Debugging Python with gdb

Debugging of Python with gdb
PyCon Ukraine 2017
Lviv, Ukraine
April 9th, 2017
by Roman Podoliaka, Development Manager at Mirantis
twitter: @rpodoliaka
blog: http://podoliaka.org
slides: http://podoliaka.org/talks/

Goals of this talk
make gdb "a known unknown", so that you consider it as an
option in the future
highlight the common gotchas

Why debugging?
working on a huge open source cloud platform ‑ OpenStack
dozens of various (micro‑)services ‑ from REST APIs to system
daemons
new features are important, but fault tolerance and overall
stability are even more important
continuous functional / performance / scale testing
numerous customer deployments
things break... pretty much all the time!

Caveats
The described debugging techniques assume that you use:
Linux
Darwin (macOS): must be similar, but lldb is the debugger
of choice there
(and things like System Integrity Protection tend to stay
in your way)
Windows: should work, if you use a recent gdb build with
Python support enabled and have debugging symbols for
CPython
CPython 2.7 or 3.x
debugging scripts are interpreter‑specific, so no
PyPy/Jython/IronPython/etc
2.6 works too, but up‑to‑date scripts are more useful

What's wrong with pdb?
It's a nice and easy to use debugger, that should be your default
choice, but it:
can't attach to a running process
can't step into native code (e.g. shared libraries, C/C++
extensions or CPython itself)
can't be used for debugging of interpreter crashes (i.e. core
dumps)

Typical problems: hung process
a process is stuck in S (sleeping) state and does not respond
strace 'ing shows that it is trying to acquire a lock (i.e.
futex(...) )
one needs a way to map this to the exact line in the application
code
especially important if you use cooperative concurrency (i.e.
asyncio, eventlet, gevent, etc)

Typical problems: going into native code
~14000 unit tests, one or a few create a temporary directory in
the git working tree and do not clean up after themselves. How
do you identify those?
pdb does not allow to set breakpoints in built‑in functions (like
os.makedirs() )

Typical problems: interpreter crashes
rarely happen in common applications
but still do with things like mod_wsgi
(https://github.com/GrahamDumpleton/mod_wsgi/issues/81)
or calls to native libraries via cffi
(https://bitbucket.org/cffi/cffi/issues/240/cffi‑crash‑on‑debian‑
unstable‑with‑gcc‑5)

gdb
a general purpose debugger, that is mostly used for debugging
of C and C++ applications (supports Objective‑C, Pascal, Rust,
Go and more)
allows attaching to a running process without instrumenting it in
advance
allows taking a core dump (a state of process memory at a
specific moment of time) in order to analyze it later
allows post‑mortem debugging of core dumps of crashed
processes saved by the kernel (if ulimit allows for it)
allows switching between threads

ptrace: the secret power behind gdb and strace
#include <sys/ptrace.h>
long ptrace(enum __ptrace_request request, pid_t pid,
void *addr, void *data);
provides a means by which one process (the "tracer") may observe
and control the execution of another process (the "tracee")

Debugging of interpreted languages
Python code is not compiled into a native binary for a target
platform. Instead there is an interpreter (e.g. CPython, the
reference implementation of Python), which executes compiled
byte‑code
when you attach to a Python process with gdb, you'll debug the
interpreter instance and introspect the process state at the
interpreter level, not the application level

Debugging of interpreted languages: interpreter
level traceback
#0 0x00007fcce9b2faf3 in __epoll_wait_nocancel () at ../sysdep
#1 0x0000000000435ef8 in pyepoll_poll (self=0x7fccdf54f240, ar
#2 0x000000000049968d in call_function (oparg=<optimized out>,
#3 PyEval_EvalFrameEx () at ../Python/ceval.c:2666
#4 0x0000000000499ef2 in fast_function () at ../Python/ceval
#5 call_function () at ../Python/ceval.c:4041
#6 PyEval_EvalFrameEx () at ../Python/ceval.c:2666

Debugging of interpreted languages: application
level traceback
/usr/local/lib/python2.7/dist-packages/eventlet/greenpool.
`func(*args, **kwargs)`
/opt/stack/neutron/neutron/agent/l3/agent.py:461 in _process_ro
`for rp, update in self._queue.each_update_to_next_router()
/opt/stack/neutron/neutron/agent/l3/router_processing_queue.
`next_update = self._queue.get()`
/usr/local/lib/python2.7/dist-packages/eventlet/queue.py:313
`return waiter.wait()`
/usr/local/lib/python2.7/dist-packages/eventlet/queue.py:141
`return get_hub().switch()`
/usr/local/lib/python2.7/dist-packages/eventlet/hubs/hub.py
`return self.greenlet.switch()`

PyEval_EvalFrameEx
PyEval_EvalFrameEx(PyFrameObject *f, int throwflag)
{
/* variable declaration and initialization stuff */
for (;;) {
/* do periodic housekeeping once in a few opcodes */
opcode = NEXTOP();
if (HAS_ARG(opcode)) oparg = NEXTARG();
switch (opcode) {
case NOP:
goto fast_next_opcode;
/* lots of more complex opcode implementations */
default:
/* become rather unhappy */
}
/* handle exceptions or runtime errors, if any */
}
/* we are finished, pop the frame stack */
tstate->frame = f->f_back;
return retval;
}

gdb and Python
gdb can be built with Python support enabled
that essentially means one can extend gdb with Python scripts
e.g. pretty‑printing for C++ STL containers:
https://sourceware.org/gdb/wiki/STLSupport
the very same mechanism is used for debugging of CPython:
https://github.com/python/cpython/blob/master/Tools/gdb/libpy
thon.py

An example of a gdb extension for debugging of
CPython
class PyBacktrace(gdb.Command):
def __init__(self):
gdb.Command.__init__(self,
"py-bt",
gdb.COMMAND_STACK,
gdb.COMPLETE_NONE)
def invoke(self, args, from_tty):
frame = Frame.get_selected_python_frame()
if not frame:
print('Unable to locate python frame')
return
sys.stdout.write('Traceback (most recent call first):n'
while frame:
if frame.is_python_frame():
frame.print_traceback()
frame = frame.older()

Prerequisites: gdb with Python support
apt-get install gdb
or
yum install gdb
or something else depending on the distro you use, then
gdb -ex 'python print("ok")' -ex quit | tail -n 1

Prerequisites: CPython debugging symbols
debugging symbols are information on the data type of each
variable or function and the correspondence between source
line numbers and addresses in the executable code
generated when applications are compiled with ‑g flag passed
to gcc/clang
consume a lot of disk space, thus, are usually stripped from
compiled binaries and shipped separately
the most popular and commonly used format of debugging
symbols is called DWARF

Prerequisites: CPython debugging symbols
apt-get install python-dbg
or
yum install python-debuginfo
CentOS/RHEL put those into a separate repo, e.g.
http://debuginfo.centos.org
debuginfo-install python
Some distros (like Arch Linux) do not ship debugging symbols at all

Prerequisites: CPython scripts for gdb
developed in CPython code tree:
https://github.com/python/cpython/blob/master/Tools/gdb/libpy
thon.py
packaged and shipped by Linux distros
loaded by gdb automatically when debugging python binary
can also be loaded manually like
(gdb) source ~/src/cpython/Tools/gdb/libpython.py

Debug a process from the start
gdb /usr/bin/python
(gdb) run my_python_script.py

Attach to a running process
gdb /usr/bin/python -p $PID
or simply
gdb -p $PID
(note: gdb will stop all process threads, unless non‑stop mode was
enabled with set non-stop on )

Load the inferior state from a core dump
get a core dump of a running process
gcore $PID
open it in gdb
gdb /usr/bin/python core.$PID

Print a traceback
(gdb) py-bt
Traceback (most recent call first):
File "/usr/lib/python2.7/logging/__init__.py", line 872, in
stream.write(ufs % msg)
File "/usr/lib/python2.7/logging/__init__.py", line 759, in
self.emit(record)
File "/usr/lib/python2.7/logging/__init__.py", line 1336,
hdlr.handle(record)
self.callHandlers(record)
self.handle(record)
self._log(DEBUG, msg, args, **kwargs)
self.logger.debug(msg, *args, **kwargs)
File "/opt/stack/nova/nova/compute/resource_tracker.py", line
'pci_devices': pci_devices})

Print Python code
(gdb) py-list
867 try:
868 if (isinstance(msg, unicode) and
869 getattr(stream, 'encoding', None)):
870 ufs = u'%sn'
871 try:
>872 stream.write(ufs % msg)
873 except UnicodeEncodeError:
874 #Printing to terminals sometimes fails. For ex
875 #with an encoding of 'cp1251', the above write
876 #work if written to a stream opened or wrapped
877 #the codecs module, but fail when writing to a

Print local variables
(gdb) py-locals
self = <ColorHandler(...)>
stream = <file at remote 0x7fa76ebb61e0>
fs = '%sn'
ufs = u'%sn'

Set a breakpoint in native code
gdb /usr/bin/python
(gdb) break mkdir
Breakpoint 1 at 0x417600
(gdb) condition 1 $_regex((char*) $rdi,
".*/instances/.*")
(gdb) commands 1
Type commands for breakpoint(s) 1, one per line.
End with a line saying just "end".
>py-bt
>end
end
(gdb) run -m testtools.run discover -s nova/tests/unit

Execute arbitrary Python code in the process
context
(gdb) call PyGILState_Ensure()
$21 = PyGILState_UNLOCKED
(gdb) call PyRun_SimpleString("print('hello')")
hello
$22 = 0
(gdb) call PyGILState_Release(PyGILState_UNLOCKED)

Gotchas: virtual environments and custom
CPython builds
when attaching to a Python process started in a virtual
environment debugging symbols may suddenly not be found
anymore
gdb -p $2975
Attaching to process 2975
Reading symbols from .../venv/bin/python2...
(no debugging symbols found)...done.
it happens because gdb looks for them in the wrong place: if
you omit the inferior binary path, gdb tries to derive it from
/proc/$PID/exe symlink and then load debugging symbols
stored in the predefined path ‑ e.g. /usr/lib/debug/$PATH .
For a virtual environment it's not
/usr/lib/debug/usr/bin/python2 , thus, loading fails

CPython builds
the solution is to always pass the inferior binary path explicitly
when attaching to a process
gdb /usr/bin/python2.7 -p $PID
alternatively, modern CPython builds (at least on Debian Testing
or Ubuntu Xenial) have an associated build-id value, that is
used to uniquely identify stripped debugging symbols
objdump -s -j .note.gnu.build-id /usr/bin/python2.7
Reading symbols from /usr/lib/debug/.build-id/8d/
04a3ae38521cb7c7928e4a7c8b1ed385e763e4.debug...done.

CPython builds
py‑ commands may be undefined for a very similar reason
(gdb) py-bt
Undefined command: "py-bt". Try "help".
gdb autoloads debugging scripts from $PATH-gdb.py
(gdb) info auto-load
gdb-scripts: No auto-load scripts.
libthread-db: No auto-loaded libthread-db.
local-gdbinit: Local .gdbinit file was not found.
python-scripts:
Loaded Script
Yes /usr/share/gdb/auto-load/usr/bin/python2.7-gdb.py

CPython builds
you can always load the scripts manually
(gdb)
source /usr/share/gdb/auto-load/usr/bin/python2.7-gdb.py
it's also useful for testing of the new versions of gdb scripts
shipped with CPython

Gotchas: PTRACE_ATTACH not permitted
Controlled by /proc/sys/kernel/yama/ptrace_scope , possible
values are
0 ‑ a process can PTRACE_ATTACH to any other
process running under the same uid
1 ‑ only descendants can be traced (default on Ubuntu)
2 ‑ admin‑only attach, or through children calling
PTRACE_TRACEME
3 ‑ no processes may use ptrace with PTRACE_ATTACH nor via
PTRACE_TRACEME

Gotchas: python‑dbg
a separate build of CPython (with --with-pydebug passed to
./configure ) with many run‑time checks enabled, thus, much
slower
not required for using of gdb
$ time python -c "print(sum(range(1, 1000000)))"
499999500000
real 0m0.096s
user 0m0.057s
sys 0m0.030s
$ time python-dbg -c "print(sum(range(1, 1000000)))"
499999500000
[18318 refs]
real 0m0.237s
user 0m0.197s
sys 0m0.016s

Gotchas: compiler build flags
some Linux distros build CPython with -g0 or -g1 flags
passed to gcc: the former produces a binary without debugging
information at all, and the latter does not allow gdb to get
information about local variables at runtime
the solution is to rebuild CPython with -g or -g2 ( 2 is the
default value when -g is passed)

Gotchas: optimized out frames
depending on the optimization level used in gcc when building
CPython or the exact compiler version used, it's possible that
information on local variables or function arguments will be lost
at runtime (e.g. with aggressive optimizations enabled by -O3 )
(gdb) py-bt
Traceback (most recent call first):
File "test.py", line 9, in g
time.sleep(1000)
File "test.py", line 5, in f
g()
(frame information optimized out)

Gotchas: optimized out frames
it's still possible to debug such builds of CPython, though it may
be tricky
(gdb) disassemble
Dump of assembler code for function PyEval_EvalFrameEx:
...
0x00007ffff7a04e88 <+8>: mov %rdi,%r12
...
(gdb) p ((PyObject*) $r12)->ob_type->tp_name
$97 = 0x7ffff7ab59f0 "frame"
(gdb) p (char*)
(&((PyUnicodeObject*) ((PyFrameObject*) $r12)->
f_code->co_name)->_base->_base + 1)
$98 = 0x7ffff6a8aca0 "main"

Gotchas: PyPy, Jython, etc
the described debugging technique is only feasible for the
CPython interpreter as is, as the gdb extension is specifically
written to introspect the state of CPython internals (e.g.
PyEval_EvalFrameEx calls)
for PyPy there is an open issue on Bitbucket, where it was
proposed to provide integration with gdb, but looks like the
attached patches have not been merged yet and the person,
who wrote those, lost interest in this
for Jython you could probably use standard tools for debugging
of JVM applications, e.g. VisualVM

Links
gdb Debugging Full Example:
http://brendangregg.com/blog/2016‑08‑09/gdb‑example‑
ncurses.html
Low‑level Python debugging with gdb:
http://grapsus.net/blog/post/Low‑level‑Python‑debugging‑with‑
GDB
a blog post on CPython internals:
https://tech.blog.aknin.name/category/my‑projects/pythons‑
innards/
pydevd: http://pydev.blogspot.com/2014/09/attaching‑
debugger‑to‑running‑process.html
pyringe: https://github.com/google/pyringe

Conclusion
gdb is a powerful tool, that allows one to debug complex
problems with crashing or hanging CPython processes, as well
as Python code, that does calls to native libraries
on modern Linux distros debugging CPython processes with
gdb must be as simple as installing of debugging symbols for
the interpreter build, although there are a few known gotchas,
especially when virtual environments are used

Questions?
Your feedback is very appreciated!
twitter: @rpodoliaka
blog: http://podoliaka.org
slides: http://podoliaka.org/talks/

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