TST: bus error on sparc: pandas/hashtable.c:7282 while pandas.io.tests.test_pytables:TestHDFStore.test_encoding

[yarikoptic]

v0.11.0-492-gb204e14

test_encoding (pandas.io.tests.test_pytables.TestHDFStore) ...
Program received signal SIGBUS, Bus error.
__pyx_pf_6pandas_9hashtable_14Int64HashTable_16map_locations (__pyx_v_values=<optimized out>, __pyx_v_self=0xf7cc0900) at pandas/hashtable.c:7282
7282        __pyx_v_val = (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int64_t *, __pyx_pybuffernd_values.rcbuffer->pybuffer.buf, __pyx_t_3, __pyx_pybuffernd_values.diminfo[0].strides));
(gdb) bt
#0  __pyx_pf_6pandas_9hashtable_14Int64HashTable_16map_locations (__pyx_v_values=<optimized out>, __pyx_v_self=0xf7cc0900) at pandas/hashtable.c:7282
#1  __pyx_pw_6pandas_9hashtable_14Int64HashTable_17map_locations (__pyx_v_self=<pandas.hashtable.Int64HashTable at remote 0xf7cc0900>, __pyx_v_values=<optimized out>) at pandas/hashtable.c:7190
#2  0x0007c2f0 in PyCFunction_Call (func=<built-in method map_locations of pandas.hashtable.Int64HashTable object at remote 0xf7cc0900>, arg=(<numpy.ndarray at remote 0x145d610>,), kw=0x0)
    at ../Objects/methodobject.c:101
#3  0x00031228 in PyObject_Call (func=<built-in method map_locations of pandas.hashtable.Int64HashTable object at remote 0xf7cc0900>, arg=(<numpy.ndarray at remote 0x145d610>,), kw=0x0) at ../Objects/abstract.c:2529
#4  0xf6536a00 in __pyx_f_6pandas_5index_11IndexEngine_initialize (__pyx_v_self=0x13515f0) at pandas/index.c:4804
#5  0xf6533124 in __pyx_f_6pandas_5index_11IndexEngine__ensure_mapping_populated (__pyx_v_self=0x13515f0) at pandas/index.c:4716
#6  __pyx_pf_6pandas_5index_11IndexEngine_2__contains__ (__pyx_v_val='columns', __pyx_v_self=0x13515f0) at pandas/index.c:2502
#7  __pyx_pw_6pandas_5index_11IndexEngine_3__contains__ (__pyx_v_self=<pandas.index.Int64Engine at remote 0x13515f0>, __pyx_v_val='columns') at pandas/index.c:2471
#8  0x000329e0 in PySequence_Contains (seq=<pandas.index.Int64Engine at remote 0x13515f0>, ob='columns') at ../Objects/abstract.c:2387
#9  0x000e96bc in cmp_outcome (w=<optimized out>, v='columns', op=<optimized out>) at ../Python/ceval.c:4463
#10 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at ../Python/ceval.c:2287

(gdb) l 7270
7265        /* "pandas/hashtable.pyx":429
7266     * 
7267     *         for i in range(n):
7268     *             val = values[i]             # <<<<<<<<<<<<<<
7269     *             k = kh_put_int64(self.table, val, &ret)
7270     *             self.table.vals[k] = i
7271     */
7272        __pyx_t_3 = __pyx_v_i;
7273        __pyx_t_4 = -1;
7274        if (__pyx_t_3 < 0) {
(gdb) 
7275          __pyx_t_3 += __pyx_pybuffernd_values.diminfo[0].shape;
7276          if (unlikely(__pyx_t_3 < 0)) __pyx_t_4 = 0;
7277        } else if (unlikely(__pyx_t_3 >= __pyx_pybuffernd_values.diminfo[0].shape)) __pyx_t_4 = 0;
7278        if (unlikely(__pyx_t_4 != -1)) {
7279          __Pyx_RaiseBufferIndexError(__pyx_t_4);
7280          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
7281        }
7282        __pyx_v_val = (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int64_t *, __pyx_pybuffernd_values.rcbuffer->pybuffer.buf, __pyx_t_3, __pyx_pybuffernd_values.diminfo[0].strides));
7283    
7284        /* "pandas/hashtable.pyx":430
(gdb) 
7285     *         for i in range(n):
7286     *             val = values[i]
7287     *             k = kh_put_int64(self.table, val, &ret)             # <<<<<<<<<<<<<<
7288     *             self.table.vals[k] = i
7289     * 
7290     */
7291        __pyx_v_k = kh_put_int64(__pyx_v_self->table, __pyx_v_val, (&__pyx_v_ret));
7292    
7293        /* "pandas/hashtable.pyx":431
7294     *             val = values[i]

cython 0.19+git51-g3078752-1 (Debian build)

[jreback]

can u show versions of Numexpr and pytables
and did they install successfully ?
what python version?

[yarikoptic]

everything installed just fine AFAIK... fresh numexpr is still in NEW queue, so now it is with an elderly one -- if you suspect that it is numexpr issue, let me know -- I could try building/installing fresh numexpr/tables

(sid)yoh@vagus:~/deb/gits/fail2ban$ dpkg -l python-{numexpr,tables}; python --version
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name                                              Version                       Architecture                  Description
+++-=================================================-=============================-=============================-=======================================================================================================
ii  python-numexpr                                    2.0.1-3                       sparc                         Fast numerical array expression evaluator for Python and NumPy
ii  python-tables                                     2.3.1-3                       sparc                         hierarchical database for Python based on HDF5
Python 2.7.5+

[jreback]

can you tell me which line it broke on in the test_encoding test?

[yarikoptic]

if I traced it right

test_pytables.py(489):             result = store.select('df',Term('columns=A',encoding='ascii'))

and then around actual bus error:

internals.py(1229):         tot_items = sum(len(x.items) for x in self.blocks)

[jreback]

can you try my PR #3898, should fix/skip all of these tests ?