Hi Fransesc,
I had a quick look now what would happen with HDF5 1.8.0 beta5 (compiled
with the api version flag in configure) and Pytables 2.0.2. To make pytables
compile with it, I specified a correct HDF5_DIR and had to edit src/
utils.c to choose the first branch in the #ifdef at src/utils.c:204.
When running the example code, I get a segfault (see below). It may
either be that I compiled HDF5 with Pytables somehow incorrectly, or that
there is at present some incompatibility b/w 1.8.0 and Pytables. I'll
have to look into this in more detail another day as it is getting late,
but possibly I could try to isolate a smaller C fragment that exhibits
the same problem.
Regards,
Pauli
***
lib/python2.5/site-packages$ cat ../../../xxx.py
#!/usr/bin/env python
import tables, numpy
print tables.__file__
print tables.hdf5Extension.__file__
N = 600
f = tables.openFile('foo.h5', 'w')
f.createCArray(f.root, 'huge_array',
tables.Float64Atom(),
shape = (2,2,N,N,50,50))
for i in xrange(50):
for j in xrange(50):
f.root.huge_array[:,:,:,:,j,i] = \
numpy.array([[1,0],[0,1]])[:,:,None,None]
lib/python2.5/site-packages$ LD_LIBRARY_PATH=../../ gdb --args python2.5
../../../xxx.py
GNU gdb 6.6-debian
Copyright (C) 2006 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you
are
welcome to change it and/or distribute copies of it under certain
conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for
details.
This GDB was configured as "i486-linux-gnu"...
Using host libthread_db library "/lib/tls/i686/cmov/libthread_db.so.1".
(gdb) run
Starting program: /usr/bin/python2.5 ../../../xxx.py
[Thread debugging using libthread_db enabled]
[New Thread -1210186064 (LWP 12304)]
/home/installer/build/hdf5/dist/tables/__init__.pyc
/home/installer/build/hdf5/dist/tables/hdf5Extension.so
/home/installer/build/hdf5/dist/tables/leaf.py:419: PerformanceWarning:
The Leaf ``/huge_array`` is exceeding the maximum recommended rowsize
(96000000 bytes);
be ready to see PyTables asking for *lots* of memory and possibly slow
I/O. You may want to reduce the rowsize by trimming the value of
dimensions that are orthogonal (and preferably close) to the main
dimension of this leave. Alternatively, in case you have specified a
very small/large chunksize, you may want to increase/decrease it.
PerformanceWarning)
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread -1210186064 (LWP 12304)]
0xb7b578b1 in H5S_close (ds=0xbfb11178) at H5S.c:464
464 H5S_SELECT_RELEASE(ds);
(gdb) bt
#0 0xb7b578b1 in H5S_close (ds=0xbfb11178) at H5S.c:464
#1 0xb7a0ab4e in H5D_destroy_chunk_map (fm=0xbfb0fff8) at H5Dio.c:2651
#2 0xb7a0b04c in H5D_create_chunk_map (fm=0xbfb0fff8,
io_info=<value optimized out>, nelmts=1440000, file_space=0x84bd140,
mem_space=0x84b40f0, mem_type=0x8363000) at H5Dio.c:2556
#3 0xb7a0cd1a in H5D_chunk_write (io_info=0xbfb13c24, nelmts=1440000,
mem_type=0x8363000, mem_space=0x84b40f0, file_space=0x84bd140,
tpath=0x8363e30, src_id=50331970, dst_id=50331966, buf=0xb57b8008)
at H5Dio.c:1765
#4 0xb7a106f9 in H5D_write (dataset=0x840a418, mem_type_id=50331970,
mem_space=0x84b40f0, file_space=0x84bd140, dxpl_id=167772168,
buf=0xb57b8008) at H5Dio.c:732
#5 0xb7a117aa in H5Dwrite (dset_id=83886080, mem_type_id=50331970,
mem_space_id=67108874, file_space_id=67108875, plist_id=167772168,
buf=0xb57b8008) at H5Dio.c:434
#6 0xb6321443 in H5ARRAYwrite_records (dataset_id=83886080,
type_id=50331970,
rank=6, start=0x8395a10, step=0x84beec8, count=0x84bfc08,
data=0xb57b8008)
at src/H5ARRAY.c:344
#7 0xb6316976 in __pyx_f_13hdf5Extension_5Array__modify (
__pyx_v_self=0xb7d62614, __pyx_args=0xb7d667ac, __pyx_kwds=0x0)
at src/hdf5Extension.c:3751
#8 0x080c8eec in PyEval_EvalFrameEx (f=0x84beb04, throwflag=0)
at ../Python/ceval.c:3564
#9 0x080ca115 in PyEval_EvalCodeEx (co=0x83b9ad0, globals=0x834bf0c,
locals=0x0, args=0xb7d77bf0, argcount=3, kws=0x0, kwcount=0,
defs=0x0,
defcount=0, closure=0x0) at ../Python/ceval.c:2831
#10 0x081123e1 in function_call (func=0x83bf3ac, arg=0xb7d77be4, kw=0x0)
at ../Objects/funcobject.c:517
#11 0x0805c9e7 in PyObject_Call (func=0x83960e0, arg=0xb7d77be4, kw=0x0)
at ../Objects/abstract.c:1860
#12 0x08062b44 in instancemethod_call (func=0x844166c, arg=0xb7d77be4,
kw=0x0)
at ../Objects/classobject.c:2509
#13 0x0805c9e7 in PyObject_Call (func=0x83960e0, arg=0x8445ccc, kw=0x0)
at ../Objects/abstract.c:1860
#14 0x080a6da1 in call_method (o=0xb7d62614, name=0x81243c0
"__setitem__",
nameobj=0x8164a6c, format=0x81296ed "(OO)") at ../Objects/
typeobject.c:929
#15 0x080a775b in slot_mp_ass_subscript (self=0x83960e0, key=0x24,
value=0x6f206568) at ../Objects/typeobject.c:4302
#16 0x080c550e in PyEval_EvalFrameEx (f=0x818510c, throwflag=0)
at ../Python/ceval.c:1497
#17 0x080ca115 in PyEval_EvalCodeEx (co=0xb7d629b0, globals=0xb7db9acc,
locals=0xb7db9acc, args=0x0, argcount=0, kws=0x0, kwcount=0,
defs=0x0,
defcount=0, closure=0x0) at ../Python/ceval.c:2831
#18 0x080ca187 in PyEval_EvalCode (co=0xb7d629b0, globals=0xb7db9acc,
locals=0xb7db9acc) at ../Python/ceval.c:494
#19 0x080e9698 in PyRun_FileExFlags (fp=0x816a008,
filename=0xbfb15648 "../../../xxx.py", start=257, globals=0xb7db9acc,
locals=0xb7db9acc, closeit=1, flags=0xbfb146d8)
at ../Python/pythonrun.c:1273
#20 0x080e9927 in PyRun_SimpleFileExFlags (fp=0x816a008,
filename=0xbfb15648 "../../../xxx.py", closeit=1, flags=0xbfb146d8)
at ../Python/pythonrun.c:879
#21 0x08059390 in Py_Main (argc=1, argv=0xbfb147a4) at ../Modules/
main.c:523
#22 0x080588c2 in main (argc=138337488, argv=0x8390fd8)
at ../Modules/python.c:23
(gdb) q
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