Bugs in the latest GPAW

See here: Bugs!

Handling segfaults

Segmentation faults are probably the hardest type of runtime error to track down, but they are also quite common during the unstable part of the release cycle. As a rule of thumb, if you get a segfault, start by checking that all array arguments passed from Python to C functions have the correct shapes and types.

Apart from appending --debug to the command line arguments when running python or gpaw-python, please familiarize yourself with the debugging tools for the Python and C code.

If you experience segfaults or unexplained MPI crashes when running GPAW in parallel, it is recommended to try a custom installation with a debugging flag in customize.py:

define_macros += [('GPAW_MPI_DEBUG', 1)]

Common sources of bugs

  • General:

    • Elements of NumPy arrays are C ordered, BLAS and LAPACK routines expect Fortran ordering.
  • Python:

    • Always give contiguous arrays to C functions. If x is contiguous with dtype=complex, then x.real is non-contiguous of dtype=float.

    • Giving array arguments to a function is a carte blanche to alter the data:

      def double(a):
          a *= 2
          return a
      
      x = np.ones(5)
      print(double(x))  # x[:] is now 2.
      
    • Forgetting a n += 1 statement in a for loop:

      n = 0
      for thing in things:
          thing.do_stuff(n)
          n += 1
      

      Use this instead:

      for n, thing in enumerate(things):
          thing.do_stuff(n)
      
    • Indentation errors like this one:

      if ok:
          x = 1.0
      else:
          x = 0.5
          do_stuff(x)
      

      where do_stuff(x) should have been reached in both cases. Emacs: always use C-c > and C-c < for shifting in and out blocks of code (mark the block first).

    • Don’t use mutables as default values:

      class A:
          def __init__(self, a=[]):
              self.a = a # All instances get the same list!
      
    • There are subtle differences between x == y and x is y.

    • If H is a numeric array, then H - x will subtract x from all elements - not only the diagonal, as in Matlab!

  • C:

    • Try building GPAW from scratch.
    • Typos like if (x = 0) which should have been if (x == 0).
    • Remember break in switch-case statements.
    • Check malloc-free pairs. Test for memory leaks by repeating the call many times.
    • Remember to update reference counts of Python objects.
    • Never put function calls inside assert’s. Compiling with -DNDEBUG will remove the call.