendel

LGTM

jreback · 2020-12-10T00:19:46Z

thanks @WillAyd

Co-authored-by: William Ayd <will_ayd@innobi.io>

Added notes on debugging extensions

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REF: de-duplicate DST tzconversion code #35077

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WillAyd and others added 2 commits July 6, 2020 15:49

Update debugging_extensions.rst

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Backport PR pandas-dev#35100: Document Tips for Debugging C Extensions

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Backport PR #35100 on branch 1.2.x (Document Tips for Debugging C Extensions) #38395

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Backport PR #35100: Document Tips for Debugging C Extensions (#38395)

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Document Tips for Debugging C Extensions #35100

Document Tips for Debugging C Extensions #35100

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pep8speaks commented Jul 6, 2020 • edited Loading

Comment last updated at 2020-12-09 00:49:35 UTC

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