glibc error in tst_compoundvar

[dopplershift]

From david.huard on February 08, 2010 09:08:06

tst_compoundvar crashes on Ubuntu 9.10 with

netcdf 4.0.1
hdf5 1.8.4
numpy 1.5.0.dev8079

Here is the backtrace, I can't make sense of any of it.
#0 0x00e2c5a6 in ?? () from /lib/tls/i686/cmov/libc.so.6
#1 0x00e2f7cd in free () from /lib/tls/i686/cmov/libc.so.6
#2 0x003498b1 in array_dealloc (self=0x867e670) at

numpy/core/src/multiarray/arrayobject.c:209
#3 0x003498fc in array_dealloc (self=0x8632010) at

numpy/core/src/multiarray/arrayobject.c:196
#4 0x0815eaba in frame_dealloc (f=0x85df994) at ../Objects/frameobject.c:420
#5 0x08101384 in tb_dealloc (tb=0x858293c) at ../Python/traceback.c:28
#6 0x08101394 in tb_dealloc (tb=0x85826bc) at ../Python/traceback.c:27
#7 0x0808e821 in PyDict_DelItem (op=0xb7fbbb54, key=0x85828b8) at

../Objects/dictobject.c:755
#8 0x0808e88c in PyDict_DelItemString (v=0xb7fbbb54, key=0x8215bdd

"exc_traceback")
at ../Objects/dictobject.c:2314
#9 0x080d8554 in reset_exc_info (f=0x85c4854, throwflag=0) at

../Python/ceval.c:3123
#10 PyEval_EvalFrameEx (f=0x85c4854, throwflag=0) at ../Python/ceval.c:2718
#11 0x080dddf2 in PyEval_EvalCodeEx (co=0xb7f94cc8, globals=0xb7f9157c,

locals=0x0, args=0x8584238,
argcount=2, kws=0x84c9390, kwcount=0, defs=0xb7ee1c18, defcount=1,
closure=0x0)
at ../Python/ceval.c:2968
#12 0x0816022f in function_call (func=0xb7ee472c, arg=0x858422c, kw=0x8581a44)

at ../Objects/funcobject.c:524

#13 0x0806120a in PyObject_Call (func=0xb7ee472c, arg=0x858422c, kw=0x8581a44)

at ../Objects/abstract.c:2492

#14 0x080daf19 in ext_do_call (f=0x85c46ec, throwflag=0) at

../Python/ceval.c:4019
#15 PyEval_EvalFrameEx (f=0x85c46ec, throwflag=0) at ../Python/ceval.c:2429
#16 0x080dddf2 in PyEval_EvalCodeEx (co=0xb7f94d10, globals=0xb7f9157c,

locals=0x0, args=0x85841f8,
argcount=2, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at
../Python/ceval.c:2968
#17 0x0816014c in function_call (func=0xb7ee4764, arg=0x85841ec, kw=0x0) at

../Objects/funcobject.c:524
#18 0x0806120a in PyObject_Call (func=0xb7ee4764, arg=0x85841ec, kw=0x0) at

../Objects/abstract.c:2492
#19 0x080684ac in instancemethod_call (func=0x858234c, arg=0x85841ec, kw=0x0)

at ../Objects/classobject.c:2579

#20 0x0806120a in PyObject_Call (func=0x858234c, arg=0x85841cc, kw=0x0) at

../Objects/abstract.c:2492
#21 0x080aedd7 in slot_tp_call (self=0x858410c, args=0x85841cc, kwds=0x0)

at ../Objects/typeobject.c:5378

#22 0x0806120a in PyObject_Call (func=0x858410c, arg=0x85841cc, kw=0x0) at

../Objects/abstract.c:2492
#23 0x080dbc3c in do_call (f=0x85c4584, throwflag=0) at ../Python/ceval.c:3924
#24 call_function (f=0x85c4584, throwflag=0) at ../Python/ceval.c:3729
#25 PyEval_EvalFrameEx (f=0x85c4584, throwflag=0) at ../Python/ceval.c:2389
#26 0x080dddf2 in PyEval_EvalCodeEx (co=0xb7fa04e8, globals=0xb7f9157c,

locals=0x0, args=0x857e758,
argcount=2, kws=0x84c9380, kwcount=0, defs=0x0, defcount=0,
closure=0x0) at ../Python/ceval.c:2968
#27 0x0816022f in function_call (func=0xb7ee4b8c, arg=0x857e74c, kw=0x85819bc)

at ../Objects/funcobject.c:524

#28 0x0806120a in PyObject_Call (func=0xb7ee4b8c, arg=0x857e74c, kw=0x85819bc)

at ../Objects/abstract.c:2492

#29 0x080daf19 in ext_do_call (f=0x85c441c, throwflag=0) at

../Python/ceval.c:4019
#30 PyEval_EvalFrameEx (f=0x85c441c, throwflag=0) at ../Python/ceval.c:2429
#31 0x080dddf2 in PyEval_EvalCodeEx (co=0xb7fa0530, globals=0xb7f9157c,

locals=0x0, args=0x8584138,
argcount=2, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at
../Python/ceval.c:2968
#32 0x0816014c in function_call (func=0xb7ee4bc4, arg=0x858412c, kw=0x0) at

../Objects/funcobject.c:524
#33 0x0806120a in PyObject_Call (func=0xb7ee4bc4, arg=0x858412c, kw=0x0) at

../Objects/abstract.c:2492
---Type to continue, or q to quit---
#34 0x080684ac in instancemethod_call (func=0x857df7c, arg=0x858412c, kw=0x0)

at ../Objects/classobject.c:2579

#35 0x0806120a in PyObject_Call (func=0x857df7c, arg=0x858408c, kw=0x0) at

../Objects/abstract.c:2492
#36 0x080aedd7 in slot_tp_call (self=0x85840ec, args=0x858408c, kwds=0x0)

at ../Objects/typeobject.c:5378

#37 0x0806120a in PyObject_Call (func=0x85840ec, arg=0x858408c, kw=0x0) at

../Objects/abstract.c:2492
#38 0x080dbc3c in do_call (f=0x85c42b4, throwflag=0) at ../Python/ceval.c:3924
#39 call_function (f=0x85c42b4, throwflag=0) at ../Python/ceval.c:3729
#40 PyEval_EvalFrameEx (f=0x85c42b4, throwflag=0) at ../Python/ceval.c:2389
#41 0x080dddf2 in PyEval_EvalCodeEx (co=0xb7fa04e8, globals=0xb7f9157c,

locals=0x0, args=0x857e878,
argcount=2, kws=0x82f12f0, kwcount=0, defs=0x0, defcount=0,
closure=0x0) at ../Python/ceval.c:2968
#42 0x0816022f in function_call (func=0xb7ee4b8c, arg=0x857e86c, kw=0x8581934)

at ../Objects/funcobject.c:524

#43 0x0806120a in PyObject_Call (func=0xb7ee4b8c, arg=0x857e86c, kw=0x8581934)

at ../Objects/abstract.c:2492

#44 0x080daf19 in ext_do_call (f=0x85c414c, throwflag=0) at

../Python/ceval.c:4019
#45 PyEval_EvalFrameEx (f=0x85c414c, throwflag=0) at ../Python/ceval.c:2429
#46 0x080dddf2 in PyEval_EvalCodeEx (co=0xb7fa0530, globals=0xb7f9157c,

locals=0x0, args=0x857e958,
argcount=2, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at
../Python/ceval.c:2968
#47 0x0816014c in function_call (func=0xb7ee4bc4, arg=0x857e94c, kw=0x0) at

../Objects/funcobject.c:524
#48 0x0806120a in PyObject_Call (func=0xb7ee4bc4, arg=0x857e94c, kw=0x0) at

../Objects/abstract.c:2492
#49 0x080684ac in instancemethod_call (func=0x857df54, arg=0x857e94c, kw=0x0)

at ../Objects/classobject.c:2579

#50 0x0806120a in PyObject_Call (func=0x857df54, arg=0x857edcc, kw=0x0) at

../Objects/abstract.c:2492
#51 0x080aedd7 in slot_tp_call (self=0x857efec, args=0x857edcc, kwds=0x0)

at ../Objects/typeobject.c:5378

#52 0x0806120a in PyObject_Call (func=0x857efec, arg=0x857edcc, kw=0x0) at

../Objects/abstract.c:2492
#53 0x080dbc3c in do_call (f=0x85c3a1c, throwflag=0) at ../Python/ceval.c:3924
#54 call_function (f=0x85c3a1c, throwflag=0) at ../Python/ceval.c:3729
#55 PyEval_EvalFrameEx (f=0x85c3a1c, throwflag=0) at ../Python/ceval.c:2389
#56 0x080dd384 in fast_function (f=0x85c38ac, throwflag=0) at

../Python/ceval.c:3792
#57 call_function (f=0x85c38ac, throwflag=0) at ../Python/ceval.c:3727
#58 PyEval_EvalFrameEx (f=0x85c38ac, throwflag=0) at ../Python/ceval.c:2389
#59 0x080dd384 in fast_function (f=0x85c0a6c, throwflag=0) at

../Python/ceval.c:3792
#60 call_function (f=0x85c0a6c, throwflag=0) at ../Python/ceval.c:3727
#61 PyEval_EvalFrameEx (f=0x85c0a6c, throwflag=0) at ../Python/ceval.c:2389
#62 0x080dddf2 in PyEval_EvalCodeEx (co=0xb7ee03c8, globals=0xb7f9157c,

locals=0x0, args=0x857ec98,
argcount=1, kws=0x0, kwcount=0, defs=0xb7ee3158, defcount=5,
closure=0x0) at ../Python/ceval.c:2968
#63 0x0816014c in function_call (func=0xb7ee53e4, arg=0x857ec8c, kw=0x0) at

../Objects/funcobject.c:524
#64 0x0806120a in Py...

Original issue: http://code.google.com/p/netcdf4-python/issues/detail?id=35

[dopplershift]

From whitaker.jeffrey@gmail.com on February 08, 2010 08:13:23

David: You need netcdf-4.1 for the compound variable stuff to work. I doubt that will
fix the crash though, seems like the backtrace emanates from numpy.

-Jeff

[dopplershift]

From david.huard on February 08, 2010 13:09:20

I created a function _netcdf_version in r840 that checks the version number of the
netcdf library. It works on *nix, but I need to check it on windows.

The version number is checked before running tst_compoundvar.

Status: Started

[dopplershift]

From whitaker.jeffrey@gmail.com on February 08, 2010 15:08:16

David: There was already a function that does this in utils.pyx

def getlibversion():
"""
getlibversion()

returns a string describing the version of the netcdf library
used to build the module, and when it was built.
"""
cdef char *libstring
libstring = nc_inq_libvers()
return PyString_FromString(libstring)

It calls the C lib, and doesn't rely on nc-config, so it should work on windows.

I'm happy to just require 4.1 anyway, since 4.0.1 is so buggy.

-Jeff

[dopplershift]

From cjgoh...@gmail.com on February 08, 2010 17:28:37

The addition of the _netcdf_version function breaks testing on Windows. Nc-config is
a Unix shell script.

python run_all.py

Traceback (most recent call last):
File "run_all.py", line 15, in
version = netCDF4._netcdf_version()
File "X:\Python26\lib\site-packages\netCDF4_utils.py", line 10, in _netcdf_version
output = subprocess.Popen(["nc-config", "--version"],
stdout=subprocess.PIPE).communicate()[0]
File "X:\Python26\lib\subprocess.py", line 621, in init
errread, errwrite)
File "X:\Python26\lib\subprocess.py", line 830, in _execute_child
startupinfo)
WindowsError: [Error 2] The system cannot find the file specified

[dopplershift]

From whitaker.jeffrey@gmail.com on February 08, 2010 19:09:58

I modified tst_compoundvar.py to use getlibversion, so it should now work on windows.

[dopplershift]

From david.huard on March 29, 2010 07:26:43

I removed the _netcdf4_version function and regenerated the .c files in r862 . Do you
want to raise an error at import if version < 4.1 ?

[dopplershift]

From whitaker.jeffrey@gmail.com on March 29, 2010 08:25:04

When netcdf 4.1 is released, I think we probably should. We might also modify setup.py to check for hdf5 >
1.8.4-patch1.

[dopplershift]

From whitaker.jeffrey@gmail.com on March 30, 2010 09:12:20

In svn trunk an ImportError is now raised if the netcdf-4 lib version < 4.1.1 and hdf5 <= 1.8.4.

[dopplershift]

From whitaker.jeffrey@gmail.com on February 25, 2014 18:04:09

Status: Fixed