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thouis opened this issue Oct 19, 2012 · 4 comments
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masked array autotest fails with bus error (Trac #1094) #1692

thouis opened this issue Oct 19, 2012 · 4 comments
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00 - Bug component: numpy.ma masked arrays Priority: high High priority, also add milestones for urgent issues
Milestone
1.6.0

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@thouis
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thouis commented Oct 19, 2012

Original ticket http://projects.scipy.org/numpy/ticket/1094 on 2009-04-24 by trac user Gerard, assigned to @charris.

Running the numpy (version 1.3.0, but also occurs on 1.2.1) autotester fails on masked array test case with a bus error. Used system is Solaris 5.8:
uname -a
SunOS wsasd529 5.8 Generic_117350-18 sun4u sparc SUNW,Sun-Blade-1500

output of "numpy.test(verbose=10)":

...
Tests how masks are initialized at the creation of Maskedarrays. ... ok
Check the use of ndmin ... ok
Make sure we're not losing the original mask w/ ndmin ... ok
Tests creaating a masked array from alist of masked arrays. ... ok
test_deepcopy (test_core.TestMaskedArray) ... ok
Test printing a masked array w/ fancy dtype. ... ok
Test filled w/ flexible dtype ... Bus error

Bus error is caused by a misaligned memory write (see output of purify below):

MAW: Misaligned memory write
  This is occurring while in:
        DOUBLE_fastputmask [arraytypes.inc.src:2282]
                   s_val = *vals;
                   for (i = 0; i < ni; i++) {
                       if (mask[i]) {
        =>                 in[i] = s_val;
                       }
                   }
               }
        PyArray_PutMask [multiarraymodule.c:4687]
                       }
                   }
                   else {
        =>             func(dest, mask->data, ni, values->data, nv);
                   }
               }

        array_putmask  [multiarraymodule.c:4600]
                                                &array, &mask, &values)) {
                   return NULL;
               }
        =>     return PyArray_PutMask((PyArrayObject *)array, values, mask);
           }

           /*NUMPY_API
        PyCFunction_Call [methodobject.c:77]
        PyEval_EvalFrameEx [ceval.c:3564]
        PyEval_EvalFrameEx [ceval.c:3650]
        PyEval_EvalCodeEx [ceval.c:2831]
        PyEval_EvalFrameEx [ceval.c:3659]
        ...

Commenting the execution of the fastputmask in multiarraymodule.c (and thus running the 'slower' version already implemented there) solves the problem:

multiarraymodule.c, line 4676 (and further):

    func = self->descr->f->fastputmask;
    /*if (func == NULL) {*/
        for (i = 0; i < ni; i++) {
            tmp = ((Bool *)(mask->data))[i];
            if (tmp) {
                src = values->data + chunk*(i % nv);
                memmove(dest + i*chunk, src, chunk);
            }
        }
    /*}
    else {
        func(dest, mask->data, ni, values->data, nv);
    }*/

added here are the comment blocks such that func is not executed anymore.

'Minimal' piece of python code to reproduce:

from numpy.ma.core import *

f = array([(1,1)], dtype=[('i',int),('f',float)])

f.mask = [1,1]

f.filled()
@thouis thouis closed this as completed Oct 19, 2012
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@charris wrote on 2009-04-24

This is probably related to #1630, which came about as an attempt to fix an earlier bus error, IIRC.

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@pierregm wrote on 2009-07-18

  • As this is not a numpy.ma problem but a multiarraymodule.c one, I kick the ball in touch.

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@mwiebe wrote on 2011-03-24

STSCI run the tests on Solaris, and report the tests are passing, so closing the issue.

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Milestone changed to 1.6.0 by @mwiebe on 2011-03-24

@numpy-gitbot numpy-gitbot mentioned this issue Oct 23, 2012
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