C2110 UNIX and programming Lesson 8 / Module 2 -1C2110
UNIX and programming
Petr Kulhanek
kulhanek@chemi.muni.cz
National Center for Biomolecular Research, Faculty of Science
Masaryk University, Kamenice 5, CZ-62500 Brno
PS / 2020 Distance form of teaching: Rev2
Lesson 8 / Module 2
C2110 UNIX and programming Lesson 8 / Module 2 -2-
Troubleshooting
➢ Syntax errors
➢ Logical errors
C2110 UNIX and programming Lesson 8 / Module 2 -3Syntax
Erros
Syntax errors
• writing errors that do not match the language specification
• program cannot be translated, place of error is printed by compiler (e.g., C/C++,
Fortran)
• script cannot be run at all (e.g. ,javascript)
• when interpreter encounters an incomprehensible notation during the run of the
script, the run is terminated and the line with the error is written to the error
output, the error may manifest only under specific run conditions (e.g., bash, awk,
gnuplot)
Attention! Beginning of the error may be at
a different location than indicated by
the error message.Troubleshooting:
• syntax highlighting
• static code analyzers
C2110 UNIX and programming Lesson 8 / Module 2 -4bash
- Syntax Check
1. The basic syntax check can be performed visually in a text editor, which allows
highlighting syntax of programming language.
2. Error message:
$ bash test.sh
Zadejte pocet: 5
test.sh: line 10: unexpected EOF while looking for matching `"'
test.sh: line 16: syntax error: unexpected end of file
unterminated string
(all in red)
turn on display of line numbers
C2110 UNIX and programming Lesson 8 / Module 2 -5bash
- Static Analysis
3. Static code analyzer:
• online
• command line
https://www.shellcheck.net/
C2110 UNIX and programming Lesson 8 / Module 2 -6Logical
Errors
Logical errors
• program/script can be run, but the result does not meet expectations or is not
reproducible
• these errors are VERY hard to find/fix - it is advisable to avoid them by thorough
design of the algorithm
Causes of logical errors:
• bad algorithm design (all languages)
• work with uninitialized variables (all languages)
• work with unallocated/freed memory, writing to unallocated memory (C/C++, Fortran)
• concurrence (race condition) for parallel tasks (OpenMP, MPI, threads)
Troubleshooting:
• dynamic run analyzers (C/C++, Fortran: valgrind)
• debugging the program run using a debugger
C2110 UNIX and programming Lesson 8 / Module 2 -7debugger
- bashdb + visual code
1. Starting the editor:
$ module add vscode
$ code
2. Install the extension (only once):
https://marketplace.visualstudio.com/items?itemName=rogalmic.bash-debug
3. Runtime environment configuration (launch.json, only once):
{
// Use IntelliSense to learn about possible attributes.
// Hover to view descriptions of existing attributes.
// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
"version": "0.2.0",
"configurations": [
{
"type": "bashdb",
"request": "launch",
"name": "Bash-Debug",
"cwd": "${workspaceFolder}",
"program": "${file}",
"args": [],
"terminalKind": "integrated"
},
]
}
Practical example of configuration and use.
C2110 UNIX and programming Lesson 8 / Module 2 -8debugger
- bashdb + visual code
Values ​​of
variables
(operator: $)
Debugger
Step Over
stops
(breakpoints)
Current position
Terminal: input/output
C2110 UNIX and programming Lesson 8 / Module 2 -9Exercise
I
1. Step through the running scripts from L08.M01.E01.T03.
C2110 UNIX and programming Lesson 8 / Module 2 -10-
Installation
Installation of shellcheck and bashdb to the Ubuntu OS
C2110 UNIX and programming Lesson 8 / Module 2 -11Notes
to Installation
1. shellcheck is part of standard packages:
2. bashdb can be installed from source code (see L13.M02) or into Ubuntu 18.04 LTS
from NCBR package repository, package name: ncbr-bashdb
3. Visual Studio Code can be installed from package (.deb) or run from a binary archive
(.tar.gz). See the documentation for instructions.
https://code.visualstudio.com/
$ sudo apt-get install shellcheck
https://wolf.ncbr.muni.cz/whitezone/packages/public/18.04/
For Infinity users (C2115): bashdb and extension bashdebug
require a system command pkill which is
redefined in the Infinity environment.
Resolve the collision by running unset command before
starting the editor.
$ unset pkill