From a680340023395a0d0d63f4feac593e0bb68b2159 Mon Sep 17 00:00:00 2001
From: Florian Ziemen <florianziemen@users.noreply.github.com>
Date: Thu, 6 Feb 2025 16:56:30 +0100
Subject: [PATCH] simple python call with stack trace
to be continued...
---
lectures/debugging-strategies/slides.qmd | 124 ++++++++++-------------
1 file changed, 53 insertions(+), 71 deletions(-)
diff --git a/lectures/debugging-strategies/slides.qmd b/lectures/debugging-strategies/slides.qmd
index 5c96f6c..69b0ab8 100644
--- a/lectures/debugging-strategies/slides.qmd
+++ b/lectures/debugging-strategies/slides.qmd
@@ -2,7 +2,17 @@
title: "Debugging Strategies"
---
-# Debugging vs. Testing {.leftalign}
+# What are we looking at?
+
+## Bugs make software misbehave
+* Crash
+* Freeze
+* Bogus result
+* Slightly wrong result
+* Security vulnerability
+* ...
+
+## Debugging vs. Testing
**Testing:** Cover as many use cases as possible to make a program more robust
@@ -11,87 +21,67 @@ title: "Debugging Strategies"
## Strategies covered in this lecture
- - Include debug output/logging mechanisms
- - Narrow down the code where the error occured (divide and conquer)
- - Use a debugger
+- Read the error message
+- Include debug output/logging mechanisms
+- Narrow down the code where the error occured (divide and conquer)
+- Use a debugger
## Other strategies
-- [Debugging compiled code](../../old_lectures/debugging-compiled-languages/)
+- Search online for the error message / problem description
- Consider the last working state and focus on what changed since
- If changes are committed in a repo,
find the last valid commit (`git bisect`)
-- Search online for this or similar issues
- Ask colleagues working with the same code
-- Call for vendor support
-
-
-
-## Locating the right error message {.leftalign}
-
-::::::::{.columns .smaller}
+- [Debugging compiled code](../../old_lectures/debugging-compiled-languages/)
-:::{.column width=50%}
-```python
-def _extend_number(num):
- return 10*num + (num % 10) -1
-
-def extend_number(num):
- try:
- for idx in range(num):
- num = _extend_number(num)
- except:
- num = extend_number(num)
-
- return num
-
-print(extend_number('6'))
-```
-Expected output:
+## Reading an error message {.special}
+Try this in python:
+```python
+import xarray as xr
+xr.open_dataset ("/scrattch/k/k202134/test.nc")
```
-6543210
-```
-
-:::
-
-:::{.column width=50% .fragment}
-
-Actual output (last 17 lines)
-
-```
+## Python output for open_dataset {.special}
+```python
Traceback (most recent call last):
- File "number_extension.py", line 6, in extend_number
- for idx in range(num):
-RecursionError: maximum recursion depth exceeded while calling a Python object
+ File "/sw/spack-levante/mambaforge-22.9.0-2-Linux-x86_64-kptncg/lib/python3.10/site-packages/xarray/backends/file_manager.py", line 210, in _acquire_with_cache_info
+ file = self._cache[self._key]
+ File "/sw/spack-levante/mambaforge-22.9.0-2-Linux-x86_64-kptncg/lib/python3.10/site-packages/xarray/backends/lru_cache.py", line 56, in __getitem__
+ value = self._cache[key]
+KeyError: [<class 'netCDF4._netCDF4.Dataset'>, ('/scrattch/k/k202134/test.nc',), 'r', (('clobber', True), ('diskless', False), ('format', 'NETCDF4'), ('persist', False)), '14687e3e-f5b3-4c71-9879-3db9386888df']
During handling of the above exception, another exception occurred:
+
Traceback (most recent call last):
- File "number_extension.py", line 13, in <module>
- print(extend_number('6'))
- File "number_extension.py", line 9, in extend_number
- num = extend_number(num)
- File "number_extension.py", line 9, in extend_number
- num = extend_number(num)
- File "number_extension.py", line 9, in extend_number
- num = extend_number(num)
- [Previous line repeated 996 more times]
-RecursionError: maximum recursion depth exceeded
+ File "<stdin>", line 1, in <module>
+ File "/sw/spack-levante/mambaforge-22.9.0-2-Linux-x86_64-kptncg/lib/python3.10/site-packages/xarray/backends/api.py", line 525, in open_dataset
+ backend_ds = backend.open_dataset(
+ File "/sw/spack-levante/mambaforge-22.9.0-2-Linux-x86_64-kptncg/lib/python3.10/site-packages/xarray/backends/netCDF4_.py", line 588, in open_dataset
+ store = NetCDF4DataStore.open(
+ File "/sw/spack-levante/mambaforge-22.9.0-2-Linux-x86_64-kptncg/lib/python3.10/site-packages/xarray/backends/netCDF4_.py", line 389, in open
+ return cls(manager, group=group, mode=mode, lock=lock, autoclose=autoclose)
+ File "/sw/spack-levante/mambaforge-22.9.0-2-Linux-x86_64-kptncg/lib/python3.10/site-packages/xarray/backends/netCDF4_.py", line 336, in __init__
+ self.format = self.ds.data_model
+ File "/sw/spack-levante/mambaforge-22.9.0-2-Linux-x86_64-kptncg/lib/python3.10/site-packages/xarray/backends/netCDF4_.py", line 398, in ds
+ return self._acquire()
+ File "/sw/spack-levante/mambaforge-22.9.0-2-Linux-x86_64-kptncg/lib/python3.10/site-packages/xarray/backends/netCDF4_.py", line 392, in _acquire
+ with self._manager.acquire_context(needs_lock) as root:
+ File "/sw/spack-levante/mambaforge-22.9.0-2-Linux-x86_64-kptncg/lib/python3.10/contextlib.py", line 135, in __enter__
+ return next(self.gen)
+ File "/sw/spack-levante/mambaforge-22.9.0-2-Linux-x86_64-kptncg/lib/python3.10/site-packages/xarray/backends/file_manager.py", line 198, in acquire_context
+ file, cached = self._acquire_with_cache_info(needs_lock)
+ File "/sw/spack-levante/mambaforge-22.9.0-2-Linux-x86_64-kptncg/lib/python3.10/site-packages/xarray/backends/file_manager.py", line 216, in _acquire_with_cache_info
+ file = self._opener(*self._args, **kwargs)
+ File "src/netCDF4/_netCDF4.pyx", line 2353, in netCDF4._netCDF4.Dataset.__init__
+ File "src/netCDF4/_netCDF4.pyx", line 1963, in netCDF4._netCDF4._ensure_nc_success
+FileNotFoundError: [Errno 2] No such file or directory: b'/scrattch/k/k202134/test.nc'
```
-<!--
-issues in line 9 and 13
--->
-
-:::
-
-::::::::
-
-
## Hands-On! (5-10min) {.handson}
1. What are the actual issues in the code from the previous slide based on the error messages?
@@ -101,19 +91,11 @@ issues in line 9 and 13
## Fixing run-time errors
- Produce sensible debug messages to determine code area with the issue
- - Use proper compiler flags for debug output
+ - Use proper flags for debug output
- Check prerequisites/environment
- Create minimal working example
- Use debugger
-
-## Prevent errors
-
- - Testing!
- - Using linters (static code analysis) like [ruff](https://github.com/astral-sh/ruff) for Python
- - Even ensure proper formatting with tools like [black](https://github.com/psf/black) for Python
- - Consider using an IDE with its tools
-
# Errors due to data access and communication
--
GitLab