Designing Reliable Python Extensions (and Debugging)

Course materials from Scientific Computing with Python. 2002.

Transcript

1. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 1 beazley@cs.uchicago.edu Designing Reliable Python Extensions (and Debugging) David M. Beazley Department of Computer Science University of Chicago beazley@cs.uchicago.edu January 21, 2002 PY-MA
2. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 2 beazley@cs.uchicago.edu Introduction Python environment is more complicated • Scripts • Shared libraries • Extension modules Applications are more flexible • Interactive interpreter • Can call any function at any time in any order • Full access to underlying data • Dynamic problem reconfiguration. • This is exactly what you want! Most scientific programs not this flexible • Written as batch processing jobs • Very predictable control flow. • Few failure modes. • Easy to debug (maybe).
3. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 3 beazley@cs.uchicago.edu Reliability Concerns Frequent crashes • When a program is first converted, it may crash a lot • Segmentation faults, failed assertions. Wrong answers • How do you know a program gave the correct result? • Missing parameters. • Use of incompatible procedures (improper integrator, etc.) This is a serious issue • Often ignored in the scientific scripting literature
4. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 4 beazley@cs.uchicago.edu Catastrophic Failure Modes Uninitialized data • User invoked function before data was initialized. • Example: calculate forces before setting up initial condition. Bad parameters • Function called with invalid parameter value • Example: bad filename, negative number, NULL pointer. Non-reentrant functions • User called the same function twice--program crashes. • Example: function assumes uninitialized state on entry. Non-graceful error handling • Program throws an assertion or calls exit() • Python interpreter just dies. No error message. Normally these errors are hidden in batch jobs • Very predictable control-flow • Internals not exposed to user.
5. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 5 beazley@cs.uchicago.edu Incorrect Results Uninitialized data • Missing parameter specification. • Missing initialization function. Bad parameters • Function given a physically meaningless parameter. • Domain error. Data manipulation • User modified data directly from interpreter. Calling functions in wrong order • Incorrect sequence of operations in an integration loop.
6. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 6 beazley@cs.uchicago.edu Strategy Defensive programming • If it might break, assume that it will break. • Always assume that user will give bad parameters. • Always assume that functions might return a bad result. Error handling • Design a uniform mechanism for returning errors to Python. • Don’t just call exit(). • Use SWIG to help with error handling (some of this can be automated). Library design • Build error handling into libraries • Even if you have to modify the original code. • The results pay off--even when Python not used.
7. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 7 beazley@cs.uchicago.edu Programming with Assertions An error-prone function: double sqrt(double x) { double r; /* Compute sqrt */ ... return r; } With assertions double sqrt(double x) { if (x < 0) { error("sqrt: domain error"); } /* Compute sqrt */ ... if (r < 0) { error("sqrt: implementation error!"); } return r; }
8. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 8 beazley@cs.uchicago.edu Assertions Pre-assertions • Checking of function input values. • Makes sure function operates on acceptable input values. Post-assertions • Checking of function output values • Makes sure function is operating correctly. Important technique for writing reliable libraries • Borrowed from "Design by contract"
9. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 9 beazley@cs.uchicago.edu Assertions Range/value checking • Make sure a variable has a proper value. • Shown in the sqrt() example. Synchronization assertion • Make sure function A executes before function B. • Implement using some kind of synchronization variable int Async = 0; void A() { ... Async = 1; } void B() { if (!Async) error("Must call A() first"); ... } • Can make this arbitrarily complex • Technique also works for non-reentrant functions.
10. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 10 beazley@cs.uchicago.edu Checking Return Codes Always check function return codes char *ptr = malloc(8192); if (!ptr) error("malloc failed!"); FILE *f = fopen(filename,"r"); if (!f) error("Can’t open file"); An amazing source of errors • Spend 10 hours debugging only to find that you didn’t check a return code.
11. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 11 beazley@cs.uchicago.edu An Exit Strategy Always provide a bailout mechanism • Error return codes • C++ exceptions • jongjmp/setjmp Don’t want • Program to keep running in an error state • Program to exit with no error message. >>> foo() foo() bar() spam() error RuntimeError: spam: domain error >>>
12. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 12 beazley@cs.uchicago.edu Designing for Reconfiguration Initialization functions • In batch jobs, usually only called once. • In scripting, may be called many times. Dynamic program reconfiguration • User may want to change important problem parameters • Grid size. • Data distribution across processors. • Problem geometry. Techniques • Make sure an application can clean up previous simulation data • Plan for dynamic memory management. • Do not rely upon fixed sized arrays. • Be careful with memory.
13. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 13 beazley@cs.uchicago.edu Use Common Sense Add error checking where it makes sense • Functions likely to be invoked directly by user • Utility functions. • I/O and system related functions. Not in the inner loop • Low-level math operations • Functions used in performance critical operations.
14. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 14 beazley@cs.uchicago.edu Case Study Adding reliability features • This was the best modification we made to our application • Cleaned up the design. • Improved stability. • More confidence in our results. • A more user friendly environment. Our Implementation • Used setjmp/longjmp to add C exception handling • Merged with Python exception handling using SWIG. • Even added line numbers Traceback (most recent call last): File "<stdin>", line 1, in ? RuntimeError: malloc(10000000) failed (memory.c, line 52)
15. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 15 beazley@cs.uchicago.edu Panic! When all else fails: $ python myscript.py Segmentation Fault (core dumped) $ Traditional debugging is difficult • What is the application being debugged? • A script? • An extension module? • Python? Usual approach • Run Python under the debugger. $ gdb python (gdb) run myscript.py ... • Not an ideal solution. Debugging with gdb is difficult. • Gives no information about script code.
16. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 16 beazley@cs.uchicago.edu Mixed Language Debugging An open area of systems research • A little work in Java-C++ debugging. • Not much with scripting environments. WAD (Wrapped Application Debugger) • A highly experimental system I am working on • A debugger encapsulated in a shared library • Linked to extension modules $ cc -shared $(OBJS) -o foomodule.so -lwadpy How it works • Fatal process errors converted into recoverable Python exceptions • Segfaults, Bus errors, assertions, etc.
17. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 17 beazley@cs.uchicago.edu Mixed Language Debugging Fatal Extension Error with WAD $ python myscript.py Traceback (most recent call last): File "<stdin>", line 1, in ? File "myscript.py", line 16, in ? foo() File "myscript.py", line 7, in spam doh.doh(a,b,c) SegFault: [ C stack trace ] #2 0x00027774 in call_builtin(func=0x1c74f0,arg=0x1a1ccc,kw=0x0) #1 0xff022f7c in _wrap_doh(0x0,0x1a1ccc,0x160ef4,0x9c,0x56b44,0x1aa3d8) #0 0xfe7e0568 in doh(a=0x3,b=0x4,c=0x0) in 'foo.c', line 28 /u0/beazley/Projects/WAD/Python/foo.c, line 28 int doh(int a, int b, int *c) { => *c = a + b; return *c; } Caveats • Highly experimental • Not portable (i386-Linux and SPARC Solaris only). • Maybe in the future...
18. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 18 beazley@cs.uchicago.edu Summary Plan for failure • Your application is going to crash • Take a defensive approach to programming. Adding reliability features is a big win • It improves your code even if you don’t use Python • Results in extremely stable modules • Gives confidence in results. Debugging • This is the biggest weakness of the scripting approach. • Traditional debuggers work. • Some research in mixed-language debugging. However, it’s immature.
19. Libraries, Shared Libraries, and Dynamic Loading, January 21, 2002 19 beazley@cs.uchicago.edu The End? Topics not covered • Numeric Python • Plotting packages • SciPy (www.scipy.org) • Working with Fortran Resources • www.python.org (Python) • www.vex.net/parnassus (Vaults of Parnassus) • www.swig.org (SWIG) Tips • Many scientific papers and tutorials in the International Python Conference. • All available online. • IEEE Computing in Science Engineering, Computers in Physics. Open discussion