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#1 2016-05-17 06:36:03

vivescere
Member
Registered: 2016-05-17
Posts: 1

Pytables (HDF5) error

I am currently working over a rather large project, that uses hdf5 to store data. The python code uses pytables to interact with the database, however I just does not work on my new machine (fresh install).
When i try to use the test method, I get the following :

$ python -c "import tables; tables.test()"
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version:    3.2.2
HDF5 version:        1.10.0
NumPy version:       1.11.0
Numexpr version:     2.5.2 (not using Intel's VML/MKL)
Zlib version:        1.2.8 (in Python interpreter)
LZO version:         2.09 (Feb 04 2015)
BZIP2 version:       1.0.6 (6-Sept-2010)
Blosc version:       1.4.4 (2015-05-05)
Blosc compressors:   blosclz (1.0.2.1), lz4 (1.2.0), lz4hc (1.2.0), snappy (1.1.1), zlib (1.2.8)
Python version:      3.5.1 (default, Mar  3 2016, 09:29:07) 
[GCC 5.3.0]
Platform:            Linux-4.4.10-1-MANJARO-x86_64-with-glibc2.3.4
Byte-ordering:       little
Detected cores:      4
Default encoding:    utf-8
Default FS encoding: utf-8
Default locale:      (en_US, UTF-8)
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing only a light (yet comprehensive) subset of the test suite.
If you want a more complete test, try passing the --heavy flag to this script
(or set the 'heavy' parameter in case you are using tables.test() call).
The whole suite will take more than 4 hours to complete on a relatively
modern CPU and around 512 MB of main memory.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
/usr/lib/python3.5/site-packages/tables/atom.py:570: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead
  for arg in inspect.getargspec(self.__init__)[0]
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE........EEss..*** Error in `python': malloc(): smallbin double linked list corrupted: 0x0000000003421fe0 ***
======= Backtrace: =========
/usr/lib/libc.so.6(+0x6ed4b)[0x7f36f3cf9d4b]
/usr/lib/libc.so.6(+0x74546)[0x7f36f3cff546]
/usr/lib/libc.so.6(+0x76981)[0x7f36f3d01981]
/usr/lib/libc.so.6(__libc_malloc+0x54)[0x7f36f3d031d4]
/usr/lib/libhdf5.so.100(+0x1b2339)[0x7f36f2ae6339]
/usr/lib/libhdf5.so.100(+0x1b4af0)[0x7f36f2ae8af0]
/usr/lib/libhdf5.so.100(+0x1b2d47)[0x7f36f2ae6d47]
/usr/lib/libhdf5.so.100(H5P_set+0xa2)[0x7f36f2aea3f2]
/usr/lib/libhdf5.so.100(H5Pset_cache+0xb0)[0x7f36f2addce0]
/usr/lib/python3.5/site-packages/tables/hdf5extension.cpython-35m-x86_64-linux-gnu.so(+0x28f95)[0x7f36ea775f95]
/usr/lib/libpython3.5m.so.1.0(PyCFunction_Call+0xe9)[0x7f36f42f8609]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x7289)[0x7f36f436fa09]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f36f43719e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f36f4371ac3]
/usr/lib/libpython3.5m.so.1.0(+0x92c85)[0x7f36f42dbc85]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f36f42b10da]
/usr/lib/libpython3.5m.so.1.0(+0x7ed64)[0x7f36f42c7d64]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f36f42b10da]
/usr/lib/libpython3.5m.so.1.0(+0xc4a10)[0x7f36f430da10]
/usr/lib/libpython3.5m.so.1.0(+0xc2de6)[0x7f36f430bde6]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f36f42b10da]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x2f6d)[0x7f36f436b6ed]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f36f43719e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x5f60)[0x7f36f436e6e0]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x81c2)[0x7f36f4370942]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f36f43719e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f36f4371ac3]
/usr/lib/libpython3.5m.so.1.0(+0x92c85)[0x7f36f42dbc85]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f36f42b10da]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x2f6d)[0x7f36f436b6ed]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f36f43719e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f36f4371ac3]
/usr/lib/libpython3.5m.so.1.0(+0x92b98)[0x7f36f42dbb98]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f36f42b10da]
/usr/lib/libpython3.5m.so.1.0(+0x7ed64)[0x7f36f42c7d64]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f36f42b10da]
/usr/lib/libpython3.5m.so.1.0(+0xc4d40)[0x7f36f430dd40]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f36f42b10da]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x1d3c)[0x7f36f436a4bc]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f36f43719e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f36f4371ac3]
/usr/lib/libpython3.5m.so.1.0(+0x92c85)[0x7f36f42dbc85]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f36f42b10da]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x2f6d)[0x7f36f436b6ed]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f36f43719e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f36f4371ac3]
/usr/lib/libpython3.5m.so.1.0(+0x92b98)[0x7f36f42dbb98]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f36f42b10da]
/usr/lib/libpython3.5m.so.1.0(+0x7ed64)[0x7f36f42c7d64]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f36f42b10da]
/usr/lib/libpython3.5m.so.1.0(+0xc4d40)[0x7f36f430dd40]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f36f42b10da]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x1d3c)[0x7f36f436a4bc]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f36f43719e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f36f4371ac3]
/usr/lib/libpython3.5m.so.1.0(+0x92c85)[0x7f36f42dbc85]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f36f42b10da]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x2f6d)[0x7f36f436b6ed]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f36f43719e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f36f4371ac3]
/usr/lib/libpython3.5m.so.1.0(+0x92b98)[0x7f36f42dbb98]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f36f42b10da]
/usr/lib/libpython3.5m.so.1.0(+0x7ed64)[0x7f36f42c7d64]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:01 8914024                            /usr/bin/python3.5
00601000-00602000 r--p 00001000 08:01 8914024                            /usr/bin/python3.5
00602000-00603000 rw-p 00002000 08:01 8914024                            /usr/bin/python3.5
01fed000-03527000 rw-p 00000000 00:00 0                                  [heap]
7f36dc000000-7f36dc021000 rw-p 00000000 00:00 0 
7f36dc021000-7f36e0000000 ---p 00000000 00:00 0 
7f36e269f000-7f36e8496000 rw-p 00000000 00:00 0 
7f36e8496000-7f36e8497000 ---p 00000000 00:00 0 
7f36e8497000-7f36e8c97000 rw-p 00000000 00:00 0                          [stack:32343]
7f36e8c97000-7f36e8c98000 ---p 00000000 00:00 0 
7f36e8c98000-7f36e9bd9000 rw-p 00000000 00:00 0                          [stack:32342]
7f36e9bd9000-7f36e9bdb000 r-xp 00000000 08:01 9178948                    /usr/lib/python3.5/lib-dynload/_bisect.cpython-35m-x86_64-linux-gnu.so
7f36e9bdb000-7f36e9dda000 ---p 00002000 08:01 9178948                    /usr/lib/python3.5/lib-dynload/_bisect.cpython-35m-x86_64-linux-gnu.so
7f36e9dda000-7f36e9ddb000 r--p 00001000 08:01 9178948                    /usr/lib/python3.5/lib-dynload/_bisect.cpython-35m-x86_64-linux-gnu.so
7f36e9ddb000-7f36e9ddc000 rw-p 00002000 08:01 9178948                    /usr/lib/python3.5/lib-dynload/_bisect.cpython-35m-x86_64-linux-gnu.so
7f36e9ddc000-7f36e9dfd000 r-xp 00000000 08:01 11799472                   /usr/lib/python3.5/site-packages/tables/indexesextension.cpython-35m-x86_64-linux-gnu.so
7f36e9dfd000-7f36e9ffc000 ---p 00021000 08:01 11799472                   /usr/lib/python3.5/site-packages/tables/indexesextension.cpython-35m-x86_64-linux-gnu.so
7f36e9ffc000-7f36e9ffd000 r--p 00020000 08:01 11799472                   /usr/lib/python3.5/site-packages/tables/indexesextension.cpython-35m-x86_64-linux-gnu.so
7f36e9ffd000-7f36ea000000 rw-p 00021000 08:01 11799472                   /usr/lib/python3.5/site-packages/tables/indexesextension.cpython-35m-x86_64-linux-gnu.so
7f36ea000000-7f36ea041000 rw-p 00000000 00:00 0 
7f36ea041000-7f36ea055000 r-xp 00000000 08:01 11799500                   /usr/lib/python3.5/site-packages/tables/lrucacheextension.cpython-35m-x86_64-linux-gnu.so
7f36ea055000-7f36ea254000 ---p 00014000 08:01 11799500                   /usr/lib/python3.5/site-packages/tables/lrucacheextension.cpython-35m-x86_64-linux-gnu.so
7f36ea254000-7f36ea255000 r--p 00013000 08:01 11799500                   /usr/lib/python3.5/site-packages/tables/lrucacheextension.cpython-35m-x86_64-linux-gnu.so
7f36ea255000-7f36ea258000 rw-p 00014000 08:01 11799500                   /usr/lib/python3.5/site-packages/tables/lrucacheextension.cpython-35m-x86_64-linux-gnu.so
7f36ea258000-7f36ea2b4000 r-xp 00000000 08:01 11799499                   /usr/lib/python3.5/site-packages/tables/tableextension.cpython-35m-x86_64-linux-gnu.so
7f36ea2b4000-7f36ea4b3000 ---p 0005c000 08:01 11799499                   /usr/lib/python3.5/site-packages/tables/tableextension.cpython-35m-x86_64-linux-gnu.so
7f36ea4b3000-7f36ea4b4000 r--p 0005b000 08:01 11799499                   /usr/lib/python3.5/site-packages/tables/tableextension.cpython-35m-x86_64-linux-gnu.so
7f36ea4b4000-7f36ea4ba000 rw-p 0005c000 08:01 11799499                   /usr/lib/python3.5/site-packages/tables/tableextension.cpython-35m-x86_64-linux-gnu.so
7f36ea4ba000-7f36ea4fd000 rw-p 00000000 00:00 0 
7f36ea4fd000-7f36ea50b000 r-xp 00000000 08:01 11799480                   /usr/lib/python3.5/site-packages/tables/linkextension.cpython-35m-x86_64-linux-gnu.so
7f36ea50b000-7f36ea70a000 ---p 0000e000 08:01 11799480                   /usr/lib/python3.5/site-packages/tables/linkextension.cpython-35m-x86_64-linux-gnu.so
7f36ea70a000-7f36ea70b000 r--p 0000d000 08:01 11799480                   /usr/lib/python3.5/site-packages/tables/linkextension.cpython-35m-x86_64-linux-gnu.so
7f36ea70b000-7f36ea70d000 rw-p 0000e000 08:01 11799480                   /usr/lib/python3.5/site-packages/tables/linkextension.cpython-35m-x86_64-linux-gnu.so
7f36ea70d000-7f36ea74d000 rw-p 00000000 00:00 0 
7f36ea74d000-7f36ea7be000 r-xp 00000000 08:01 11799503                   /usr/lib/python3.5/site-packages/tables/hdf5extension.cpython-35m-x86_64-linux-gnu.so
7f36ea7be000-7f36ea9bd000 ---p 00071000 08:01 11799503                   /usr/lib/python3.5/site-packages/tables/hdf5extension.cpython-35m-x86_64-linux-gnu.so
7f36ea9bd000-7f36ea9be000 r--p 00070000 08:01 11799503                   /usr/lib/python3.5/site-packages/tables/hdf5extension.cpython-35m-x86_64-linux-gnu.so
7f36ea9be000-7f36ea9c6000 rw-p 00071000 08:01 11799503                   /usr/lib/python3.5/site-packages/tables/hdf5extension.cpython-35m-x86_64-linux-gnu.so
7f36ea9c6000-7f36ea9c9000 rw-p 00000000 00:00 0 
7f36ea9c9000-7f36ea9ca000 ---p 00000000 00:00 0 
7f36ea9ca000-7f36eb1ca000 rw-p 00000000 00:00 0                          [stack:31949]
7f36eb1ca000-7f36eb1cb000 ---p 00000000 00:00 0 
7f36eb1cb000-7f36eb9cb000 rw-p 00000000 00:00 0                          [stack:31948]
7f36eb9cb000-7f36eb9cc000 ---p 00000000 00:00 0 
7f36eb9cc000-7f36ec1cc000 rw-p 00000000 00:00 0                          [stack:31947]
7f36ec1cc000-7f36ec1cd000 ---p 00000000 00:00 0 
7f36ec1cd000-7f36eca0d000 rw-p 00000000 00:00 0                          [stack:31946]
7f36eca0d000-7f36eca4c000 r-xp 00000000 08:01 11799419                   /usr/lib/python3.5/site-packages/numexpr/interpreter.cpython-35m-x86_64-linux-gnu.so
7f36eca4c000-7f36ecc4b000 ---p 0003f000 08:01 11799419                   /usr/lib/python3.5/site-packages/numexpr/interpreter.cpython-35m-x86_64-linux-gnu.so
7f36ecc4b000-7f36ecc4c000 r--p 0003e000 08:01 11799419                   /usr/lib/python3.5/site-packages/numexpr/interpreter.cpython-35m-x86_64-linux-gnu.so
7f36ecc4c000-7f36ecc4d000 rw-p 0003f000 08:01 11799419                   /usr/lib/python3.5/site-packages/numexpr/interpreter.cpython-35m-x86_64-linux-gnu.so
7f36ecc4d000-7f36eccb1000 rw-p 00000000 00:00 0 
7f36eccb1000-7f36eccb5000 r-xp 00000000 08:01 11799464                   /usr/lib/python3.5/site-packages/tables/_comp_bzip2.cpython-35m-x86_64-linux-gnu.so
7f36eccb5000-7f36eceb5000 ---p 00004000 08:01 11799464                   /usr/lib/python3.5/site-packages/tables/_comp_bzip2.cpython-35m-x86_64-linux-gnu.so
7f36eceb5000-7f36eceb6000 r--p 00004000 08:01 11799464                   /usr/lib/python3.5/site-packages/tables/_comp_bzip2.cpython-35m-x86_64-linux-gnu.so
7f36eceb6000-7f36eceb7000 rw-p 00005000 08:01 11799464                   /usr/lib/python3.5/site-packages/tables/_comp_bzip2.cpython-35m-x86_64-linux-gnu.so
7f36eceb7000-7f36eced8000 r-xp 00000000 08:01 8918277                    /usr/lib/liblzo2.so.2.0.0
7f36eced8000-7f36ed0d7000 ---p 00021000 08:01 8918277                    /usr/lib/liblzo2.so.2.0.0
7f36ed0d7000-7f36ed0d8000 r--p 00020000 08:01 8918277                    /usr/lib/liblzo2.so.2.0.0
7f36ed0d8000-7f36ed0d9000 rw-p 00021000 08:01 8918277                    /usr/lib/liblzo2.so.2.0.0
7f36ed0d9000-7f36ed0dd000 r-xp 00000000 08:01 11799501                   /usr/lib/python3.5/site-packages/tables/_comp_lzo.cpython-35m-x86_64-linux-gnu.so
7f36ed0dd000-7f36ed2dc000 ---p 00004000 08:01 11799501                   /usr/lib/python3.5/site-packages/tables/_comp_lzo.cpython-35m-x86_64-linux-gnu.so
7f36ed2dc000-7f36ed2dd000 r--p 00003000 08:01 11799501                   /usr/lib/python3.5/site-packages/tables/_comp_lzo.cpython-35m-x86_64-linux-gnu.so
7f36ed2dd000-7f36ed2de000 rw-p 00004000 08:01 11799501                   /usr/lib/python3.5/site-packages/tables/_comp_lzo.cpython-35m-x86_64-linux-gnu.so
7f36ed2de000-7f36ed35e000 rw-p 00000000 00:00 0 
7f36ed35e000-7f36ed363000 r-xp 00000000 08:01 9179005                    /usr/lib/python3.5/lib-dynload/select.cpython-35m-x86_64-linux-gnu.so
7f36ed363000-7f36ed562000 ---p 00005000 08:01 9179005                    /usr/lib/python3.5/lib-dynload/select.cpython-35m-x86_64-linux-gnu.so
7f36ed562000-7f36ed563000 r--p 00004000 08:01 9179005                    /usr/lib/python3.5/lib-dynload/select.cpython-35m-x86_64-linux-gnu.so
7f36ed563000-7f36ed565000 rw-p 00005000 08:01 9179005                    /usr/lib/python3.5/lib-dynload/select.cpython-35m-x86_64-linux-gnu.so
7f36ed565000-7f36ed568000 r-xp 00000000 08:01 9178977                    /usr/lib/python3.5/lib-dynload/_posixsubprocess.cpython-35m-x86_64-linux-gnu.so
7f36ed568000-7f36ed767000 ---p 00003000 08:01 9178977                    /usr/lib/python3.5/lib-dynload/_posixsubprocess.cpython-35m-x86_64-linux-gnu.so
7f36ed767000-7f36ed768000 r--p 00002000 08:01 9178977                    /usr/lib/python3.5/lib-dynload/_posixsubprocess.cpython-35m-x86_64-linux-gnu.so
7f36ed768000-7f36ed769000 rw-p 00003000 08:01 9178977                    /usr/lib/python3.5/lib-dynload/_posixsubprocess.cpython-35m-x86_64-linux-gnu.so
7f36ed769000-7f36ed76a000 r-xp 00000000 08:01 9178975                    /usr/lib/python3.5/lib-dynload/_opcode.cpython-35m-x86_64-linux-gnu.so
7f36ed76a000-7f36ed969000 ---p 00001000 08:01 9178975                    /usr/lib/python3.5/lib-dynload/_opcode.cpython-35m-x86_64-linux-gnu.so
7f36ed969000-7f36ed96a000 r--p 00000000 08:01 9178975                    /usr/lib/python3.5/lib-dynload/_opcode.cpython-35m-x86_64-linux-gnu.so
7f36ed96a000-7f36ed96b000 rw-p 00001000 08:01 9178975                    /usr/lib/python3.5/lib-dynload/_opcode.cpython-35m-x86_64-linux-gnu.so
7f36ed96b000-7f36ed9eb000 rw-p 00000000 00:00 0 
7f36ed9eb000-7f36ed9f0000 r-xp 00000000 08:01 9179011                    /usr/lib/python3.5/lib-dynload/zlib.cpython-35m-x86_64-linux-gnu.so
7f36ed9f0000-7f36edbef000 ---p 00005000 08:01 9179011                    /usr/lib/python3.5/lib-dynload/zlib.cpython-35m-x86_64-linux-gnu.so
7f36edbef000-7f36edbf0000 r--p 00004000 08:01 9179011                    /usr/lib/python3.5/lib-dynload/zlib.cpython-35m-x86_64-linux-gnu.so
7f36edbf0000-7f36edbf2000 rw-p 00005000 08:01 9179011                    /usr/lib/python3.5/lib-dynload/zlib.cpython-35m-x86_64-linux-gnu.so
7f36edbf2000-7f36edc72000 rw-p 00000000 00:00 0 
7f36edc72000-7f36edce8000 r-xp 00000000 08:01 9577278                    /usr/lib/python3.5/site-packages/numpy/random/mtrand.cpython-35m-x86_64-linux-gnu.so
7f36edce8000-7f36edee7000 ---p 00076000 08:01 9577278                    /usr/lib/python3.5/site-packages/numpy/random/mtrand.cpython-35m-x86_64-linux-gnu.so
7f36edee7000-7f36edee8000 r--p 00075000 08:01 9577278                    /usr/lib/python3.5/site-packages/numpy/random/mtrand.cpython-35m-x86_64-linux-gnu.so
7f36edee8000-7f36edf23000 rw-p 00076000 08:01 9577278                    /usr/lib/python3.5/site-packages/numpy/random/mtrand.cpython-35m-x86_64-linux-gnu.so
7f36edf23000-7f36edf24000 rw-p 00000000 00:00 0 
7f36edf24000-7f36edf2d000 r-xp 00000000 08:01 9313245                    /usr/lib/python3.5/site-packages/numpy/fft/fftpack_lite.cpython-35m-x86_64-linux-gnu.so
7f36edf2d000-7f36ee12c000 ---p 00009000 08:01 9313245                    /usr/lib/python3.5/site-packages/numpy/fft/fftpack_lite.cpython-35m-x86_64-linux-gnu.so
7f36ee12c000-7f36ee12d000 r--p 00008000 08:01 9313245                    /usr/lib/python3.5/site-packages/numpy/fft/fftpack_lite.cpython-35m-x86_64-linux-gnu.so
7f36ee12d000-7f36ee12e000 rw-p 00009000 08:01 9313245                    /usr/lib/python3.5/site-packages/numpy/fft/fftpack_lite.cpython-35m-x86_64-linux-gnu.so
7f36ee12e000-7f36ee22f000 rw-p 00000000 00:00 0 
7f36ee22f000-7f36ee24f000 r-xp 00000000 08:01 9313225                    /usr/lib/python3.5/site-packages/numpy/linalg/_umath_linalg.cpython-35m-x86_64-linux-gnu.so
7f36ee24f000-7f36ee44e000 ---p 00020000 08:01 9313225                    /usr/lib/python3.5/site-packages/numpy/linalg/_umath_linalg.cpython-35m-x86_64-linux-gnu.so
7f36ee44e000-7f36ee44f000 r--p 0001f000 08:01 9313225                    /usr/lib/python3.5/site-packages/numpy/linalg/_umath_linalg.cpython-35m-x86_64-linux-gnu.so
7f36ee44f000-7f36ee450000 rw-p 00020000 08:01 9313225                    /usr/lib/python3.5/site-packages/numpy/linalg/_umath_linalg.cpython-35m-x86_64-linux-gnu.so
7f36ee450000-7f36eea36000 r-xp 00000000 08:01 8931804                    /usr/lib/liblapack.so.3.6.0
7f36eea36000-7f36eec35000 ---p 005e6000 08:01 8931804                    /usr/lib/liblapack.so.3.6.0
7f36eec35000-7f36eec36000 r--p 005e5000 08:01 8931804                    /usr/lib/liblapack.so.3.6.0
7f36eec36000-7f36eec39000 rw-p 005e6000 08:01 8931804                    /usr/lib/liblapack.so.3.6.0
7f36eec39000-7f36eec84000 rw-p 00000000 00:00 0 
7f36eec84000-7f36eec87000 r-xp 00000000 08:01 9313222                    /usr/lib/python3.5/site-packages/numpy/linalg/lapack_lite.cpython-35m-x86_64-linux-gnu.so
7f36eec87000-7f36eee86000 ---p 00003000 08:01 9313222                    /usr/lib/python3.5/site-packages/numpy/linalg/lapack_lite.cpython-35m-x86_64-linux-gnu.so
7f36eee86000-7f36eee87000 r--p 00002000 08:01 9313222                    /usr/lib/python3.5/site-packages/numpy/linalg/lapack_lite.cpython-35m-x86_64-linux-gnu.so
7f36eee87000-7f36eee88000 rw-p 00003000 08:01 9313222                    /usr/lib/python3.5/site-packages/numpy/linalg/lapack_lite.cpython-35m-x86_64-linux-gnu.so
7f36eee88000-7f36eef08000 rw-p 00000000 00:00 0 
7f36eef08000-7f36eef0a000 r-xp 00000000 08:01 9178978                    /usr/lib/python3.5/lib-dynload/_random.cpython-35m-x86_64-linux-gnu.so
7f36eef0a000-7f36ef10a000 ---p 00002000 08:01 9178978                    /usr/lib/python3.5/lib-dynload/_random.cpython-35m-x86_64-linux-gnu.so
7f36ef10a000-7f36ef10b000 r--p 00002000 08:01 9178978                    /usr/lib/python3.5/lib-dynload/_random.cpython-35m-x86_64-linux-gnu.so
7f36ef10b000-7f36ef10c000 rw-p 00003000 08:01 9178978                    /usr/lib/python3.5/lib-dynload/_random.cpython-35m-x86_64-linux-gnu.so
7f36ef10c000-7f36ef358000 r-xp 00000000 08:01 8918166                    /usr/lib/libcrypto.so.1.0.0
7f36ef358000-7f36ef558000 ---p 0024c000 08:01 8918166                    /usr/lib/libcrypto.so.1.0.0
7f36ef558000-7f36ef574000 r--p 0024c000 08:01 8918166                    /usr/lib/libcrypto.so.1.0.0
7f36ef574000-7f36ef580000 rw-p 00268000 08:01 8918166                    /usr/lib/libcrypto.so.1.0.0
7f36ef580000-7f36ef583000 rw-p 00000000 00:00 0 
7f36ef583000-7f36ef588000 r-xp 00000000 08:01 9178967                    /usr/lib/python3.5/lib-dynload/_hashlib.cpython-35m-x86_64-linux-gnu.so
7f36ef588000-7f36ef787000 ---p 00005000 08:01 9178967                    /usr/lib/python3.5/lib-dynload/_hashlib.cpython-35m-x86_64-linux-gnu.so
7f36ef787000-7f36ef788000 r--p 00004000 08:01 9178967                    /usr/lib/python3.5/lib-dynload/_hashlib.cpython-35m-x86_64-linux-gnu.so
7f36ef788000-7f36ef789000 rw-p 00005000 08:01 9178967                    /usr/lib/python3.5/lib-dynload/_hashlib.cpython-35m-x86_64-linux-gnu.so
7f36ef789000-7f36ef7ae000 r-xp 00000000 08:01 8918276                    /usr/lib/liblzma.so.5.2.2
7f36ef7ae000-7f36ef9ad000 ---p 00025000 08:01 8918276                    /usr/lib/liblzma.so.5.2.2
7f36ef9ad000-7f36ef9ae000 r--p 00024000 08:01 8918276                    /usr/lib/liblzma.so.5.2.2
7f36ef9ae000-7f36ef9af000 rw-p 00025000 08:01 8918276                    /usr/lib/liblzma.so.5.2.2
7f36ef9af000-7f36ef9b5000 r-xp 00000000 08:01 9178971                    /usr/lib/python3.5/lib-dynload/_lzma.cpython-35m-x86_64-linux-gnu.so
7f36ef9b5000-7f36efbb4000 ---p 00006000 08:01 9178971                    /usr/lib/python3.5/lib-dynload/_lzma.cpython-35m-x86_64-linux-gnu.so
7f36efbb4000-7f36efbb5000 r--p 00005000 08:01 9178971                    /usr/lib/python3.5/lib-dynload/_lzma.cpython-35m-x86_64-linux-gnu.so
7f36efbb5000-7f36efbb7000 rw-p 00006000 08:01 9178971                    /usr/lib/python3.5/lib-dynload/_lzma.cpython-35m-x86_64-linux-gnu.so
7f36efbb7000-7f36efbc6000 r-xp 00000000 08:01 8918150                    /usr/lib/libbz2.so.1.0.6
7f36efbc6000-7f36efdc5000 ---p 0000f000 08:01 8918150                    /usr/lib/libbz2.so.1.0.6
7f36efdc5000-7f36efdc7000 rw-p 0000e000 08:01 8918150                    /usr/lib/libbz2.so.1.0.6
7f36efdc7000-7f36efdca000 r-xp 00000000 08:01 9178949                    /usr/lib/python3.5/lib-dynload/_bz2.cpython-35m-x86_64-linux-gnu.so
7f36efdca000-7f36effc9000 ---p 00003000 08:01 9178949                    /usr/lib/python3.5/lib-dynload/_bz2.cpython-35m-x86_64-linux-gnu.so
7f36effc9000-7f36effca000 r--p 00002000 08:01 9178949                    /usr/lib/python3.5/lib-dynload/_bz2.cpython-35m-x86_64-linux-gnu.so
7f36effca000-7f36effcb000 rw-p 00003000 08:01 9178949                    /usr/lib/python3.5/lib-dynload/_bz2.cpython-35m-x86_64-linux-gnu.so
7f36effcb000-7f36f000b000 rw-p 00000000 00:00 0 
7f36f000b000-7f36f000d000 r-xp 00000000 08:01 9178996                    /usr/lib/python3.5/lib-dynload/grp.cpython-35m-x86_64-linux-gnu.so
7f36f000d000-7f36f020c000 ---p 00002000 08:01 9178996                    /usr/lib/python3.5/lib-dynload/grp.cpython-35m-x86_64-linux-gnu.so
7f36f020c000-7f36f020d000 r--p 00001000 08:01 9178996                    /usr/lib/python3.5/lib-dynload/grp.cpython-35m-x86_64-linux-gnu.so
7f36f020d000-7f36f020e000 rw-p 00002000 08:01 9178996                    /usr/lib/python3.5/lib-dynload/grp.cpython-35m-x86_64-linux-gnu.so
7f36f020e000-7f36f038e000 rw-p 00000000 00:00 0 
7f36f038e000-7f36f03a1000 r-xp 00000000 08:01 9178976                    /usr/lib/python3.5/lib-dynload/_pickle.cpython-35m-x86_64-linux-gnu.so
7f36f03a1000-7f36f05a0000 ---p 00013000 08:01 9178976                    /usr/lib/python3.5/lib-dynload/_pickle.cpython-35m-x86_64-linux-gnu.so
7f36f05a0000-7f36f05a1000 r--p 00012000 08:01 9178976                    /usr/lib/python3.5/lib-dynload/_pickle.cpython-35m-x86_64-linux-gnu.so
7f36f05a1000-7f36f05a5000 rw-p 00013000 08:01 9178976                    /usr/lib/python3.5/lib-dynload/_pickle.cpython-35m-x86_64-linux-gnu.so
7f36f05a5000-7f36f05e5000 rw-p 00000000 00:00 0 
7f36f05e5000-7f36f05ed000 r-xp 00000000 08:01 9178985                    /usr/lib/python3.5/lib-dynload/_struct.cpython-35m-x86_64-linux-gnu.so
7f36f05ed000-7f36f07ec000 ---p 00008000 08:01 9178985                    /usr/lib/python3.5/lib-dynload/_struct.cpython-35m-x86_64-linux-gnu.so
7f36f07ec000-7f36f07ed000 r--p 00007000 08:01 9178985                    /usr/lib/python3.5/lib-dynload/_struct.cpython-35m-x86_64-linux-gnu.so
7f36f07ed000-7f36f07f0000 rw-p 00008000 08:01 9178985                    /usr/lib/python3.5/lib-dynload/_struct.cpython-35m-x86_64-linux-gnu.so
7f36f07f0000-7f36f0830000 rw-p 00000000 00:00 0 
7f36f0830000-7f36f0838000 r-xp 00000000 08:01 8918207                    /usr/lib/libffi.so.6.0.4
7f36f0838000-7f36f0a37000 ---p 00008000 08:01 8918207                    /usr/lib/libffi.so.6.0.4
7f36f0a37000-7f36f0a38000 r--p 00007000 08:01 8918207                    /usr/lib/libffi.so.6.0.4
7f36f0a38000-7f36f0a39000 rw-p 00008000 08:01 8918207                    /usr/lib/libffi.so.6.0.4
7f36f0a39000-7f36f0a52000 r-xp 00000000 08:01 9178958                    /usr/lib/python3.5/lib-dynload/_ctypes.cpython-35m-x86_64-linux-gnu.so
7f36f0a52000-7f36f0c52000 ---p 00019000 08:01 9178958                    /usr/lib/python3.5/lib-dynload/_ctypes.cpython-35m-x86_64-linux-gnu.so
7f36f0c52000-7f36f0c53000 r--p 00019000 08:01 9178958                    /usr/lib/python3.5/lib-dynload/_ctypes.cpython-35m-x86_64-linux-gnu.so
7f36f0c53000-7f36f0c57000 rw-p 0001a000 08:01 9178958                    /usr/lib/python3.5/lib-dynload/_ctypes.cpython-35m-x86_64-linux-gnu.so
7f36f0c78000-7f36f0cb8000 rw-p 00000000 00:00 0 
7f36f0cb8000-7f36f0d6b000 r-xp 00000000 08:01 9708258                    /usr/lib/python3.5/site-packages/numpy/core/umath.cpython-35m-x86_64-linux-gnu.so
7f36f0d6b000-7f36f0f6a000 ---p 000b3000 08:01 9708258                    /usr/lib/python3.5/site-packages/numpy/core/umath.cpython-35m-x86_64-linux-gnu.so
7f36f0f6a000-7f36f0f6b000 r--p 000b2000 08:01 9708258                    /usr/lib/python3.5/site-packages/numpy/core/umath.cpython-35m-x86_64-linux-gnu.so
7f36f0f6b000-7f36f0f71000 rw-p 000b3000 08:01 9708258                    /usr/lib/python3.5/site-packages/numpy/core/umath.cpython-35m-x86_64-linux-gnu.so
7f36f0f71000-7f36f0fb3000 rw-p 00000000 00:00 0 
7f36f0fb3000-7f36f0fc3000 r-xp 00000000 08:01 9178962                    /usr/lib/python3.5/lib-dynload/_datetime.cpython-35m-x86_64-linux-gnu.so
7f36f0fc3000-7f36f11c3000 ---p 00010000 08:01 9178962                    /usr/lib/python3.5/lib-dynload/_datetime.cpython-35m-x86_64-linux-gnu.so
7f36f11c3000-7f36f11c4000 r--p 00010000 08:01 9178962                    /usr/lib/python3.5/lib-dynload/_datetime.cpython-35m-x86_64-linux-gnu.so
7f36f11c4000-7f36f11c7000 rw-p 00011000 08:01 9178962                    /usr/lib/python3.5/lib-dynload/_datetime.cpython-35m-x86_64-linux-gnu.so
7f36f11c7000-7f36f1207000 rw-p 00000000 00:00 0 
7f36f1207000-7f36f1246000 r-xp 00000000 08:01 8918364                    /usr/lib/libquadmath.so.0.0.0
7f36f1246000-7f36f1445000 ---p 0003f000 08:01 8918364                    /usr/lib/libquadmath.so.0.0.0
7f36f1445000-7f36f1446000 rw-p 0003e000 08:01 8918364                    /usr/lib/libquadmath.so.0.0.0
7f36f1446000-7f36f1574000 r-xp 00000000 08:01 8918223                    /usr/lib/libgfortran.so.3.0.0
7f36f1574000-7f36f1774000 ---p 0012e000 08:01 8918223                    /usr/lib/libgfortran.so.3.0.0
7f36f1774000-7f36f1776000 rw-p 0012e000 08:01 8918223                    /usr/lib/libgfortran.so.3.0.0
7f36f1776000-7f36f17cd000 r-xp 00000000 08:01 8931800                    /usr/lib/libblas.so.3.6.0
7f36f17cd000-7f36f19cc000 ---p 00057000 08:01 8931800                    /usr/lib/libblas.so.3.6.0
7f36f19cc000-7f36f19cd000 r--p 00056000 08:01 8931800                    /usr/lib/libblas.so.3.6.0
7f36f19cd000-7f36f19ce000 rw-p 00057000 08:01 8931800                    /usr/lib/libblas.so.3.6.0
7f36f19ce000-7f36f19e7000 r-xp 00000000 08:01 8931806                    /usr/lib/libcblas.so
7f36f19e7000-7f36f1be6000 ---p 00019000 08:01 8931806                    /usr/lib/libcblas.so
7f36f1be6000-7f36f1be7000 r--p 00018000 08:01 8931806                    /usr/lib/libcblas.so
7f36f1be7000-7f36f1be8000 rw-p 00019000 08:01 8931806                    /usr/lib/libcblas.so
7f36f1be8000-7f36f1d57000 r-xp 00000000 08:01 9708268                    /usr/lib/python3.5/site-packages/numpy/core/multiarray.cpython-35m-x86_64-linux-gnu.so
7f36f1d57000-7f36f1f56000 ---p 0016f000 08:01 9708268                    /usr/lib/python3.5/site-packages/numpy/core/multiarray.cpython-35m-x86_64-linux-gnu.so
7f36f1f56000-7f36f1f58000 r--p 0016e000 08:01 9708268                    /usr/lib/python3.5/site-packages/numpy/core/multiarray.cpython-35m-x86_64-linux-gnu.so
7f36f1f58000-7f36f1f65000 rw-p 00170000 08:01 9708268                    /usr/lib/python3.5/site-packages/numpy/core/multiarray.cpython-35m-x86_64-linux-gnu.so
7f36f1f65000-7f36f1f77000 rw-p 00000000 00:00 0 
7f36f1f77000-7f36f1f7f000 r-xp 00000000 08:01 9178997                    /usr/lib/python3.5/lib-dynload/math.cpython-35m-x86_64-linux-gnu.so
7f36f1f7f000-7f36f217e000 ---p 00008000 08:01 9178997                    /usr/lib/python3.5/lib-dynload/math.cpython-35m-x86_64-linux-gnu.so
7f36f217e000-7f36f217f000 r--p 00007000 08:01 9178997                    /usr/lib/python3.5/lib-dynload/math.cpython-35m-x86_64-linux-gnu.so
7f36f217f000-7f36f2181000 rw-p 00008000 08:01 9178997                    /usr/lib/python3.5/lib-dynload/math.cpython-35m-x86_64-linux-gnu.so
7f36f2181000-7f36f2196000 r-xp 00000000 08:01 8918443                    /usr/lib/libz.so.1.2.8
7f36f2196000-7f36f2395000 ---p 00015000 08:01 8918443                    /usr/lib/libz.so.1.2.8
7f36f2395000-7f36f2396000 r--p 00014000 08:01 8918443                    /usr/lib/libz.so.1.2.8
7f36f2396000-7f36f2397000 rw-p 00015000 08:01 8918443                    /usr/lib/libz.so.1.2.8
7f36f2397000-7f36f23ad000 r-xp 00000000 08:01 8918216                    /usr/lib/libgcc_s.so.1
7f36f23ad000-7f36f25ac000 ---p 00016000 08:01 8918216                    /usr/lib/libgcc_s.so.1
7f36f25ac000-7f36f25ad000 rw-p 00015000 08:01 8918216                    /usr/lib/libgcc_s.so.1
7f36f25ad000-7f36f2725000 r-xp 00000000 08:01 8918386                    /usr/lib/libstdc++.so.6.0.22
7f36f2725000-7f36f2924000 ---p 00178000 08:01 8918386                    /usr/lib/libstdc++.so.6.0.22
7f36f2924000-7f36f292e000 r--p 00177000 08:01 8918386                    /usr/lib/libstdc++.so.6.0.22
7f36f292e000-7f36f2930000 rw-p 00181000 08:01 8918386                    /usr/lib/libstdc++.so.6.0.22
7f36f2930000-7f36f2934000 rw-p 00000000 00:00 0 
7f36f2934000-7f36f2c63000 r-xp 00000000 08:01 8929345                    /usr/lib/libhdf5.so.100.0.0
7f36f2c63000-7f36f2e62000 ---p 0032f000 08:01 8929345                    /usr/lib/libhdf5.so.100.0.0
7f36f2e62000-7f36f2e6b000 r--p 0032e000 08:01 8929345                    /usr/lib/libhdf5.so.100.0.0
7f36f2e6b000-7f36f2e73000 rw-p 00337000 08:01 8929345                    /usr/lib/libhdf5.so.100.0.0
7f36f2e73000-7f36f2e76000 rw-p 00000000 00:00 0 
7f36f2eb5000-7f36f2f11000 r-xp 00000000 08:01 11799490                   /usr/lib/python3.5/site-packages/tables/utilsextension.cpython-35m-x86_64-linux-gnu.so
7f36f2f11000-7f36f3110000 ---p 0005c000 08:01 11799490                   /usr/lib/python3.5/site-packages/tables/utilsextension.cpython-35m-x86_64-linux-gnu.so
7f36f3110000-7f36f3111000 r--p 0005b000 08:01 11799490                   /usr/lib/python3.5/site-packages/tables/utilsextension.cpython-35m-x86_64-linux-gnu.so
7f36f3111000-7f36f3119000 rw-p 0005c000 08:01 11799490                   /usr/lib/python3.5/site-packages/tables/utilsextension.cpython-35m-x86_64-linux-gnu.so
7f36f3119000-7f36f315c000 rw-p 00000000 00:00 0 
7f36f315c000-7f36f315e000 r-xp 00000000 08:01 9178968                    /usr/lib/python3.5/lib-dynload/_heapq.cpython-35m-x86_64-linux-gnu.so
7f36f315e000-7f36f335d000 ---p 00002000 08:01 9178968                    /usr/lib/python3.5/lib-dynload/_heapq.cpython-35m-x86_64-linux-gnu.so
7f36f335d000-7f36f335e000 r--p 00001000 08:01 9178968                    /usr/lib/python3.5/lib-dynload/_heapq.cpython-35m-x86_64-linux-gnu.so
7f36f335e000-7f36f3360000 rw-p 00002000 08:01 9178968                    /usr/lib/python3.5/lib-dynload/_heapq.cpython-35m-x86_64-linux-gnu.so
7f36f3360000-7f36f33a0000 rw-p 00000000 00:00 0 
7f36f33a0000-7f36f3580000 r--p 00000000 08:01 8930010                    /usr/lib/locale/locale-archive
7f36f3580000-7f36f3683000 r-xp 00000000 08:01 8918278                    /usr/lib/libm-2.23.soAborted (core dumped)

And when I try to use a simple script :

import tables


class Particle(tables.IsDescription):
        name = tables.StringCol(16)


file = tables.open_file('hello.py', 'w')
table = file.create_table(file.root, 'particles', Particle)

particle = table.row

for i in range(10):
        particle['name'] = 'Particle: {}'.format(i)
        particle.append()

table.flush()
file.close()

I get :

Traceback (most recent call last):
  File "s.py", line 9, in <module>
    table = file.create_table(file.root, 'particles', Particle)
  File "/usr/lib/python3.5/site-packages/tables/file.py", line 1060, in create_table
    chunkshape=chunkshape, byteorder=byteorder)
  File "/usr/lib/python3.5/site-packages/tables/table.py", line 873, in __init__
    byteorder, _log)
  File "/usr/lib/python3.5/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/usr/lib/python3.5/site-packages/tables/node.py", line 267, in __init__
    self._v_objectid = self._g_create()
  File "/usr/lib/python3.5/site-packages/tables/table.py", line 1066, in _g_create
    self._v_new_title, self.filters.complib or '', obversion)
  File "tables/tableextension.pyx", line 222, in tables.tableextension.Table._create_table (tables/tableextension.c:3322)
tables.exceptions.HDF5ExtError: HDF5 error back trace

  File "H5A.c", line 265, in H5Acreate2
    not a location
  File "H5Gloc.c", line 253, in H5G_loc
    invalid object ID

End of HDF5 error back trace

Can't set attribute 'CLASS' in table:
 particles.
Closing remaining open files:hello.py...done

Thank you for any help that you can provide !

Offline

#2 2016-05-18 13:20:37

asphere
Member
Registered: 2016-05-18
Posts: 2

Re: Pytables (HDF5) error

I am having the same issue for both python2 and python3 pytables.

Python2:

$ python2 -c "import tables; tables.test()" 
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version:    3.2.2
HDF5 version:        1.10.0
NumPy version:       1.11.0
Numexpr version:     2.5.2 (not using Intel's VML/MKL)
Zlib version:        1.2.8 (in Python interpreter)
LZO version:         2.09 (Feb 04 2015)
BZIP2 version:       1.0.6 (6-Sept-2010)
Blosc version:       1.4.4 (2015-05-05)
Blosc compressors:   blosclz (1.0.2.1), lz4 (1.2.0), lz4hc (1.2.0), snappy (1.1.1), zlib (1.2.8)
Cython version:      0.24
Python version:      2.7.11 (default, Mar 31 2016, 06:18:34) 
[GCC 5.3.0]
Platform:            Linux-4.5.4-1-ARCH-x86_64-with-glibc2.2.5
Byte-ordering:       little
Detected cores:      8
Default encoding:    ascii
Default FS encoding: UTF-8
Default locale:      (en_US, UTF-8)
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing only a light (yet comprehensive) subset of the test suite.
If you want a more complete test, try passing the --heavy flag to this script
(or set the 'heavy' parameter in case you are using tables.test() call).
The whole suite will take more than 4 hours to complete on a relatively
modern CPU and around 512 MB of main memory.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE........EE.*** Error in `python2': malloc(): smallbin double linked list corrupted: 0x000055fc1ed68d80 ***
======= Backtrace: =========
/usr/lib/libc.so.6(+0x6ed4b)[0x7f7eb527ad4b]
/usr/lib/libc.so.6(+0x74546)[0x7f7eb5280546]
/usr/lib/libc.so.6(+0x76981)[0x7f7eb5282981]
/usr/lib/libc.so.6(__libc_malloc+0x54)[0x7f7eb52841d4]
/usr/lib/libhdf5.so.100(H5MM_xstrdup+0x1c)[0x7f7eb40ca8dc]
/usr/lib/libhdf5.so.100(H5E_push_stack+0x152)[0x7f7eb4037712]
/usr/lib/libhdf5.so.100(H5E_printf_stack+0x10d)[0x7f7eb403788d]
/usr/lib/libhdf5.so.100(H5FD_open+0x491)[0x7f7eb405d781]
/usr/lib/libhdf5.so.100(H5F_open+0xdd)[0x7f7eb404a65d]
/usr/lib/libhdf5.so.100(H5Fcreate+0x1e0)[0x7f7eb40429f0]
/usr/lib/python2.7/site-packages/tables/hdf5extension.so(+0x3bcb2)[0x7f7ea90decb2]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x741b)[0x7f7eb58b540b]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x86c)[0x7f7eb58b7adc]
/usr/lib/libpython2.7.so.1.0(+0x72c0d)[0x7f7eb583cc0d]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(+0x5bdef)[0x7f7eb5825def]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(+0xa6896)[0x7f7eb5870896]
/usr/lib/libpython2.7.so.1.0(+0xa54e2)[0x7f7eb586f4e2]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3fa8)[0x7f7eb58b1f98]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x86c)[0x7f7eb58b7adc]
/usr/lib/libpython2.7.so.1.0(+0x72c0d)[0x7f7eb583cc0d]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3fa8)[0x7f7eb58b1f98]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x86c)[0x7f7eb58b7adc]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x68cc)[0x7f7eb58b48bc]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x86c)[0x7f7eb58b7adc]
/usr/lib/libpython2.7.so.1.0(+0x72c0d)[0x7f7eb583cc0d]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3fa8)[0x7f7eb58b1f98]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x86c)[0x7f7eb58b7adc]
/usr/lib/libpython2.7.so.1.0(+0x72b2b)[0x7f7eb583cb2b]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(+0x5bdef)[0x7f7eb5825def]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(+0xa6c76)[0x7f7eb5870c76]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x58c3)[0x7f7eb58b38b3]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x86c)[0x7f7eb58b7adc]
/usr/lib/libpython2.7.so.1.0(+0x72c0d)[0x7f7eb583cc0d]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3fa8)[0x7f7eb58b1f98]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x86c)[0x7f7eb58b7adc]
/usr/lib/libpython2.7.so.1.0(+0x72b2b)[0x7f7eb583cb2b]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(+0x5bdef)[0x7f7eb5825def]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(+0xa6c76)[0x7f7eb5870c76]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x58c3)[0x7f7eb58b38b3]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x86c)[0x7f7eb58b7adc]
/usr/lib/libpython2.7.so.1.0(+0x72c0d)[0x7f7eb583cc0d]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3fa8)[0x7f7eb58b1f98]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x86c)[0x7f7eb58b7adc]
/usr/lib/libpython2.7.so.1.0(+0x72b2b)[0x7f7eb583cb2b]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(+0x5bdef)[0x7f7eb5825def]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(+0xa6c76)[0x7f7eb5870c76]
/usr/lib/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f7eb58164a2]
/usr/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x58c3)[0x7f7eb58b38b3]
======= Memory map: ========
55fc1b9c9000-55fc1b9ca000 r-xp 00000000 fe:01 11669590                   /usr/bin/python2.7
55fc1bbc9000-55fc1bbca000 r--p 00000000 fe:01 11669590                   /usr/bin/python2.7
55fc1bbca000-55fc1bbcb000 rw-p 00001000 fe:01 11669590                   /usr/bin/python2.7
55fc1d9d2000-55fc1ee54000 rw-p 00000000 00:00 0                          [heap]
7f7e9c000000-7f7e9c021000 rw-p 00000000 00:00 0 
7f7e9c021000-7f7ea0000000 ---p 00000000 00:00 0 
7f7ea09ad000-7f7ea6864000 rw-p 00000000 00:00 0 
7f7ea6864000-7f7ea6865000 ---p 00000000 00:00 0 
7f7ea6865000-7f7ea7065000 rw-p 00000000 00:00 0 
7f7ea7065000-7f7ea7066000 ---p 00000000 00:00 0 
7f7ea7066000-7f7ea8227000 rw-p 00000000 00:00 0 
7f7ea8227000-7f7ea822d000 r-xp 00000000 fe:01 14040102                   /usr/lib/python2.7/lib-dynload/_multiprocessing.so
7f7ea822d000-7f7ea842c000 ---p 00006000 fe:01 14040102                   /usr/lib/python2.7/lib-dynload/_multiprocessing.so
7f7ea842c000-7f7ea842d000 r--p 00005000 fe:01 14040102                   /usr/lib/python2.7/lib-dynload/_multiprocessing.so
7f7ea842d000-7f7ea842e000 rw-p 00006000 fe:01 14040102                   /usr/lib/python2.7/lib-dynload/_multiprocessing.so
7f7ea842e000-7f7ea852e000 rw-p 00000000 00:00 0 
7f7ea852e000-7f7ea8530000 r-xp 00000000 fe:01 14040136                   /usr/lib/python2.7/lib-dynload/_bisect.so
7f7ea8530000-7f7ea872f000 ---p 00002000 fe:01 14040136                   /usr/lib/python2.7/lib-dynload/_bisect.so
7f7ea872f000-7f7ea8730000 r--p 00001000 fe:01 14040136                   /usr/lib/python2.7/lib-dynload/_bisect.so
7f7ea8730000-7f7ea8731000 rw-p 00002000 fe:01 14040136                   /usr/lib/python2.7/lib-dynload/_bisect.so
7f7ea8731000-7f7ea8752000 r-xp 00000000 fe:01 14037872                   /usr/lib/python2.7/site-packages/tables/indexesextension.so
7f7ea8752000-7f7ea8951000 ---p 00021000 fe:01 14037872                   /usr/lib/python2.7/site-packages/tables/indexesextension.so
7f7ea8951000-7f7ea8952000 r--p 00020000 fe:01 14037872                   /usr/lib/python2.7/site-packages/tables/indexesextension.so
7f7ea8952000-7f7ea8955000 rw-p 00021000 fe:01 14037872                   /usr/lib/python2.7/site-packages/tables/indexesextension.so
7f7ea8955000-7f7ea8996000 rw-p 00000000 00:00 0 
7f7ea8996000-7f7ea89aa000 r-xp 00000000 fe:01 14037824                   /usr/lib/python2.7/site-packages/tables/lrucacheextension.so
7f7ea89aa000-7f7ea8ba9000 ---p 00014000 fe:01 14037824                   /usr/lib/python2.7/site-packages/tables/lrucacheextension.so
7f7ea8ba9000-7f7ea8baa000 r--p 00013000 fe:01 14037824                   /usr/lib/python2.7/site-packages/tables/lrucacheextension.so
7f7ea8baa000-7f7ea8bad000 rw-p 00014000 fe:01 14037824                   /usr/lib/python2.7/site-packages/tables/lrucacheextension.so
7f7ea8bad000-7f7ea8c0a000 r-xp 00000000 fe:01 14037847                   /usr/lib/python2.7/site-packages/tables/tableextension.so
7f7ea8c0a000-7f7ea8e09000 ---p 0005d000 fe:01 14037847                   /usr/lib/python2.7/site-packages/tables/tableextension.so
7f7ea8e09000-7f7ea8e0a000 r--p 0005c000 fe:01 14037847                   /usr/lib/python2.7/site-packages/tables/tableextension.so
7f7ea8e0a000-7f7ea8e10000 rw-p 0005d000 fe:01 14037847                   /usr/lib/python2.7/site-packages/tables/tableextension.so
7f7ea8e10000-7f7ea8e53000 rw-p 00000000 00:00 0 
7f7ea8e53000-7f7ea8e61000 r-xp 00000000 fe:01 14037805                   /usr/lib/python2.7/site-packages/tables/linkextension.so
7f7ea8e61000-7f7ea9060000 ---p 0000e000 fe:01 14037805                   /usr/lib/python2.7/site-packages/tables/linkextension.so
7f7ea9060000-7f7ea9061000 r--p 0000d000 fe:01 14037805                   /usr/lib/python2.7/site-packages/tables/linkextension.so
7f7ea9061000-7f7ea9063000 rw-p 0000e000 fe:01 14037805                   /usr/lib/python2.7/site-packages/tables/linkextension.so
7f7ea9063000-7f7ea90a3000 rw-p 00000000 00:00 0 
7f7ea90a3000-7f7ea9115000 r-xp 00000000 fe:01 14037859                   /usr/lib/python2.7/site-packages/tables/hdf5extension.so
7f7ea9115000-7f7ea9314000 ---p 00072000 fe:01 14037859                   /usr/lib/python2.7/site-packages/tables/hdf5extension.so
7f7ea9314000-7f7ea9315000 r--p 00071000 fe:01 14037859                   /usr/lib/python2.7/site-packages/tables/hdf5extension.so
7f7ea9315000-7f7ea931d000 rw-p 00072000 fe:01 14037859                   /usr/lib/python2.7/site-packages/tables/hdf5extension.so
7f7ea931d000-7f7ea9320000 rw-p 00000000 00:00 0 
7f7ea9320000-7f7ea9321000 ---p 00000000 00:00 0 
7f7ea9321000-7f7ea9b21000 rw-p 00000000 00:00 0 
7f7ea9b21000-7f7ea9b22000 ---p 00000000 00:00 0 
7f7ea9b22000-7f7eaa322000 rw-p 00000000 00:00 0 
7f7eaa322000-7f7eaa323000 ---p 00000000 00:00 0 
7f7eaa323000-7f7eaab23000 rw-p 00000000 00:00 0 
7f7eaab23000-7f7eaab24000 ---p 00000000 00:00 0 
7f7eaab24000-7f7eab324000 rw-p 00000000 00:00 0 
7f7eab324000-7f7eab325000 ---p 00000000 00:00 0 
7f7eab325000-7f7eabb25000 rw-p 00000000 00:00 0 
7f7eabb25000-7f7eabb26000 ---p 00000000 00:00 0 
7f7eabb26000-7f7eac326000 rw-p 00000000 00:00 0 
7f7eac326000-7f7eac327000 ---p 00000000 00:00 0 
7f7eac327000-7f7eacb27000 rw-p 00000000 00:00 0 
7f7eacb27000-7f7eacb28000 ---p 00000000 00:00 0 
7f7eacb28000-7f7ead368000 rw-p 00000000 00:00 0 
7f7ead368000-7f7ead3a8000 r-xp 00000000 fe:01 14035790                   /usr/lib/python2.7/site-packages/numexpr/interpreter.so
7f7ead3a8000-7f7ead5a7000 ---p 00040000 fe:01 14035790                   /usr/lib/python2.7/site-packages/numexpr/interpreter.so
7f7ead5a7000-7f7ead5a8000 r--p 0003f000 fe:01 14035790                   /usr/lib/python2.7/site-packages/numexpr/interpreter.so
7f7ead5a8000-7f7ead5a9000 rw-p 00040000 fe:01 14035790                   /usr/lib/python2.7/site-packages/numexpr/interpreter.so
7f7ead5a9000-7f7ead5cd000 rw-p 00000000 00:00 0 
7f7ead5cd000-7f7ead5dc000 r-xp 00000000 fe:01 11689640                   /usr/lib/libbz2.so.1.0.6
7f7ead5dc000-7f7ead7db000 ---p 0000f000 fe:01 11689640                   /usr/lib/libbz2.so.1.0.6
7f7ead7db000-7f7ead7dd000 rw-p 0000e000 fe:01 11689640                   /usr/lib/libbz2.so.1.0.6
7f7ead7dd000-7f7ead7e1000 r-xp 00000000 fe:01 14037820                   /usr/lib/python2.7/site-packages/tables/_comp_bzip2.so
7f7ead7e1000-7f7ead9e0000 ---p 00004000 fe:01 14037820                   /usr/lib/python2.7/site-packages/tables/_comp_bzip2.so
7f7ead9e0000-7f7ead9e1000 r--p 00003000 fe:01 14037820                   /usr/lib/python2.7/site-packages/tables/_comp_bzip2.so
7f7ead9e1000-7f7ead9e2000 rw-p 00004000 fe:01 14037820                   /usr/lib/python2.7/site-packages/tables/_comp_bzip2.so
7f7ead9e2000-7f7eada03000 r-xp 00000000 fe:01 11690397                   /usr/lib/liblzo2.so.2.0.0
7f7eada03000-7f7eadc02000 ---p 00021000 fe:01 11690397                   /usr/lib/liblzo2.so.2.0.0
7f7eadc02000-7f7eadc03000 r--p 00020000 fe:01 11690397                   /usr/lib/liblzo2.so.2.0.0
7f7eadc03000-7f7eadc04000 rw-p 00021000 fe:01 11690397                   /usr/lib/liblzo2.so.2.0.0
7f7eadc09000-7f7eadc89000 rw-p 00000000 00:00 0 
7f7eadc89000-7f7eadc8d000 r-xp 00000000 fe:01 14037848                   /usr/lib/python2.7/site-packages/tables/_comp_lzo.so
7f7eadc8d000-7f7eade8c000 ---p 00004000 fe:01 14037848                   /usr/lib/python2.7/site-packages/tables/_comp_lzo.so
7f7eade8c000-7f7eade8d000 r--p 00003000 fe:01 14037848                   /usr/lib/python2.7/site-packages/tables/_comp_lzo.so
7f7eade8d000-7f7eade8e000 rw-p 00004000 fe:01 14037848                   /usr/lib/python2.7/site-packages/tables/_comp_lzo.so
7f7eade8e000-7f7eadece000 rw-p 00000000 00:00 0 
7f7eadece000-7f7eaded3000 r-xp 00000000 fe:01 14040105                   /usr/lib/python2.7/lib-dynload/select.so
7f7eaded3000-7f7eae0d2000 ---p 00005000 fe:01 14040105                   /usr/lib/python2.7/lib-dynload/select.so
7f7eae0d2000-7f7eae0d3000 r--p 00004000 fe:01 14040105                   /usr/lib/python2.7/lib-dynload/select.so
7f7eae0d3000-7f7eae0d5000 rw-p 00005000 fe:01 14040105                   /usr/lib/python2.7/lib-dynload/select.so
7f7eae0d5000-7f7eae115000 rw-p 00000000 00:00 0 
7f7eae115000-7f7eae11a000 r-xp 00000000 fe:01 14040155                   /usr/lib/python2.7/lib-dynload/strop.so
7f7eae11a000-7f7eae319000 ---p 00005000 fe:01 14040155                   /usr/lib/python2.7/lib-dynload/strop.so
7f7eae319000-7f7eae31a000 r--p 00004000 fe:01 14040155                   /usr/lib/python2.7/lib-dynload/strop.so
7f7eae31a000-7f7eae31c000 rw-p 00005000 fe:01 14040155                   /usr/lib/python2.7/lib-dynload/strop.so
7f7eae31c000-7f7eae35c000 rw-p 00000000 00:00 0 
7f7eae35c000-7f7eae360000 r-xp 00000000 fe:01 14040108                   /usr/lib/python2.7/lib-dynload/zlib.so
7f7eae360000-7f7eae55f000 ---p 00004000 fe:01 14040108                   /usr/lib/python2.7/lib-dynload/zlib.so
7f7eae55f000-7f7eae560000 r--p 00003000 fe:01 14040108                   /usr/lib/python2.7/lib-dynload/zlib.so
7f7eae560000-7f7eae562000 rw-p 00004000 fe:01 14040108                   /usr/lib/python2.7/lib-dynload/zlib.so
7f7eae562000-7f7eae5a2000 rw-p 00000000 00:00 0 
7f7eae5da000-7f7eae61a000 rw-p 00000000 00:00 0 
7f7eae61a000-7f7eae690000 r-xp 00000000 fe:01 14292088                   /usr/lib/python2.7/site-packages/numpy/random/mtrand.so
7f7eae690000-7f7eae88f000 ---p 00076000 fe:01 14292088                   /usr/lib/python2.7/site-packages/numpy/random/mtrand.so
7f7eae88f000-7f7eae890000 r--p 00075000 fe:01 14292088                   /usr/lib/python2.7/site-packages/numpy/random/mtrand.so
7f7eae890000-7f7eae8cb000 rw-p 00076000 fe:01 14292088                   /usr/lib/python2.7/site-packages/numpy/random/mtrand.so
7f7eae8cb000-7f7eae8cc000 rw-p 00000000 00:00 0 
7f7eae8cc000-7f7eae8d5000 r-xp 00000000 fe:01 14292355                   /usr/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so
7f7eae8d5000-7f7eaead4000 ---p 00009000 fe:01 14292355                   /usr/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so
7f7eaead4000-7f7eaead5000 r--p 00008000 fe:01 14292355                   /usr/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so
7f7eaead5000-7f7eaead6000 rw-p 00009000 fe:01 14292355                   /usr/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so
7f7eaead6000-7f7eaead7000 r-xp 00000000 fe:01 14040132                   /usr/lib/python2.7/lib-dynload/future_builtins.so
7f7eaead7000-7f7eaecd6000 ---p 00001000 fe:01 14040132                   /usr/lib/python2.7/lib-dynload/future_builtins.so
7f7eaecd6000-7f7eaecd7000 r--p 00000000 fe:01 14040132                   /usr/lib/python2.7/lib-dynload/future_builtins.so
7f7eaecd7000-7f7eaecd8000 rw-p 00001000 fe:01 14040132                   /usr/lib/python2.7/lib-dynload/future_builtins.so
7f7eaecd8000-7f7eaecf8000 r-xp 00000000 fe:01 14292260                   /usr/lib/python2.7/site-packages/numpy/linalg/_umath_linalg.so
7f7eaecf8000-7f7eaeef7000 ---p 00020000 fe:01 14292260                   /usr/lib/python2.7/site-packages/numpy/linalg/_umath_linalg.so
7f7eaeef7000-7f7eaeef8000 r--p 0001f000 fe:01 14292260                   /usr/lib/python2.7/site-packages/numpy/linalg/_umath_linalg.so
7f7eaeef8000-7f7eaeef9000 rw-p 00020000 fe:01 14292260                   /usr/lib/python2.7/site-packages/numpy/linalg/_umath_linalg.so
7f7eaeef9000-7f7eaf4df000 r-xp 00000000 fe:01 11694948                   /usr/lib/liblapack.so.3.6.0
7f7eaf4df000-7f7eaf6de000 ---p 005e6000 fe:01 11694948                   /usr/lib/liblapack.so.3.6.0
7f7eaf6de000-7f7eaf6df000 r--p 005e5000 fe:01 11694948                   /usr/lib/liblapack.so.3.6.0
7f7eaf6df000-7f7eaf6e2000 rw-p 005e6000 fe:01 11694948                   /usr/lib/liblapack.so.3.6.0
7f7eaf6e2000-7f7eaf72d000 rw-p 00000000 00:00 0 
7f7eaf732000-7f7eaf7b2000 rw-p 00000000 00:00 0 
7f7eaf7b2000-7f7eaf7b5000 r-xp 00000000 fe:01 14292248                   /usr/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
7f7eaf7b5000-7f7eaf9b4000 ---p 00003000 fe:01 14292248                   /usr/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
7f7eaf9b4000-7f7eaf9b5000 r--p 00002000 fe:01 14292248                   /usr/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
7f7eaf9b5000-7f7eaf9b6000 rw-p 00003000 fe:01 14292248                   /usr/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
7f7eaf9b6000-7f7eaf9b9000 r-xp 00000000 fe:01 14040096                   /usr/lib/python2.7/lib-dynload/fcntl.so
7f7eaf9b9000-7f7eafbb8000 ---p 00003000 fe:01 14040096                   /usr/lib/python2.7/lib-dynload/fcntl.so
7f7eafbb8000-7f7eafbb9000 r--p 00002000 fe:01 14040096                   /usr/lib/python2.7/lib-dynload/fcntl.so
7f7eafbb9000-7f7eafbba000 rw-p 00003000 fe:01 14040096                   /usr/lib/python2.7/lib-dynload/fcntl.so
7f7eafbba000-7f7eafbbd000 r-xp 00000000 fe:01 14040099                   /usr/lib/python2.7/lib-dynload/_random.so
7f7eafbbd000-7f7eafdbc000 ---p 00003000 fe:01 14040099                   /usr/lib/python2.7/lib-dynload/_random.so
7f7eafdbc000-7f7eafdbd000 r--p 00002000 fe:01 14040099                   /usr/lib/python2.7/lib-dynload/_random.so
7f7eafdbd000-7f7eafdbe000 rw-p 00003000 fe:01 14040099                   /usr/lib/python2.7/lib-dynload/_random.so
7f7eafdbe000-7f7eb000a000 r-xp 00000000 fe:01 11694906                   /usr/lib/libcrypto.so.1.0.0
7f7eb000a000-7f7eb020a000 ---p 0024c000 fe:01 11694906                   /usr/lib/libcrypto.so.1.0.0
7f7eb020a000-7f7eb0226000 r--p 0024c000 fe:01 11694906                   /usr/lib/libcrypto.so.1.0.0
7f7eb0226000-7f7eb0232000 rw-p 00268000 fe:01 11694906                   /usr/lib/libcrypto.so.1.0.0
7f7eb0232000-7f7eb0235000 rw-p 00000000 00:00 0 
7f7eb023a000-7f7eb02ba000 rw-p 00000000 00:00 0 
7f7eb02ba000-7f7eb02be000 r-xp 00000000 fe:01 14040143                   /usr/lib/python2.7/lib-dynload/_hashlib.so
7f7eb02be000-7f7eb04bd000 ---p 00004000 fe:01 14040143                   /usr/lib/python2.7/lib-dynload/_hashlib.so
7f7eb04bd000-7f7eb04be000 r--p 00003000 fe:01 14040143                   /usr/lib/python2.7/lib-dynload/_hashlib.so
7f7eb04be000-7f7eb04bf000 rw-p 00004000 fe:01 14040143                   /usr/lib/python2.7/lib-dynload/_hashlib.so
7f7eb04bf000-7f7eb04c4000 r-xp 00000000 fe:01 14040131                   /usr/lib/python2.7/lib-dynload/binascii.so
7f7eb04c4000-7f7eb06c3000 ---p 00005000 fe:01 14040131                   /usr/lib/python2.7/lib-dynload/binascii.so
7f7eb06c3000-7f7eb06c4000 r--p 00004000 fe:01 14040131                   /usr/lib/python2.7/lib-dynload/binascii.so
7f7eb06c4000-7f7eb06c5000 rw-p 00005000 fe:01 14040131                   /usr/lib/python2.7/lib-dynload/binascii.so
7f7eb06c5000-7f7eb06e2000 r-xp 00000000 fe:01 14040115                   /usr/lib/python2.7/lib-dynload/_io.so
7f7eb06e2000-7f7eb08e1000 ---p 0001d000 fe:01 14040115                   /usr/lib/python2.7/lib-dynload/_io.so
7f7eb08e1000-7f7eb08e2000 r--p 0001c000 fe:01 14040115                   /usr/lib/python2.7/lib-dynload/_io.so
7f7eb08e2000-7f7eb08ec000 rw-p 0001d000 fe:01 14040115                   /usr/lib/python2.7/lib-dynload/_io.so
7f7eb08ec000-7f7eb08ee000 r-xp 00000000 fe:01 14040153                   /usr/lib/python2.7/lib-dynload/grp.so
7f7eb08ee000-7f7eb0aed000 ---p 00002000 fe:01 14040153                   /usr/lib/python2.7/lib-dynload/grp.so
7f7eb0aed000-7f7eb0aee000 r--p 00001000 fe:01 14040153                   /usr/lib/python2.7/lib-dynload/grp.so
7f7eb0aee000-7f7eb0aef000 rw-p 00002000 fe:01 14040153                   /usr/lib/python2.7/lib-dynload/grp.so
7f7eb0aef000-7f7eb0b2f000 rw-p 00000000 00:00 0 
7f7eb0b2f000-7f7eb0b33000 r-xp 00000000 fe:01 14040119                   /usr/lib/python2.7/lib-dynload/time.so
7f7eb0b33000-7f7eb0d32000 ---p 00004000 fe:01 14040119                   /usr/lib/python2.7/lib-dynload/time.so
7f7eb0d32000-7f7eb0d33000 r--p 00003000 fe:01 14040119                   /usr/lib/python2.7/lib-dynload/time.so
7f7eb0d33000-7f7eb0d35000 rw-p 00004000 fe:01 14040119                   /usr/lib/python2.7/lib-dynload/time.so
7f7eb0d35000-7f7eb0db5000 rw-p 00000000 00:00 0 
7f7eb0db5000-7f7eb0db8000 r-xp 00000000 fe:01 14040101                   /usr/lib/python2.7/lib-dynload/_functools.so
7f7eb0db8000-7f7eb0fb7000 ---p 00003000 fe:01 14040101                   /usr/lib/python2.7/lib-dynload/_functools.so
7f7eb0fb7000-7f7eb0fb8000 r--p 00002000 fe:01 14040101                   /usr/lib/python2.7/lib-dynload/_functools.so
7f7eb0fb8000-7f7eb0fb9000 rw-p 00003000 fe:01 14040101                   /usr/lib/python2.7/lib-dynload/_functools.so
7f7eb0fb9000-7f7eb107a000 rw-p 00000000 00:00 0 
7f7eb107a000-7f7eb107e000 r-xp 00000000 fe:01 14040133                   /usr/lib/python2.7/lib-dynload/cStringIO.so
7f7eb107e000-7f7eb127d000 ---p 00004000 fe:01 14040133                   /usr/lib/python2.7/lib-dynload/cStringIO.so
7f7eb127d000-7f7eb127e000 r--p 00003000 fe:01 14040133                   /usr/lib/python2.7/lib-dynload/cStringIO.so
7f7eb127e000-7f7eb1280000 rw-p 00004000 fe:01 14040133                   /usr/lib/python2.7/lib-dynload/cStringIO.so
7f7eb1280000-7f7eb1293000 r-xp 00000000 fe:01 14040157                   /usr/lib/python2.7/lib-dynload/cPickle.so
7f7eb1293000-7f7eb1492000 ---p 00013000 fe:01 14040157                   /usr/lib/python2.7/lib-dynload/cPickle.so
7f7eb1492000-7f7eb1493000 r--p 00012000 fe:01 14040157                   /usr/lib/python2.7/lib-dynload/cPickle.so
7f7eb1493000-7f7eb1494000 rw-p 00013000 fe:01 14040157                   /usr/lib/python2.7/lib-dynload/cPickle.so
7f7eb1494000-7f7eb1497000 r-xp 00000000 fe:01 14040118                   /usr/lib/python2.7/lib-dynload/_heapq.so
7f7eb1497000-7f7eb1696000 ---p 00003000 fe:01 14040118                   /usr/lib/python2.7/lib-dynload/_heapq.so[1]    2758 abort (core dumped)  python2 -c "import tables; tables.test()"

Python3:

$ python3 -c "import tables; tables.test()"
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version:    3.2.2
HDF5 version:        1.10.0
NumPy version:       1.11.0
Numexpr version:     2.5.2 (not using Intel's VML/MKL)
Zlib version:        1.2.8 (in Python interpreter)
LZO version:         2.09 (Feb 04 2015)
BZIP2 version:       1.0.6 (6-Sept-2010)
Blosc version:       1.4.4 (2015-05-05)
Blosc compressors:   blosclz (1.0.2.1), lz4 (1.2.0), lz4hc (1.2.0), snappy (1.1.1), zlib (1.2.8)
Cython version:      0.24
Python version:      3.5.1 (default, Mar  3 2016, 09:29:07) 
[GCC 5.3.0]
Platform:            Linux-4.5.4-1-ARCH-x86_64-with-arch
Byte-ordering:       little
Detected cores:      8
Default encoding:    utf-8
Default FS encoding: utf-8
Default locale:      (en_US, UTF-8)
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing only a light (yet comprehensive) subset of the test suite.
If you want a more complete test, try passing the --heavy flag to this script
(or set the 'heavy' parameter in case you are using tables.test() call).
The whole suite will take more than 4 hours to complete on a relatively
modern CPU and around 512 MB of main memory.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
/usr/lib/python3.5/site-packages/tables/atom.py:570: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead
  for arg in inspect.getargspec(self.__init__)[0]
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE........EEss..*** Error in `python3': malloc(): smallbin double linked list corrupted: 0x0000000002f72160 ***
======= Backtrace: =========
/usr/lib/libc.so.6(+0x6ed4b)[0x7f078c8f5d4b]
/usr/lib/libc.so.6(+0x74546)[0x7f078c8fb546]
/usr/lib/libc.so.6(+0x76981)[0x7f078c8fd981]
/usr/lib/libc.so.6(__libc_malloc+0x54)[0x7f078c8ff1d4]
/usr/lib/libhdf5.so.100(+0x1b2339)[0x7f078b6dc339]
/usr/lib/libhdf5.so.100(+0x1b46c6)[0x7f078b6de6c6]
/usr/lib/libhdf5.so.100(H5P_create_id+0x170)[0x7f078b6dde40]
/usr/lib/libhdf5.so.100(H5Pcreate+0x4b)[0x7f078b6bc0bb]
/usr/lib/python3.5/site-packages/tables/hdf5extension.cpython-35m-x86_64-linux-gnu.so(+0x28e7a)[0x7f07813efe7a]
/usr/lib/libpython3.5m.so.1.0(PyCFunction_Call+0xe9)[0x7f078cef4609]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x7289)[0x7f078cf6ba09]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f078cf6d9e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f078cf6dac3]
/usr/lib/libpython3.5m.so.1.0(+0x92c85)[0x7f078ced7c85]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f078cead0da]
/usr/lib/libpython3.5m.so.1.0(+0x7ed64)[0x7f078cec3d64]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f078cead0da]
/usr/lib/libpython3.5m.so.1.0(+0xc4a10)[0x7f078cf09a10]
/usr/lib/libpython3.5m.so.1.0(+0xc2de6)[0x7f078cf07de6]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f078cead0da]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x2f6d)[0x7f078cf676ed]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f078cf6d9e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x5f60)[0x7f078cf6a6e0]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x81c2)[0x7f078cf6c942]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f078cf6d9e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f078cf6dac3]
/usr/lib/libpython3.5m.so.1.0(+0x92c85)[0x7f078ced7c85]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f078cead0da]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x2f6d)[0x7f078cf676ed]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f078cf6d9e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f078cf6dac3]
/usr/lib/libpython3.5m.so.1.0(+0x92b98)[0x7f078ced7b98]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f078cead0da]
/usr/lib/libpython3.5m.so.1.0(+0x7ed64)[0x7f078cec3d64]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f078cead0da]
/usr/lib/libpython3.5m.so.1.0(+0xc4d40)[0x7f078cf09d40]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f078cead0da]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x1d3c)[0x7f078cf664bc]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f078cf6d9e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f078cf6dac3]
/usr/lib/libpython3.5m.so.1.0(+0x92c85)[0x7f078ced7c85]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f078cead0da]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x2f6d)[0x7f078cf676ed]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f078cf6d9e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f078cf6dac3]
/usr/lib/libpython3.5m.so.1.0(+0x92b98)[0x7f078ced7b98]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f078cead0da]
/usr/lib/libpython3.5m.so.1.0(+0x7ed64)[0x7f078cec3d64]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f078cead0da]
/usr/lib/libpython3.5m.so.1.0(+0xc4d40)[0x7f078cf09d40]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f078cead0da]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x1d3c)[0x7f078cf664bc]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f078cf6d9e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f078cf6dac3]
/usr/lib/libpython3.5m.so.1.0(+0x92c85)[0x7f078ced7c85]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f078cead0da]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x2f6d)[0x7f078cf676ed]
/usr/lib/libpython3.5m.so.1.0(+0x1289e2)[0x7f078cf6d9e2]
/usr/lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f078cf6dac3]
/usr/lib/libpython3.5m.so.1.0(+0x92b98)[0x7f078ced7b98]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f078cead0da]
/usr/lib/libpython3.5m.so.1.0(+0x7ed64)[0x7f078cec3d64]
/usr/lib/libpython3.5m.so.1.0(PyObject_Call+0x6a)[0x7f078cead0da]
======= Memory map: ========
00400000-00401000 r-xp 00000000 fe:01 11666049                           /usr/bin/python3.5
00601000-00602000 r--p 00001000 fe:01 11666049                           /usr/bin/python3.5
00602000-00603000 rw-p 00002000 fe:01 11666049                           /usr/bin/python3.5
01b04000-03077000 rw-p 00000000 00:00 0                                  [heap]
7f0774000000-7f0774021000 rw-p 00000000 00:00 0 
7f0774021000-7f0778000000 ---p 00000000 00:00 0 
7f0779258000-7f0779298000 rw-p 00000000 00:00 0 
7f0779319000-7f077f0d0000 rw-p 00000000 00:00 0 
7f077f0d0000-7f077f0d1000 ---p 00000000 00:00 0 
7f077f0d1000-7f077f8d1000 rw-p 00000000 00:00 0 
7f077f8d1000-7f077f8d2000 ---p 00000000 00:00 0 
7f077f8d2000-7f0780853000 rw-p 00000000 00:00 0 
7f0780853000-7f0780855000 r-xp 00000000 fe:01 13111759                   /usr/lib/python3.5/lib-dynload/_bisect.cpython-35m-x86_64-linux-gnu.so
7f0780855000-7f0780a54000 ---p 00002000 fe:01 13111759                   /usr/lib/python3.5/lib-dynload/_bisect.cpython-35m-x86_64-linux-gnu.so
7f0780a54000-7f0780a55000 r--p 00001000 fe:01 13111759                   /usr/lib/python3.5/lib-dynload/_bisect.cpython-35m-x86_64-linux-gnu.so
7f0780a55000-7f0780a56000 rw-p 00002000 fe:01 13111759                   /usr/lib/python3.5/lib-dynload/_bisect.cpython-35m-x86_64-linux-gnu.so
7f0780a56000-7f0780a77000 r-xp 00000000 fe:01 36048818                   /usr/lib/python3.5/site-packages/tables/indexesextension.cpython-35m-x86_64-linux-gnu.so
7f0780a77000-7f0780c76000 ---p 00021000 fe:01 36048818                   /usr/lib/python3.5/site-packages/tables/indexesextension.cpython-35m-x86_64-linux-gnu.so
7f0780c76000-7f0780c77000 r--p 00020000 fe:01 36048818                   /usr/lib/python3.5/site-packages/tables/indexesextension.cpython-35m-x86_64-linux-gnu.so
7f0780c77000-7f0780c7a000 rw-p 00021000 fe:01 36048818                   /usr/lib/python3.5/site-packages/tables/indexesextension.cpython-35m-x86_64-linux-gnu.so
7f0780c7a000-7f0780cbb000 rw-p 00000000 00:00 0 
7f0780cbb000-7f0780ccf000 r-xp 00000000 fe:01 36048855                   /usr/lib/python3.5/site-packages/tables/lrucacheextension.cpython-35m-x86_64-linux-gnu.so
7f0780ccf000-7f0780ece000 ---p 00014000 fe:01 36048855                   /usr/lib/python3.5/site-packages/tables/lrucacheextension.cpython-35m-x86_64-linux-gnu.so
7f0780ece000-7f0780ecf000 r--p 00013000 fe:01 36048855                   /usr/lib/python3.5/site-packages/tables/lrucacheextension.cpython-35m-x86_64-linux-gnu.so
7f0780ecf000-7f0780ed2000 rw-p 00014000 fe:01 36048855                   /usr/lib/python3.5/site-packages/tables/lrucacheextension.cpython-35m-x86_64-linux-gnu.so
7f0780ed2000-7f0780f2e000 r-xp 00000000 fe:01 36048854                   /usr/lib/python3.5/site-packages/tables/tableextension.cpython-35m-x86_64-linux-gnu.so
7f0780f2e000-7f078112d000 ---p 0005c000 fe:01 36048854                   /usr/lib/python3.5/site-packages/tables/tableextension.cpython-35m-x86_64-linux-gnu.so
7f078112d000-7f078112e000 r--p 0005b000 fe:01 36048854                   /usr/lib/python3.5/site-packages/tables/tableextension.cpython-35m-x86_64-linux-gnu.so
7f078112e000-7f0781134000 rw-p 0005c000 fe:01 36048854                   /usr/lib/python3.5/site-packages/tables/tableextension.cpython-35m-x86_64-linux-gnu.so
7f0781134000-7f0781177000 rw-p 00000000 00:00 0 
7f0781177000-7f0781185000 r-xp 00000000 fe:01 36048826                   /usr/lib/python3.5/site-packages/tables/linkextension.cpython-35m-x86_64-linux-gnu.so
7f0781185000-7f0781384000 ---p 0000e000 fe:01 36048826                   /usr/lib/python3.5/site-packages/tables/linkextension.cpython-35m-x86_64-linux-gnu.so
7f0781384000-7f0781385000 r--p 0000d000 fe:01 36048826                   /usr/lib/python3.5/site-packages/tables/linkextension.cpython-35m-x86_64-linux-gnu.so
7f0781385000-7f0781387000 rw-p 0000e000 fe:01 36048826                   /usr/lib/python3.5/site-packages/tables/linkextension.cpython-35m-x86_64-linux-gnu.so
7f0781387000-7f07813c7000 rw-p 00000000 00:00 0 
7f07813c7000-7f0781438000 r-xp 00000000 fe:01 36048858                   /usr/lib/python3.5/site-packages/tables/hdf5extension.cpython-35m-x86_64-linux-gnu.so
7f0781438000-7f0781637000 ---p 00071000 fe:01 36048858                   /usr/lib/python3.5/site-packages/tables/hdf5extension.cpython-35m-x86_64-linux-gnu.so
7f0781637000-7f0781638000 r--p 00070000 fe:01 36048858                   /usr/lib/python3.5/site-packages/tables/hdf5extension.cpython-35m-x86_64-linux-gnu.so
7f0781638000-7f0781640000 rw-p 00071000 fe:01 36048858                   /usr/lib/python3.5/site-packages/tables/hdf5extension.cpython-35m-x86_64-linux-gnu.so
7f0781640000-7f0781643000 rw-p 00000000 00:00 0 
7f0781643000-7f0781644000 ---p 00000000 00:00 0 
7f0781644000-7f0781e44000 rw-p 00000000 00:00 0 
7f0781e44000-7f0781e45000 ---p 00000000 00:00 0 
7f0781e45000-7f0782645000 rw-p 00000000 00:00 0 
7f0782645000-7f0782646000 ---p 00000000 00:00 0 
7f0782646000-7f0782e46000 rw-p 00000000 00:00 0 
7f0782e46000-7f0782e47000 ---p 00000000 00:00 0 
7f0782e47000-7f0783647000 rw-p 00000000 00:00 0 
7f0783647000-7f0783648000 ---p 00000000 00:00 0 
7f0783648000-7f0783e48000 rw-p 00000000 00:00 0 
7f0783e48000-7f0783e49000 ---p 00000000 00:00 0 
7f0783e49000-7f0784649000 rw-p 00000000 00:00 0 
7f0784649000-7f078464a000 ---p 00000000 00:00 0 
7f078464a000-7f0784e4a000 rw-p 00000000 00:00 0 
7f0784e4a000-7f0784e4b000 ---p 00000000 00:00 0 
7f0784e4b000-7f078564b000 rw-p 00000000 00:00 0 
7f078564b000-7f078568a000 r-xp 00000000 fe:01 35922505                   /usr/lib/python3.5/site-packages/numexpr/interpreter.cpython-35m-x86_64-linux-gnu.so
7f078568a000-7f0785889000 ---p 0003f000 fe:01 35922505                   /usr/lib/python3.5/site-packages/numexpr/interpreter.cpython-35m-x86_64-linux-gnu.so
7f0785889000-7f078588a000 r--p 0003e000 fe:01 35922505                   /usr/lib/python3.5/site-packages/numexpr/interpreter.cpython-35m-x86_64-linux-gnu.so
7f078588a000-7f078588b000 rw-p 0003f000 fe:01 35922505                   /usr/lib/python3.5/site-packages/numexpr/interpreter.cpython-35m-x86_64-linux-gnu.so
7f078588b000-7f07858af000 rw-p 00000000 00:00 0 
7f07858af000-7f07858b3000 r-xp 00000000 fe:01 36048809                   /usr/lib/python3.5/site-packages/tables/_comp_bzip2.cpython-35m-x86_64-linux-gnu.so
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7f078898d000-7f078898f000 rw-p 0000e000 fe:01 11689640                   /usr/lib/libbz2.so.1.0.6
7f0788994000-7f0788a14000 rw-p 00000000 00:00 0 
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7f0788a17000-7f0788c16000 ---p 00003000 fe:01 13111799                   /usr/lib/python3.5/lib-dynload/_bz2.cpython-35m-x86_64-linux-gnu.so
7f0788c16000-7f0788c17000 r--p 00002000 fe:01 13111799                   /usr/lib/python3.5/lib-dynload/_bz2.cpython-35m-x86_64-linux-gnu.so
7f0788c17000-7f0788c18000 rw-p 00003000 fe:01 13111799                   /usr/lib/python3.5/lib-dynload/_bz2.cpython-35m-x86_64-linux-gnu.so
7f0788c18000-7f0788c1a000 r-xp 00000000 fe:01 13111771                   /usr/lib/python3.5/lib-dynload/grp.cpython-35m-x86_64-linux-gnu.so
7f0788c1a000-7f0788e19000 ---p 00002000 fe:01 13111771                   /usr/lib/python3.5/lib-dynload/grp.cpython-35m-x86_64-linux-gnu.so
7f0788e19000-7f0788e1a000 r--p 00001000 fe:01 13111771                   /usr/lib/python3.5/lib-dynload/grp.cpython-35m-x86_64-linux-gnu.so
7f0788e1a000-7f0788e1b000 rw-p 00002000 fe:01 13111771                   /usr/lib/python3.5/lib-dynload/grp.cpython-35m-x86_64-linux-gnu.so
7f0788e1b000-7f0788f9b000 rw-p 00000000 00:00 0 
7f0788f9b000-7f0788fae000 r-xp 00000000 fe:01 13111761                   /usr/lib/python3.5/lib-dynload/_pickle.cpython-35m-x86_64-linux-gnu.so
7f0788fae000-7f07891ad000 ---p 00013000 fe:01 13111761                   /usr/lib/python3.5/lib-dynload/_pickle.cpython-35m-x86_64-linux-gnu.so
7f07891ad000-7f07891ae000 r--p 00012000 fe:01 13111761                   /usr/lib/python3.5/lib-dynload/_pickle.cpython-35m-x86_64-linux-gnu.so
7f07891ae000-7f07891b2000 rw-p 00013000 fe:01 13111761                   /usr/lib/python3.5/lib-dynload/_pickle.cpython-35m-x86_64-linux-gnu.so
7f07891b2000-7f07891ba000 r-xp 00000000 fe:01 13111752                   /usr/lib/python3.5/lib-dynload/_struct.cpython-35m-x86_64-linux-gnu.so[1]    3248 abort (core dumped)  python3 -c "import tables; tables.test()"

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#3 2016-06-01 20:21:13

asphere
Member
Registered: 2016-05-18
Posts: 2

Re: Pytables (HDF5) error

The package maintainers appear to have fixed this issue for us. With my latest pacman upgrade I got pytables 3.2.2-6. I also had to install the new extra/hdf5_18 package (it didn't automatically come in as a dependency). But the pytables test suite for python2 and 3 now runs all the way through.

Last edited by asphere (2016-06-01 20:21:44)

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#4 2016-10-11 15:02:48

mehdi
Member
Registered: 2016-10-05
Posts: 13

Re: Pytables (HDF5) error

Updating pytables totables-3.3.0-cp27-cp27mu-manylinux1_x86_64.whl solved my problem.

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