diff --git a/_quarto.yml b/_quarto.yml
index f0fbb58e4abfb671b2c26cce5744483b73b37880..a196151a9b7a993f8fee7f03566c53ca8acbbea8 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -31,7 +31,7 @@ website:
- "lectures/programming-paradigms/slides.qmd"
- "lectures/data-structures/slides.qmd"
- "lectures/complexity/slides.qmd"
- # - "lectures/debugging/slides.qmd"
+ - "lectures/debugging-strategies/slides.qmd"
# - "lectures/good-scientific-practice/slides.qmd"
# - "lectures/user-experience/slides.qmd"
# - "lectures/testing/slides.qmd"
@@ -47,7 +47,7 @@ website:
- "exercises/programming_paradigms.qmd"
- "exercises/data_structures.qmd"
- "exercises/complexity.qmd"
- # - "exercises/debugging.qmd"
+ - "exercises/debugging-strategies.qmd"
# - "exercises/good_scientific_practice.qmd"
# - "exercises/user_experience.qmd"
# - "exercises/testing.qmd"
diff --git a/exercises/debugging-strategies.qmd b/exercises/debugging-strategies.qmd
new file mode 100644
index 0000000000000000000000000000000000000000..0b62253b8997a46650234ac4dcd71a5785e71723
--- /dev/null
+++ b/exercises/debugging-strategies.qmd
@@ -0,0 +1,45 @@
+---
+title: "Debugging strategies"
+---
+
+### 1. Approach on locating Python bugs
+
+_The tasks should be done using the test repository <https://github.com/gweis/isodate>,
+specifically commit 8856fdf0 (HEAD of `master` branch at the moment of writing this)._
+
+_It is a Python library to parse date and times according to the ISO 8601 standard.
+Although it works great in many use cases, there are some documented bugs in the code.
+But the linked repository was not chosen to cast a bad light on it in any way.
+In fact, it does a good job providing tests and stating which problems still occur in the code._
+
+**Tasks**
+
+1. Check out the code and run the test suite. This can typically be done by issueing
+`python -m unittest` in the `src/isodate` directory (not within the `tests` directory).
+You should find that it reports two failures and one error.
+Document the actual output stating that.
+
+2. Pick one of the three issues and investigate it. Narrow down the code area, where the issue occurs.
+Document your strategy of narrowing it down step by step.
+**This task is NOT about fixing any of the issues^[You can try, if you want. But this is NOT part of the homework]!**
+
+
+### 2. Approach on locating Fortran bugs
+
+For this exercise, check out the Fortran code [schnecke_flt.f90](../lectures/debugging-strategies/static/schnecke_flt.f90).
+You can compile it on Levante e.g. by loading GCC 11.2.0 compilers with
+
+```bash
+module load gcc/11.2.0-gcc-11.2.0
+```
+
+and then run
+
+```bash
+gfortran schnecke_flt.f90
+```
+
+**Task**
+
+- Use additional compiler flags and `gdb` to locate the error. Document your approach.
+
diff --git a/lectures/custom.scss b/lectures/custom.scss
index d09613149e5861343d7041a189a8708b98d5eae2..31184f94364a323c47038e59f9a522abdf33e52b 100644
--- a/lectures/custom.scss
+++ b/lectures/custom.scss
@@ -95,7 +95,7 @@ kbd, .kbd {
background-position: right top;
}
-.sourceCode > pre.fortran > code.fortran {
+.sourceCode > pre.fortranfree > code.fortranfree {
background: url('data:image/png;base64,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');
background-repeat: no-repeat;
background-attachment: fixed;
diff --git a/lectures/debugging-strategies/slides.qmd b/lectures/debugging-strategies/slides.qmd
new file mode 100644
index 0000000000000000000000000000000000000000..ada31330097fcf7f4a113042004e6ee78f476fbd
--- /dev/null
+++ b/lectures/debugging-strategies/slides.qmd
@@ -0,0 +1,880 @@
+---
+title: "Debugging Strategies"
+author: "Dominik Zobel and René Redler"
+---
+
+# Debugging vs. Testing {.leftalign}
+
+**Testing:** Cover as many use cases as possible to make a program more robust
+
+**Debugging:** Identify issue(s) and fix a broken program
+
+
+## Different kind of errors
+
+```{dot}
+digraph {
+ node [ shape="box" ];
+
+ compile_ask [ label="Compile program\nSuccessfull?", shape="invhouse", style="filled", fillcolor="#ccccff" ];
+ compile_fail [ label="Fix compile-time error(s)" ];
+ compile_ok [ label="Run it!\nDid everything\nwork as intended?", shape="hexagon", style="filled", fillcolor="#dddddd" ];
+ run_fail [ label="Fix run-time error(s)" ];
+ run_ok [ label="Great!", shape="house", style="filled", fillcolor="#ccccff" ];
+
+ compile_ask -> compile_fail [ label="no", color="#ff0000", fontcolor="#ff0000" ];
+ compile_ask -> compile_ok [ label="yes", color="#32dd32", fontcolor="#32dd32" ];
+ compile_ok -> run_fail [ label="no", color="#ff0000", fontcolor="#ff0000" ];
+ compile_ok -> run_ok [ label="yes", color="#32dd32", fontcolor="#32dd32" ];
+}
+```
+
+## Strategies covered in this lecture
+
+ - Understand compiler usage and messages
+ - Include debug output/logging mechanisms
+ - Narrow down the code where the error occured (divide and conquer)
+ - Use a debugger
+
+
+## Other strategies
+
+ - 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
+
+
+
+# Compile-time errors {.leftalign}
+
+ - Make the compiler say what you need to know
+ - Learn to understand what the compiler tries to tell you
+
+
+## GCC C++ compiler examples {auto-animate=true}
+
+::::::::{.columns}
+
+:::{.column width=45%}
+
+```cpp
+int main() {
+ return 0
+}
+
+
+
+
+
+```
+
+Compiling with
+
+`gcc test.cpp -o test`
+
+:::
+
+:::{.column width=55% .smaller}
+
+
+```
+test.cpp: In function ‘int main()’:
+test.cpp:2:12: error: expected ‘;’ before ‘}’ token
+ 2 | return 0
+ | ^
+ | ;
+ 3 | }
+ | ~
+
+
+
+
+
+
+
+
+
+
+
+
+
+```
+
+:::
+
+::::::::
+
+
+## GCC C++ compiler examples {auto-animate=true}
+
+::::::::{.columns}
+
+:::{.column width=45%}
+
+```cpp
+int main() {
+ using namespace std;
+ cout << "Hello" << endl;
+ return 0;
+}
+
+
+
+```
+
+Compiling with
+
+`gcc test.cpp -o test`
+
+:::
+
+:::{.column width=55% .smaller}
+
+
+```
+test.cpp: In function ‘int main()’:
+test.cpp:3:4: error: ‘cout’ was not declared in this scope
+ 3 | cout << "Hello" << endl;
+ | ^~~~
+test.cpp:1:1: note: ‘std::cout’ is defined in header ‘<iostream>’; did you forget to ‘#include <iostream>’?
+ +++ |+#include <iostream>
+ 1 | int main() {
+test.cpp:3:23: error: ‘endl’ was not declared in this scope
+ 3 | cout << "Hello" << endl;
+ | ^~~~
+test.cpp:1:1: note: ‘std::endl’ is defined in header ‘<ostream>’; did you forget to ‘#include <ostream>’?
+ +++ |+#include <ostream>
+ 1 | int main() {
+
+
+
+
+
+
+```
+
+:::
+
+::::::::
+
+
+## GCC C++ compiler examples {auto-animate=true}
+
+::::::::{.columns}
+
+:::{.column width=45%}
+
+```cpp
+#include <iostream>
+
+int main {
+ using namespace std;
+ cout << "Hello" << endl;
+ return 0;
+}
+```
+
+Compiling with
+
+`gcc test.cpp -o test`
+
+:::
+
+:::{.column width=55% .smaller}
+
+
+```
+test.cpp:3:5: error: cannot declare ‘::main’ to be a global variable
+ 3 | int main {
+ | ^~~~
+test.cpp:4:4: error: expected primary-expression before ‘using’
+ 4 | using namespace std;
+ | ^~~~~
+test.cpp:4:4: error: expected ‘}’ before ‘using’
+test.cpp:3:10: note: to match this ‘{’
+ 3 | int main {
+ | ^
+test.cpp:5:4: error: ‘cout’ does not name a type
+ 5 | cout << "Hello" << endl;
+ | ^~~~
+test.cpp:6:4: error: expected unqualified-id before ‘return’
+ 6 | return 0;
+ | ^~~~~~
+test.cpp:7:1: error: expected declaration before ‘}’ token
+ 7 | }
+ | ^
+```
+
+:::
+
+::::::::
+
+
+## GCC C++ compiler examples {auto-animate=true}
+
+::::::::{.columns}
+
+:::{.column width=45%}
+
+```cpp
+#include <iostream>
+
+int main() {
+ using namespace std;
+ cout << "Hello" << endl;
+ return 0;
+}
+```
+
+Compiling with
+
+`gcc test.cpp -o test`
+
+:::
+
+:::{.column width=55% .smaller}
+
+
+```
+/usr/bin/ld: /tmp/ccrbNm7k.o: warning: relocation against `_ZSt4cout' in read-only section `.text'
+/usr/bin/ld: /tmp/ccrbNm7k.o: in function `main':
+test.cpp:(.text+0x15): undefined reference to `std::cout'
+/usr/bin/ld: test.cpp:(.text+0x1d): undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::operator<< <std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*)'
+/usr/bin/ld: test.cpp:(.text+0x24): undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::endl<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&)'
+/usr/bin/ld: test.cpp:(.text+0x2f): undefined reference to `std::ostream::operator<<(std::ostream& (*)(std::ostream&))'
+/usr/bin/ld: /tmp/ccrbNm7k.o: in function `__static_initialization_and_destruction_0(int, int)':
+test.cpp:(.text+0x66): undefined reference to `std::ios_base::Init::Init()'
+/usr/bin/ld: test.cpp:(.text+0x81): undefined reference to `std::ios_base::Init::~Init()'
+/usr/bin/ld: warning: creating DT_TEXTREL in a PIE
+collect2: error: ld returned 1 exit status
+```
+
+:::
+
+::::::::
+
+
+## GCC C++ compiler examples {auto-animate=true}
+
+::::::::{.columns}
+
+:::{.column width=45%}
+
+```cpp
+#include <iostream>
+
+int main() {
+ using namespace std;
+ cout << "Hello" << endl;
+ return 0;
+}
+```
+
+Compiling with
+
+`g++ test.cpp -o test`
+
+:::
+
+:::{.column width=55% .smaller}
+
+
+Compilation succeeded
+
+:::
+
+::::::::
+
+
+
+## Remarks
+
+ - The issue is always at or before the first error
+ - Most compilers give good feedback by default
+
+
+
+## Compiler flags for compilation output {.leftalign}
+
+_Setting compiler flags for compiled languages like Fortran and C_
+
+Check the manuals
+
+ - [GCC manuals](https://gcc.gnu.org/onlinedocs/)
+ - [Intel Fortran compiler options](https://www.intel.com/content/www/us/en/docs/fortran-compiler/developer-guide-reference/2024-1/compiler-options-001.html)
+
+Also gcc compile time checks and options like
+
+ - `-Wall` and
+ - `-Wextra`
+
+
+
+# Run-time errors {.leftalign}
+
+ - Let the compiler help you if something goes wrong
+ - Understand where to look for issues
+
+
+
+## Look out for compiler warnings {.leftalign auto-animate=true}
+
+::::::::{.columns}
+
+:::{.column width=48%}
+
+```c
+#include <stdlib.h>
+
+int main() {
+ int number = 1;
+ int* ptr;
+ ptr = &number;
+
+ free(ptr);
+ // ERROR: Trying to free
+ // memory from stack
+
+ return 0;
+}
+```
+
+Compiling with
+
+`gcc inv_ptr.c -o inv_ptr`
+
+:::
+
+:::{.column width=52% .fragment}
+
+Compiler output
+
+```
+inv_ptr.c: In function ‘main’:
+inv_ptr.c:8:4: warning: ‘free’ called on unallocated object ‘number’ [-Wfree-nonheap-object]
+ 8 | free(ptr);
+ | ^~~~~~~~~
+inv_ptr.c:4:8: note: declared here
+ 4 | int number = 1;
+ | ^~~~~~
+```
+
+Run output e.g.
+
+```
+Segmentation fault
+```
+
+:::
+
+::::::::
+
+
+## Look out for compiler warnings {.leftalign auto-animate=true}
+
+::::::::{.columns}
+
+:::{.column width=48%}
+
+```c
+#include <stdlib.h>
+
+int main() {
+ int number = 1;
+ int* ptr;
+ ptr = &number;
+
+ free(ptr);
+ // ERROR: Trying to free
+ // memory from stack
+
+ return 0;
+}
+```
+
+Compiling with
+
+`gcc inv_ptr.c -Werror -o inv_ptr`
+
+:::
+
+:::{.column width=52%}
+
+Compiler output
+
+```
+inv_ptr.c: In function ‘main’:
+inv_ptr.c:8:4: error: ‘free’ called on unallocated object ‘number’ [-Werror=free-nonheap-object]
+ 8 | free(ptr);
+ | ^~~~~~~~~
+inv_ptr.c:4:8: note: declared here
+ 4 | int number = 1;
+ | ^~~~~~
+cc1: all warnings being treated as errors
+```
+
+:::
+
+::::::::
+
+
+
+## Compiler flags for run-time output (1/2) {.leftalign}
+
+_Setting compiler flags for compiled languages like Fortran and C_
+
+Typically using `-g` for Intel, GCC and many other compilers
+
+In the Fortran world, also
+
+- gfortran: `-fbacktrace`, `-fbounds-check`
+- intel (ifort): `-traceback`, `-check bounds`, `-check all`
+
+
+## Compiler flags for run-time output (2/2) {.leftalign}
+
+Try with more than just one compiler
+
+$\Rightarrow$ HPC systems usally provide native compiler plus gcc/gfortan. Try both variants.
+
+
+
+## Locating the right error message {.leftalign}
+
+::::::::{.columns .smaller}
+
+:::{.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:
+
+```
+6543210
+```
+
+:::
+
+:::{.column width=50% .fragment}
+
+
+Actual output (last 17 lines)
+
+```
+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
+
+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
+```
+
+<!--
+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?
+2. How to rectify them?
+
+
+## Fixing run-time errors
+
+ - Produce sensible debug messages to determine code area with the issue
+ - Use proper compiler 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
+
+## Accessing data {.leftalign}
+
+ - Data has to be available and accessible
+ - Typical errors are out-of-bounds accesses
+ (resulting in a segmentation fault in languages like C)
+ - Usually manual checks are needed
+
+
+## Postprocessing example (1/4)
+
+ - Extract data from netCDF file and calculate interpolation weights
+ - Python script located [here](static/postprocessing_example.py), netCDF file [here](static/vmro3_input4MIPs_ozone_1850-1855_rev.nc)
+ - Works for the active time stamps, but not for the ones in the comment
+
+```python{.python startFrom="46"}
+filename = 'vmro3_input4MIPs_ozone_1850-1855_rev.nc'
+timestamp_start = '1851-01-01T00:00:00.000' # '1850-01-01T00:00:00.000'
+timestamp_end = '1851-03-31T00:00:00.000' # '1850-03-31T00:00:00.000'
+timestep_days = 10
+
+Calculate_Weights(filename, timestamp_start, timestamp_end, timestep_days)
+```
+
+
+## Postprocessing example (2/4)
+
+:::{.smaller}
+
+```{.python startFrom="23"}
+def Calculate_Weights(filename, timestamp_start, timestamp_end, timestep_days):
+ start_date, end_date, timestep = Get_Time_Objects(
+ timestamp_start=timestamp_start, timestamp_end=timestamp_end,
+ timestep_days=10)
+
+ ds = Open_File(filename=filename)
+
+ model_date = start_date
+ while ( model_date < end_date ):
+ o3_prev_date = Select_Date(ds=ds, model_date=model_date, method='ffill')
+ o3_next_date = Select_Date(ds=ds, model_date=model_date, method='bfill')
+
+ if ( o3_next_date == o3_prev_date ):
+ prev_weight = 0.5
+ else :
+ delta_step_sec = (o3_next_date - o3_prev_date).total_seconds()
+ delta_sec = (model_date - o3_prev_date).total_seconds()
+ prev_weight = 1.0 - delta_sec/delta_step_sec
+
+ next_weight = 1.0 - prev_weight
+ print('weights for', model_date, 'are', prev_weight, 'and', next_weight)
+ model_date = model_date + timestep
+```
+
+:::
+
+
+## Postprocessing example (3/4)
+
+
+```python
+def Open_File(filename):
+ import xarray as xr
+
+ return xr.open_dataset(filename)\
+ .convert_calendar('standard', use_cftime=True)
+
+def Select_Date(ds, model_date, method):
+ import datetime as dt
+
+ ds_elem = ds.sel(time=model_date, method=method)
+ return dt.datetime.strptime(str(ds_elem['time'].values),
+ '%Y-%m-%d %H:%M:%S')
+```
+
+<!--
+```python
+def Select_Date(ds, model_date, method='ffill'):
+ import datetime as dt
+
+ if ( model_date < dt.datetime(1850, 1, 16, 12, 0, 0) ) \
+ or ( model_date > dt.datetime(1854, 12, 31, 12, 0, 0) ):
+ ds_elem = ds.sel(time=model_date, method='nearest')
+ else :
+ ds_elem = ds.sel(time=model_date, method=method)
+
+ return dt.datetime.strptime(str(ds_elem['time'].values),
+ '%Y-%m-%d %H:%M:%S')
+```
+-->
+
+
+## Postprocessing example (4/4)
+
+
+```{.python startFrom="14"}
+def Get_Time_Objects(timestamp_start, timestamp_end, timestep_days):
+ import datetime as dt
+
+ time_format = '%Y-%m-%dT%H:%M:%S.%f'
+ start_date = dt.datetime.strptime(timestamp_start, time_format)
+ end_date = dt.datetime.strptime(timestamp_end, time_format)
+ timestep = dt.timedelta(days=timestep_days)
+ return [start_date, end_date, timestep]
+```
+
+
+## Hands-On! (~15min) {.handson}
+
+1. Which command in the code causes the problem?
+2. Describe what would you need to do?
+ (you can inspect the data e.g. with `print(ds['time'])`
+ or in your terminal with `cdo infon <file>.nc`)
+
+<!--
+```
+ncdump -h
+```
+-->
+
+## Parallel programs
+
+Possible issues due to mishandled communication or data access
+
+ - "Just" wrong results
+ - Deadlock
+ - Race conditions
+
+
+## Remarks {.leftalign}
+
+If you found a bug in someone's code:
+
+ - Communicate with the developer(s)
+ - Try to write a reproducer
+
+If you also managed to solve the bug
+
+ - Share your solution (developers, colleagues, support)
+ - Write a test for it
+
+
+
+# Debugging broken code
+
+## Logging (1/2)
+
+_Make debugging easier with proper logging_
+
+ - Very minimal logger for Python
+
+```Python
+import logging
+
+logging.warning('Example warning message')
+logging.error('Example error message')
+```
+
+## Logging (2/2) {.leftalign}
+
+Optionally: Adjust the logger to your needs
+
+ - Set output parameters
+ - Set log level and formatting
+
+Example:
+
+```python
+logging.basicConfig(filename='output.log', level=logging.WARNING,
+ datefmt='%H:%M:%S', format='[%(asctime)s] %(levelname)-8s in ' \
+ + '%(pathname)s:%(lineno)d %(message)s')
+```
+
+
+## Hands-On! (~10min) {.handson .leftalign}
+
+Use the Python code for the Postprocessing example and add logging output at appropriate points.
+Afterwards your code should log
+
+ - if a file is opened and which,
+ - what date is being processed, and
+ - the calculated weights.
+
+
+## Using debuggers {.leftalign}
+
+::::::::{.columns}
+
+:::{.column width=50%}
+
+Idea of debuggers:
+
+ - Investigate code before/at the issue interactively
+ - Set breakpoints to check actual values at specific code positions
+
+:::
+
+:::{.column width=50%}
+
+Some debuggers:
+
+ - `pdb` (Python debugger)
+ - `gdb` (GNU debugger)
+ - commercial debuggers (like `ddt` on Levante, see also [Tech Talk](https://www.youtube.com/watch?v=q-JTpxsT0wA))
+
+:::
+
+::::::::
+
+
+_Debuggers can also be used in IDEs and JupyterHub_
+
+
+
+## gdb {.leftalign}
+
+Using gdb to inspect a core dump
+
+ - to get a core dump
+
+```bash
+ulimit -c unlimited
+a.out
+```
+
+:::{.smaller}
+
+For core dumps, also `man 5 core`
+
+:::
+
+ - to inspect the `core` dump
+
+```bash
+gdb a.out core
+```
+
+
+## gdb example
+
+
+::::::::{.columns .smaller}
+
+:::{.column width=50%}
+
+```fortranfree
+program loop_count_2d
+ implicit none
+ integer, parameter :: leni = 3
+ integer, parameter :: lenj = 5
+ integer, parameter :: len = leni*leni
+ ! ERROR: leni used twice for len
+
+ integer :: my_ij(2,len)
+ integer :: i, j, n, ii, jj
+
+ n = 0
+ do j = 1, lenj
+ do i = 1, leni
+ n = n+1
+ my_ij(1,n) = i
+ my_ij(2,n) = j
+ enddo
+ enddo
+```
+
+:::
+
+:::{.column width=50%}
+
+```{.fortranfree startFrom="20"}
+ do n = 1, len
+ jj = ( n - 1) / leni + 1
+ ii = n - (jj-1) * leni
+
+ if ( ii /= my_ij(1,n) ) then
+ print *, ' wrong i ', n, &
+ ii, my_ij(1,n)
+ end if
+
+ if ( jj /= my_ij(2,n) ) then
+ print *, ' wrong j ', n, &
+ jj, my_ij(2,n)
+ end if
+ enddo
+end program loop_count_2d
+```
+
+:::
+
+::::::::
+
+
+## Some gdb Commands
+
+::::::::{.columns .smaller}
+
+:::{.column width=50%}
+
+ - `b <line>`: Add breakpoint at given line number
+ - `info b`: Show current breakpoints
+ - `clear`: Clear current breakpoint
+ - `d`: Clear all breakpoints
+ - `run`: Run the program
+ - `l`: Print code
+ - `info locals`: Print value of local variables
+
+:::
+
+:::{.column width=50%}
+
+ - `p <var>`: Print value of variable
+ - `up`, `down` or `frame <num>`: Navigate stack
+ - `n`: Next line (without descending)
+ - `step`: Next command
+ - `h`: Show help
+ - `bt`: Create backtrace
+ - `c`: Continue execution
+ - `q`: Quit gdb
+
+:::
+
+::::::::
+
+
+## gdb Live Demo
+
+
+# Debugging Flowchart
+
+::::::::{.columns}
+
+:::{.column width=35%}
+
+[](static/debug-flow.png)
+
+:::
+
+:::{.column width=60%}
+
+ - Click on flowchart to enlarge
+ - Intended as a guideline, not strict rule
+
+:::
+
+::::::::
+
+
diff --git a/lectures/debugging-strategies/static/debug-flow.dot b/lectures/debugging-strategies/static/debug-flow.dot
new file mode 100644
index 0000000000000000000000000000000000000000..74300618d7f3ed481a8d885f08f19aeceaeb1bc7
--- /dev/null
+++ b/lectures/debugging-strategies/static/debug-flow.dot
@@ -0,0 +1,99 @@
+digraph {
+ node [ shape="box" ];
+
+ compile_stmt [ label="Compile program", shape="invhouse", style="filled", fillcolor="#ccccff" ];
+ compile_ask [ label="Compilation\nsuccessfull?", shape="hexagon", style="filled", fillcolor="#dddddd" ];
+ compile_fail [ label="Locate first\nerror message" ];
+ compile_ok [ label="Nice! Try running\nthe program" ];
+
+ compile_stmt -> compile_ask;
+ compile_ask -> compile_ok [ label="yes", color="#32dd32", fontcolor="#32dd32" ];
+ compile_ask -> compile_fail [ label="no", color="#ff0000", fontcolor="#ff0000" ];
+
+ run_ask [ label="Did everything\nwork as intended?", shape="hexagon", style="filled", fillcolor="#dddddd" ];
+ run_ok [ label="Great! That's how\nthings should be", shape="house", style="filled", fillcolor="#ccccff" ];
+ run_fail [ label="Was there an error\nmessage/stack trace?", shape="hexagon", style="filled", fillcolor="#dddddd" ];
+
+ compile_ok -> run_ask;
+ run_ask -> run_ok [ label="yes", color="#32dd32", fontcolor="#32dd32" ];
+ run_ask -> run_fail [ label="no", color="#ff0000", fontcolor="#ff0000" ];
+
+ fix_first_ask [ label="Do you know\nhow to fix\nthis error?", shape="hexagon", style="filled", fillcolor="#dddddd" ];
+ fix_first_ok [ label="Fix it and\nrecompile" ];
+ fix_first_fail [ label="Search online for the error\nmessage (stackoverflow, ...).\nSee if anybody has had a\nsimilar issue" ];
+
+ compile_fail -> fix_first_ask;
+ fix_first_ask -> fix_first_ok [ label="yes", color="#32dd32", fontcolor="#32dd32" ];
+ fix_first_ok -> compile_ask;
+ fix_first_ask -> fix_first_fail [ label="no", color="#ff0000", fontcolor="#ff0000" ];
+
+ online_ask [ label="Is this a known issue\nand you can apply the fix\nfor your situation?", shape="hexagon", style="filled", fillcolor="#dddddd" ];
+ online_ok [ label="Apply the fix and recompile" ];
+ online_fail [ label="Do you have read the\ndocumentation and FAQs?", shape="hexagon", style="filled", fillcolor="#dddddd" ];
+
+ fix_first_fail -> online_ask;
+ online_ask -> online_ok [ label="yes", color="#32dd32", fontcolor="#32dd32" ];
+ online_ok -> compile_ask;
+ online_ask -> online_fail [ label="no", color="#ff0000", fontcolor="#ff0000" ];
+
+ trace_ok [ label="Does it provide\nenough information\nto fix this error?", shape="hexagon", style="filled", fillcolor="#dddddd" ];
+ trace_fail [ label="Recompile program with\nproper debugging support\nand rerun it" ];
+
+ run_fail -> trace_ok [ label="yes", color="#32dd32", fontcolor="#32dd32" ];
+ run_fail -> trace_fail [ label="no", color="#ff0000", fontcolor="#ff0000" ];
+ trace_fail -> compile_ask;
+
+ docread_ok [ label="Try running a simpler\nversion of that program\n(deactivate components,\ncomment out code) or\nincrease output verbosity" ];
+ docread_fail [ label="Locate documentation\nand FAQ of this program\n(and for machine/site if needed)" ];
+
+ online_fail -> doc_fail [ label="yes", color="#32dd32", fontcolor="#32dd32" ];
+ online_fail -> docread_fail [ label="no", color="#ff0000", fontcolor="#ff0000" ];
+
+ doc_ask [ label="Do you see\ndifferences which\nmight be related\nto this error?", shape="hexagon", style="filled", fillcolor="#dddddd" ];
+ doc_ok [ label="Follow closer\nto the official\ndocumentation and\nrecompile" ];
+ doc_fail [ label="Ask your colleagues or\nworking group if anybody\nknows about that issue" ];
+
+ docread_fail -> doc_ask;
+ doc_ask -> doc_ok [ label="yes", color="#32dd32", fontcolor="#32dd32" ];
+ doc_ok -> compile_ask;
+ doc_ask -> doc_fail [ label="no", color="#ff0000", fontcolor="#ff0000" ];
+
+ cmphint_ask [ label="Are there any suggestions\nfor what to do in your\nsituation?", shape="hexagon", style="filled", fillcolor="#dddddd" ];
+ cmphint_ok [ label="Try to adapt them\nto your situation and\nrecompile" ];
+
+ doc_fail -> cmphint_ask;
+ cmphint_ask -> cmphint_ok [ label="yes", color="#32dd32", fontcolor="#32dd32" ];
+ cmphint_ok -> compile_ask;
+ cmphint_ask -> docread_ok [ label="no", color="#ff0000", fontcolor="#ff0000" ];
+
+ autofix_ask [ label="Can you fix it\nby iteratively using\nthis approach?", shape="hexagon", style="filled", fillcolor="#dddddd" ];
+ autofix_ok [ label="Well done! If the issue is\nnot specific to your situation,\nconsider reporting it with\nyour solution how to fix it", shape="house", style="filled", fillcolor="#ccccff" ];
+ autofix_fail [ label="Try to create a minimal\nreproducer, i.e. a very\nsmall program which (still)\nhas the same issue" ];
+ autofix_ask -> docread_ok;
+
+ docread_ok -> autofix_ask;
+ autofix_ask -> autofix_ok [ label="yes", color="#32dd32", fontcolor="#32dd32" ];
+ autofix_ask -> autofix_fail [ label="no", color="#ff0000", fontcolor="#ff0000" ];
+
+ debug_ok [ label="Fix it and recompile/rerun" ];
+ debug_fail [ label="Use a debugger or\nincrease output verbosity\nto locate the issue" ];
+
+ trace_ok -> debug_ok [ label="yes", color="#32dd32", fontcolor="#32dd32" ];
+ debug_ok -> compile_ask;
+ trace_ok -> debug_fail [ label="no", color="#ff0000", fontcolor="#ff0000" ];
+
+ pinpoint_ask [ label="Can you pinpoint the\nissue to a specific part\nor region in the code?", shape="hexagon", style="filled", fillcolor="#dddddd" ];
+ pinpoint_ok [ label="Fix it and recompile/rerun" ];
+
+ debug_fail -> pinpoint_ask
+ pinpoint_ask -> pinpoint_ok [ label="yes", color="#32dd32", fontcolor="#32dd32" ];
+ pinpoint_ok -> compile_ask;
+ pinpoint_ask -> docread_ok [ label="no", color="#ff0000", fontcolor="#ff0000" ];
+
+ reproducer_ask [ label="Did creating the reproducer\nprovide new insights which can\nbe used to solve the issue?", shape="hexagon", style="filled", fillcolor="#dddddd" ];
+ support [ label="Gather relevant information\n(error message and log files,\nprogram version, what you tried,\nminimal reproducible expample,\ncontext and job IDs) and reach\nout for support. If supported by\nDKRZ, contact support@dkrz.de", shape="house", style="filled", fillcolor="#ccccff" ];
+
+ autofix_fail -> reproducer_ask;
+ reproducer_ask -> autofix_ok [ label="yes", color="#32dd32", fontcolor="#32dd32" ];
+ reproducer_ask -> support [ label="no", color="#ff0000", fontcolor="#ff0000" ];
+}
diff --git a/lectures/debugging-strategies/static/debug-flow.png b/lectures/debugging-strategies/static/debug-flow.png
new file mode 100644
index 0000000000000000000000000000000000000000..c0c45f2ba7e50ae5672848a76f66662e3af245e5
Binary files /dev/null and b/lectures/debugging-strategies/static/debug-flow.png differ
diff --git a/lectures/debugging-strategies/static/postprocessing_example.py b/lectures/debugging-strategies/static/postprocessing_example.py
new file mode 100644
index 0000000000000000000000000000000000000000..54700831451e2f89a9fafbbc138b0a98c7f01cb0
--- /dev/null
+++ b/lectures/debugging-strategies/static/postprocessing_example.py
@@ -0,0 +1,53 @@
+def Open_File(filename):
+ import xarray as xr
+
+ return xr.open_dataset(filename).convert_calendar("standard", use_cftime=True)
+
+
+def Select_Date(ds, model_date, method):
+ import datetime as dt
+
+ ds_elem = ds.sel(time=model_date, method=method)
+ return dt.datetime.strptime(str(ds_elem["time"].values), "%Y-%m-%d %H:%M:%S")
+
+
+def Get_Time_Objects(timestamp_start, timestamp_end, timestep_days):
+ import datetime as dt
+
+ time_format = "%Y-%m-%dT%H:%M:%S.%f"
+ start_date = dt.datetime.strptime(timestamp_start, time_format)
+ end_date = dt.datetime.strptime(timestamp_end, time_format)
+ timestep = dt.timedelta(days=timestep_days)
+ return [start_date, end_date, timestep]
+
+
+def Calculate_Weights(filename, timestamp_start, timestamp_end, timestep_days):
+ start_date, end_date, timestep = Get_Time_Objects(
+ timestamp_start=timestamp_start, timestamp_end=timestamp_end, timestep_days=10
+ )
+
+ ds = Open_File(filename=filename)
+
+ model_date = start_date
+ while model_date < end_date:
+ o3_prev_date = Select_Date(ds=ds, model_date=model_date, method="ffill")
+ o3_next_date = Select_Date(ds=ds, model_date=model_date, method="bfill")
+
+ if o3_next_date == o3_prev_date:
+ prev_weight = 0.5
+ else:
+ delta_step_sec = (o3_next_date - o3_prev_date).total_seconds()
+ delta_sec = (model_date - o3_prev_date).total_seconds()
+ prev_weight = 1.0 - delta_sec / delta_step_sec
+
+ next_weight = 1.0 - prev_weight
+ print("weights for", model_date, "are", prev_weight, "and", next_weight)
+ model_date = model_date + timestep
+
+
+filename = "vmro3_input4MIPs_ozone_1850-1855_rev.nc"
+timestamp_start = "1851-01-01T00:00:00.000" # '1850-01-01T00:00:00.000'
+timestamp_end = "1851-03-31T00:00:00.000" # '1850-03-31T00:00:00.000'
+timestep_days = 10
+
+Calculate_Weights(filename, timestamp_start, timestamp_end, timestep_days)
diff --git a/lectures/debugging-strategies/static/schnecke_flt.f90 b/lectures/debugging-strategies/static/schnecke_flt.f90
new file mode 100644
index 0000000000000000000000000000000000000000..584d56f7eacbed6ccd63374b90ee172fed231d19
--- /dev/null
+++ b/lectures/debugging-strategies/static/schnecke_flt.f90
@@ -0,0 +1,211 @@
+program schnecke
+
+ ! The code flags 42 pairs of (i,j) indices as True
+ ! and relocates these in a larger domain by starting
+ ! at index (is,js)
+
+
+ implicit none
+
+ Integer, parameter :: m = 1
+ Integer, parameter :: idim = 128
+ Integer, parameter :: jdim = 64
+
+ Type memo
+ Integer :: i
+ Integer :: j
+ Integer :: dir
+ End Type
+
+ Integer :: i, j
+ Integer :: index, nn
+ Integer :: is, js
+
+ Integer :: stacksize
+ Integer :: current_stacksize
+
+ Integer :: nbr_cells_tot
+ Integer :: nbr_cells_inc
+
+ Type (memo), Pointer :: stack(:)
+ Type (memo), Pointer :: new_stack(:)
+
+ Integer :: nbr_cells(m)
+
+ Integer, Pointer :: tmp_neighcells_3d(:,:)
+ Integer, Pointer :: new_neighcells_3d(:,:)
+
+ Logical :: cyclic(2)
+
+ Logical :: flagged(idim,jdim)
+ Integer :: visited(idim,jdim)
+
+ Integer :: direction(2,4)
+
+ data direction / -1, 0, 0, -1, 1, 0, 0, 1 /
+
+!
+! Initialise variables for test case
+!-----------------------------------
+
+ cyclic = .false.
+
+ current_stacksize = 0
+
+ flagged = .false.
+
+ do j = 45, 50
+ do i = 30, 36
+ flagged(i,j) = .true.
+ enddo
+ enddo
+
+ is = 34
+ js = 48
+!
+! ----------------------------------
+!
+ stacksize = 4
+ nbr_cells_inc = 4
+ nbr_cells_tot = nbr_cells_inc
+
+ allocate(stack(stacksize))
+
+ allocate(tmp_neighcells_3d(2,nbr_cells_tot))
+
+ visited = 0
+ nbr_cells = 0
+
+ !
+ ! Initialise first stack entry
+ !
+ index = 1
+ stack(index)%i = is
+ stack(index)%j = js
+ stack(index)%dir = 0
+ !
+ ! ... maybe we should test first whether our initial guess is really good
+ !
+ visited(is,js) = m
+
+ nn = 1
+
+ tmp_neighcells_3d(1,nn) = stack(index)%i
+ tmp_neighcells_3d(2,nn) = stack(index)%j
+
+ nbr_cells(1) = 1
+ !
+ ! Andreas Algorithmus
+ !
+ do while ( index > 0 )
+ !
+ ! Change direction
+ !
+ stack(index)%dir = stack(index)%dir + 1
+
+ if ( stack(index)%dir > 4 ) then
+ !
+ ! All 4 directions are already tested
+ ! for this cell so we have to go back
+ !
+ index = index - 1
+ cycle
+ endif
+ !
+ ! Go to the next cell
+ !
+ is = stack(index)%i + direction(1,stack(index)%dir)
+ js = stack(index)%j + direction(2,stack(index)%dir)
+ !
+ ! Apply cyclic boundary conditions if required
+ !
+ if ( cyclic(1) ) is = mod(is-1,idim)+1
+ if ( cyclic(2) ) js = mod(js-1,jdim)+1
+ !
+ ! Check that indices are in the allowed range
+ !
+ if ( is < 1 .or. is > idim ) cycle
+ if ( js < 1 .or. js > jdim ) cycle
+ !
+ ! When cell is already checked for this target ...
+ !
+ if ( visited(is,js) == m ) cycle
+ !
+ ! Test current cell
+ !
+ if ( .not. flagged(is,js) ) then
+ !
+ ! Mark cell as checked for this cycle
+ !
+ visited(is,js) = m
+ cycle
+
+ else
+ !
+ ! We found a new source cell
+ !
+ nbr_cells(m) = nbr_cells(m) + 1
+ !
+ ! ... allocate new memory if necessary
+ !
+ if ( nn + 1 > nbr_cells_tot ) then
+ nbr_cells_tot = nbr_cells_tot + nbr_cells_inc
+ allocate(new_neighcells_3d(2,nbr_cells_tot))
+ new_neighcells_3d(1:2,1:nn) = tmp_neighcells_3d(1:2,1:nn)
+ deallocate(tmp_neighcells_3d)
+ tmp_neighcells_3d => new_neighcells_3d
+ endif
+
+ nn = nn + 1
+
+ tmp_neighcells_3d(1,nn) = is
+ tmp_neighcells_3d(2,nn) = js
+ !
+ ! Prepare for the next source cell to test
+ !
+ ! ... allocate new memory for the stack if necessary
+ !
+ if ( index + 1 > current_stacksize ) then
+ current_stacksize = stacksize
+ allocate(new_stack(current_stacksize))
+ new_stack(1:index) = stack(1:index)
+ deallocate(stack)
+ stack => new_stack
+ endif
+
+ index = index + 1
+ stack(index)%i = is
+ stack(index)%j = js
+ stack(index)%dir = 0
+
+ visited(is,js) = m
+
+ endif
+
+ enddo
+ !
+ ! Finally shrink tmp_neighcells_3d to required size
+ !
+ if ( nn < nbr_cells_tot ) then
+ nbr_cells_tot = nn
+ allocate(new_neighcells_3d(2,nbr_cells_tot))
+ new_neighcells_3d(1:2,1:nn) = tmp_neighcells_3d(1:2,1:nn)
+ deallocate(tmp_neighcells_3d)
+ tmp_neighcells_3d => new_neighcells_3d
+ endif
+ !
+ ! Test
+ !
+ do i = 1, nbr_cells_tot
+ if ( tmp_neighcells_3d(2,i) < 45 .or. tmp_neighcells_3d(2,i) > 50 .or. &
+ tmp_neighcells_3d(1,i) < 30 .or. tmp_neighcells_3d(1,i) > 36 ) then
+ print *, 'WARNING at i ', i, tmp_neighcells_3d(1,i), tmp_neighcells_3d(2,i)
+ endif
+ print *, ' Found ', tmp_neighcells_3d(1,i), tmp_neighcells_3d(2,i)
+ enddo
+
+ print *, ' Found ', nbr_cells, ' cells.'
+
+end program schnecke
+
+
diff --git a/lectures/debugging-strategies/static/vmro3_input4MIPs_ozone_1850-1855_rev.nc b/lectures/debugging-strategies/static/vmro3_input4MIPs_ozone_1850-1855_rev.nc
new file mode 100644
index 0000000000000000000000000000000000000000..b102115868e3b14a465796935fb8d74ac573921e
Binary files /dev/null and b/lectures/debugging-strategies/static/vmro3_input4MIPs_ozone_1850-1855_rev.nc differ