simple python call with stack trace

to be continued...

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