[issue27480] Cannot link _crypt and _nis modules on a host with glibc-2.12

2016-07-11 Thread Martin Mokrejs

Changes by Martin Mokrejs <mmokr...@users.sourceforge.net>:


Added file: http://bugs.python.org/file43693/nohup-gentoo-prefix.out

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[issue27480] Cannot link _crypt and _nis modules on a host with glibc-2.12

2016-07-11 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Interesting, using the system-wide RedHat stuff I can compile vanilla 
Python-3.4.5. See attached nohup.out. I tried to stick to the same configure 
arguments as Gentoo's package manager used.

I also tried to compile the vanilla tarball under Gentoo::Prefix and wow, it 
also went through (as fat as _crypt is concerned). See nohup-gentoo-prefix.out

--
Added file: http://bugs.python.org/file43692/nohup.out

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[issue27480] Cannot link _crypt and _nis modules on a host with glibc-2.12

2016-07-11 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Ah, thank you for a quick answer.

The problem is not with a Gentoo, the problem is with python which needs too 
new libc or libnss or libcrypt.

I am re-opening, why cannot I compile newer python version on glibc-2.12 host? 
This is not a problme with python-2.7, at least.

https://bugs.gentoo.org/show_bug.cgi?id=587664

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[issue27480] Cannot link _crypt and _nis modules on a host with glibc-2.12

2016-07-11 Thread Martin Mokrejs

Changes by Martin Mokrejs <mmokr...@users.sourceforge.net>:


--
versions: +Python 3.5

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[issue27480] Cannot link _crypt and _nis modules on a host with glibc-2.12

2016-07-11 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Also is an issue with 3.5.1-r3:

x86_64-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -L. 
-L/scratch/mmokrejs/gentoo/lib -L/scratch/mmokrejs/gentoo/usr/lib 
-Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -O2 
-pipe -march=native -fwrapv 
build/temp.linux-x86_64-3.5/scratch/mmokrejs/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/_decimal.o
 
build/temp.linux-x86_64-3.5/scratch/mmokrejs/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/libmpdec/basearith.o
 
build/temp.linux-x86_64-3.5/scratch/mmokrejs/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/libmpdec/constants.o
 
build/temp.linux-x86_64-3.5/scratch/mmokrejs/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/libmpdec/context.o
 
build/temp.linux-x86_64-3.5/scratch/mmokrejs/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/libmpdec/convolute.o
 build/temp.linux-x86_64-3.5/scratch/mmokre
 
js/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/libmpdec/crt.o
 
build/temp.linux-x86_64-3.5/scratch/mmokrejs/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/libmpdec/difradix2.o
 
build/temp.linux-x86_64-3.5/scratch/mmokrejs/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/libmpdec/fnt.o
 
build/temp.linux-x86_64-3.5/scratch/mmokrejs/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/libmpdec/fourstep.o
 
build/temp.linux-x86_64-3.5/scratch/mmokrejs/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/libmpdec/io.o
 
build/temp.linux-x86_64-3.5/scratch/mmokrejs/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/libmpdec/memory.o
 
build/temp.linux-x86_64-3.5/scratch/mmokrejs/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/libmpdec/mpdecimal.o
 build/temp.linux-x8
 
6_64-3.5/scratch/mmokrejs/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/libmpdec/numbertheory.o
 
build/temp.linux-x86_64-3.5/scratch/mmokrejs/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/libmpdec/sixstep.o
 
build/temp.linux-x86_64-3.5/scratch/mmokrejs/gentoo/var/tmp/portage/dev-lang/python-3.5.1-r3/work/Python-3.5.1/Modules/_decimal/libmpdec/transpose.o
 -L. -L/scratch/mmokrejs/gentoo/lib -L/scratch/mmokrejs/gentoo/usr/lib 
-lpython3.5 -o 
build/lib.linux-x86_64-3.5/_decimal.cpython-35-x86_64-linux-gnu.so
*** WARNING: renaming "_crypt" since importing it failed: 
build/lib.linux-x86_64-3.5/_crypt.cpython-35-x86_64-linux-gnu.so: undefined 
symbol: crypt
*** WARNING: renaming "nis" since importing it failed: 
build/lib.linux-x86_64-3.5/nis.cpython-35-x86_64-linux-gnu.so: undefined 
symbol: yp_master

Following modules built successfully but were removed because they could not be 
imported:
_cryptnis

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[issue27480] Cannot link _crypt and _nis modules on a host with glibc-2.12

2016-07-11 Thread Martin Mokrejs

New submission from Martin Mokrejs:

Hi,
  it seems at least python 3.4.3-r5 on a Gentoo Linux.

Failed to build these modules:
_cryptnis

--
files: build.log
messages: 270163
nosy: mmokrejs
priority: normal
severity: normal
status: open
title: Cannot link _crypt and _nis modules on a host with glibc-2.12
type: compile error
versions: Python 3.4
Added file: http://bugs.python.org/file43684/build.log

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[issue25965] decimal.py: issues reprted by pychecker

2015-12-28 Thread Martin Mokrejs

New submission from Martin Mokrejs:

I use pychecker to check my code. It complains about decimal.py from 
python-2.7.10 itself:

[system path]/decimal.py:1345: INTERNAL ERROR -- STOPPED PROCESSING FUNCTION --
Traceback (most recent call last):
  File "/usr/lib64/python2.7/site-packages/pychecker/warn.py", line 
242, in _checkFunction
_checkCode(code, codeSource)
  File "/usr/lib64/python2.7/site-packages/pychecker/warn.py", line 
155, in _checkCode
raise NotImplementedError('No DISPATCH member for op %r' % op)
NotImplementedError: No DISPATCH member for op 28

[system path]/decimal.py:1546: Invalid arguments to (__floordiv__), got 3, 
expected 2
[system path]/decimal.py:1574: Invalid arguments to (__rfloordiv__), got 3, 
expected 2
[system path]/decimal.py:1997: INTERNAL ERROR -- STOPPED PROCESSING FUNCTION --
Traceback (most recent call last):
  File "/usr/lib64/python2.7/site-packages/pychecker/warn.py", line 
242, in _checkFunction
_checkCode(code, codeSource)
  File "/usr/lib64/python2.7/site-packages/pychecker/warn.py", line 
155, in _checkCode
raise NotImplementedError('No DISPATCH member for op %r' % op)
NotImplementedError: No DISPATCH member for op 28

[system path]/decimal.py:2173: Invalid arguments to (__pow__), got 4, expected 3
[system path]/decimal.py:2389: Invalid arguments to (__rpow__), got 3, expected 
2
[system path]/decimal.py:2692: INTERNAL ERROR -- STOPPED PROCESSING FUNCTION --
Traceback (most recent call last):
  File "/usr/lib64/python2.7/site-packages/pychecker/warn.py", line 
242, in _checkFunction
_checkCode(code, codeSource)
  File "/usr/lib64/python2.7/site-packages/pychecker/warn.py", line 
155, in _checkCode
raise NotImplementedError('No DISPATCH member for op %r' % op)
NotImplementedError: No DISPATCH member for op 28

--
components: Library (Lib)
messages: 257111
nosy: mmokrejs
priority: normal
severity: normal
status: open
title: decimal.py: issues reprted by pychecker
versions: Python 2.7

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[issue25965] decimal.py: issues reported by pychecker

2015-12-28 Thread Martin Mokrejs

Changes by Martin Mokrejs <mmokr...@users.sourceforge.net>:


--
title: decimal.py: issues reprted by pychecker -> decimal.py: issues reported 
by pychecker

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[issue25964] optparse.py:1668: (file) shadows builtin

2015-12-28 Thread Martin Mokrejs

Martin Mokrejs added the comment:

But couldn't somebody just rename the variable for example to _file? I see 
optparse also in python-3.5 so I did not think it could be Deprecated.

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[issue25964] optparse.py:1668: (file) shadows builtin

2015-12-28 Thread Martin Mokrejs

New submission from Martin Mokrejs:

I use pychecker for checking my python code. Seems optparse.py distributed with 
python-2.7 could be improved as well:

[system path]/optparse.py:1191: Function (__init__) has too many arguments (11)
[system path]/optparse.py:1206: Local variable (version) shadows global defined 
on line 10 in file my-test-code.py
[system path]/optparse.py:1400: Local variable (stop) not used
[system path]/optparse.py:1668: (file) shadows builtin


Interestingly, my version variable is overridden by one from optparse.py. But 
more worrisome is the 'file' variable name.

--
messages: 257110
nosy: mmokrejs
priority: normal
severity: normal
status: open
title: optparse.py:1668: (file) shadows builtin
type: enhancement
versions: Python 2.7

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[issue18897] Illegal instruction at Python-2.7.5/Modules/_sre.c:1173

2013-12-01 Thread Martin Mokrejs

Martin Mokrejs added the comment:

The issue could have been caused the malfunctioning memory or CPU.
http://bugs.python.org/issue18843#msg204954

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-12-01 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Hi,
  I think I should report back what I found on the hardware side. While memory 
testing tools like memtest86+ and other did not find any error, the built in 
Dell ePSA test suite likely does compute a checksum of tested memory regions. 
It reported some addresses/regions as failed, sadly nobody seems to know 
details of the failing tests. On repeated testing different memory regions were 
reported, so I never understood whether that is a bad CPU cache or something 
randomizing the issue observed. At least, only one of the two SO-DIMMs caused 
the problems so lets conclude it was partly baked up and failing randomly. At 
that time it seemed the cause was either bad CPU producing just too much heat 
or the fan. Fan was replaced, max temps went down from 92 oC to 82 oC. Two 
months later I faced more and more often that an external HDMI-connected 
display did not receive signal, so even the CPU got replaced. I got another 
drop in max temperatures, now max are about 70 oC. Cool!

Back to python, the random crashes of my apps stopped after the memory module 
being replaced, actually who pair was replaced. I started to dream about linux 
kernel making mirroring inside memory for failure resiliency but there is 
nothing like that available.

In summary, this lesson was hard and showed that there are no good tools to 
test hardware. Checksums should be used always and bits tested for fading over 
the time. The mirroring trick could have also uncovered a failing memory or 
CPU. Seems there is still way to go to a perfect computer.

Thanks to everybody for their efforts on this issue. Whether python takes 
something from this lesson is up to you.

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status: pending - open

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[issue18845] 2.7.5-r2: Fatal Python error: Segmentation fault

2013-12-01 Thread Martin Mokrejs

Martin Mokrejs added the comment:

The issue could have been caused the malfunctioning memory or CPU.
http://bugs.python.org/issue18843#msg204954

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-31 Thread Martin Mokrejs

Martin Mokrejs added the comment:

So with your test program I did not yet hit the error. It used in the end 1.3GB 
of RAM, maybe in the good region. while this was python-2.7.5 configures as 
--without-pymalloc maybe the output from valgrind becomes more useful.

--
Added file: http://bugs.python.org/file31532/stress.valgrind.stderr

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[issue18897] Illegal instruction at Python-2.7.5/Modules/_sre.c:1173

2013-08-31 Thread Martin Mokrejs

New submission from Martin Mokrejs:

I was trying to use DUMA to find errors in python runtime and it indeed killed 
python-based utility called emerge. Let's see what you say now:

# export LD_PRELOAD=/usr/lib64/libduma.so.0.0.0
# sysctl -w vm.max_map_count=100

# emerge dev-lang/python:2.7 
DUMA 2.5.15 (shared library, NO_LEAKDETECTION)
Copyright (C) 2006 Michael Eddington medding...@gmail.com
Copyright (C) 2002-2008 Hayati Ayguen h_ayg...@web.de, Procitec GmbH
Copyright (C) 1987-1999 Bruce Perens br...@perens.com

DUMA 2.5.15 (shared library, NO_LEAKDETECTION)
Copyright (C) 2006 Michael Eddington medding...@gmail.com
Copyright (C) 2002-2008 Hayati Ayguen h_ayg...@web.de, Procitec GmbH
Copyright (C) 1987-1999 Bruce Perens br...@perens.com

DUMA 2.5.15 (shared library, NO_LEAKDETECTION)
Copyright (C) 2006 Michael Eddington medding...@gmail.com
Copyright (C) 2002-2008 Hayati Ayguen h_ayg...@web.de, Procitec GmbH
Copyright (C) 1987-1999 Bruce Perens br...@perens.com


DUMA Aborting: mprotect() failed: Cannot allocate memory.
Check README section 'MEMORY USAGE AND EXECUTION SPEED'
  if your (Linux) system may limit the number of different page mappings per 
process
Illegal instruction (core dumped)
# ulimit -a
core file size  (blocks, -c) unlimited
data seg size   (kbytes, -d) unlimited
scheduling priority (-e) 0
file size   (blocks, -f) unlimited
pending signals (-i) 127104
max locked memory   (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files  (-n) 1024
pipe size(512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority  (-r) 0
stack size  (kbytes, -s) 8192
cpu time   (seconds, -t) unlimited
max user processes  (-u) 127104
virtual memory  (kbytes, -v) unlimited
file locks  (-x) unlimited
#

(gdb) where
#0  0x7febd6ed84d7 in kill () from /lib64/libc.so.6
#1  0x7febd78e2f9c in DUMA_Abort () from /usr/lib64/libduma.so.0.0.0
#2  0x7febd78e1b77 in _duma_allocate () from /usr/lib64/libduma.so.0.0.0
#3  0x7febd78e1fef in _duma_malloc () from /usr/lib64/libduma.so.0.0.0
#4  0x7febd7626c60 in sre_umatch (state=0x7fff96f0de10, 
pattern=0x7feb2804ecb8) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Modules/_sre.c:1173
#5  0x7febd762932f in pattern_match (self=0x7feb2804ec58, 
args=(u'=gnome-base/libbonobo-2.32::gentoo-haskell',), kw=0x0) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Modules/_sre.c:1896
#6  0x7febd751ffcc in PyCFunction_Call (func=built-in method match of 
_sre.SRE_Pattern object at remote 0x7feb2804ec58, 
arg=(u'=gnome-base/libbonobo-2.32::gentoo-haskell',), kw=0x0) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Objects/methodobject.c:85
#7  0x7febd75c4b81 in call_function (pp_stack=0x7fff96f0e6d0, oparg=1) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Python/ceval.c:4021
#8  0x7febd75bf6c6 in PyEval_EvalFrameEx (f=Frame 0x7feb374ebce8, for file 
/usr/lib64/portage/pym/portage/dep/__init__.py, line 1227, in __init__ 
(self=Atom(blocker=False, eapi=None) at remote 0x7fea931d5fb0, 
s=u'=gnome-base/libbonobo-2.32::gentoo-haskell', unevaluated_atom=None, 
allow_wildcard=True, allow_repo=True, _use=None, eapi=None, is_valid_flag=None, 
eapi_attrs=_eapi_attrs at remote 0x7feb31931f48, atom_re=_sre.SRE_Pattern at 
remote 0x7feb2804ec58, blocker_prefix=u'', blocker=False), throwflag=0) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Python/ceval.c:2666

[cut]

(gdb) bt full
#0  0x7febd6ed84d7 in kill () from /lib64/libc.so.6
No symbol table info available.
#1  0x7febd78e2f9c in DUMA_Abort () from /usr/lib64/libduma.so.0.0.0
No symbol table info available.
#2  0x7febd78e1b77 in _duma_allocate () from /usr/lib64/libduma.so.0.0.0
No symbol table info available.
#3  0x7febd78e1fef in _duma_malloc () from /usr/lib64/libduma.so.0.0.0
No symbol table info available.
#4  0x7febd7626c60 in sre_umatch (state=0x7fff96f0de10, 
pattern=0x7feb2804ecb8) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Modules/_sre.c:1173
end = 0x7fea931cfffc
alloc_pos = 1648
ctx_pos = 1648
i = 128
ret = 0
jump = 2
sigcount = 187
ctx = 0x7fea931fbcf8
nextctx = 0x7fea931fbcf8
__PRETTY_FUNCTION__ = sre_umatch
#5  0x7febd762932f in pattern_match (self=0x7feb2804ec58, 
args=(u'=gnome-base/libbonobo-2.32::gentoo-haskell',), kw=0x0) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Modules/_sre.c:1896
state = {ptr = 0x7fea931cffbc, beginning = 0x7fea931cff50, start = 
0x7fea931cff50, end = 0x7fea931cfffc, string = 
u'=gnome-base/libbonobo-2.32::gentoo-haskell', pos = 0, endpos = 43, charsize 
= 4, lastindex = 2

[issue18897] Illegal instruction at Python-2.7.5/Modules/_sre.c:1173

2013-08-31 Thread Martin Mokrejs

Martin Mokrejs added the comment:

To a naive user two places with numbers are in the stacktrace:

size = -1282872823

and
instr_ub = -1
instr_lb = 0
instr_prev = -1

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[issue18897] Illegal instruction at Python-2.7.5/Modules/_sre.c:1173

2013-08-31 Thread Martin Mokrejs

Martin Mokrejs added the comment:

I was actually printing every 10 seconds how much memory it was using, the last 
before got killed was:

  PIDVSZ   RSS TIME ELAPSED %CPU %MEM COMMAND
 4097 4938188 2445712 00:22:4425:04 90.7 15.0 /usr/bin/python2.7 
/usr/bin/emerge dev-lang/python:2.7

Provided I have 16GB RAM then maybe it was really some limit in the Bourne 
shell or OS which prevented DUMA to obtain more memory. But my own python-based 
app can can grow to even 12GB RSS on this computer so I wonder what limit would 
be the cause. Probably some overhead due to DUMA.



I increased shell limits and looks it can continue further so far:

vostro crashtest # ulimit -l unlimited
vostro crashtest # ulimit -s unlimited
vostro crashtest # ulimit -i unlimited
vostro crashtest # 
vostro crashtest # ulimit -a
core file size  (blocks, -c) unlimited
data seg size   (kbytes, -d) unlimited
scheduling priority (-e) 0
file size   (blocks, -f) unlimited
pending signals (-i) unlimited
max locked memory   (kbytes, -l) unlimited
max memory size (kbytes, -m) unlimited
open files  (-n) 1024
pipe size(512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority  (-r) 0
stack size  (kbytes, -s) unlimited
cpu time   (seconds, -t) unlimited
max user processes  (-u) 127104
virtual memory  (kbytes, -v) unlimited
file locks  (-x) unlimited
#


Currently the emerge through DUMA is at:

  PIDVSZ   RSS TIME ELAPSED %CPU %MEM COMMAND
 9528 6121764 3041960 00:34:1656:05 61.1 18.6 /usr/bin/python2.7 
/usr/bin/emerge dev-lang/python:2.7

and still continues ...


Sorry, should better read the main STDERR output before diving into gdb 
stacktraces. I thought those negative numbers are a true sign of an error. ;)

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[issue17628] str==str: compare the first character before calling memcmp()

2013-08-31 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Regarding benchmarking and code performance inspection, maybe you want to try 
on your linux box:

perf top
perf stat /usr/bin/python mytest.py

http://perf.wiki.kernel.org/

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-30 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Hi Stephen,
  I discussed the USE=debug here 
(https://bugs.gentoo.org/show_bug.cgi?id=482348) and it is denied by portage 
maintainers because it is not only a debug addition but a whole API change. We 
have to live with:

mkdir -p /etc/portage/env
echo 'EXTRA_ECONF=--with-pydebug'  /etc/portage/env/pydebug.conf
echo dev-lang/python pydebug.conf  /etc/portage/package.env


The above what I had originally. Yesterday I tried even:

# cat /etc/portage/env/pydebug.conf 
EXTRA_ECONF=--with-pydebug --without-pymalloc --with-valgrind
#

but I don't know what the valgrind option really does and, whether that means:
a) python will run itself under valgrind, don't both doing it yourself
b) you don't have to bother with uncommenting the lines in valgrind.supp
c) make install will install the valgrind.supp but you have to edit it on 
your own
d) you may use valgrind but don't use other tool replacing malloc(), like 
electric fence, DUMA, etc.

Or some combination of them? :( The Readme.valgrind does not answer this at all.

I let DUMA inspect emerge boost run overnight but my computer stopped 
responding (16GB RAM).

I tried only gcc-4.7.3 and python-2.7.5-r2.

CFLAGS=-ggdb -pipe -msse  -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4 -mavx 
-maes -mpclmul -mpopcnt -march=corei7-avx
CXXFLAGS=${CFLAGS}


Per comment from Charles-François, so you mean that this single-bit change 
won't be caught by valgrind, right? Why does not memtest86+ detect that? Could 
python when compiled with the --with-pydebug print also physical, hardware 
address of the wrong value? That would be really helpful here! Thanks.

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[issue18883] python-3.3.2-r2: Modules/xxlimited.c:17:error: #error Py_LIMITED_API is incompatible with Py_DEBUG, Py_TRACE_REFS, and Py_REF_DEBUG

2013-08-30 Thread Martin Mokrejs

New submission from Martin Mokrejs:

Looks I cannot compile when python-3.3 was configured with --with-pydebug. I 
use Gentoo Linux, the -r2 shows they added some patches but should not matter I 
think.

building 'xxlimited' extension
x86_64-pc-linux-gnu-gcc -pthread -fPIC -Wno-unused-result 
-DDYNAMIC_ANNOTATIONS_ENABLED=1 -O2 -pipe -msse -msse2 -msse3 -mssse3 -msse4.1 
-msse4.2 -msse4 -mavx -maes -mpclmul -mpopcnt -march=corei7-avx 
-fstack-protector-all -fwrapv -DPy_LIMITED_API=1 -IInclude -I. 
-I/mnt/1TB/var/tmp/portage/dev-lang/python-3.3.2-r2/work/Python-3.3.2/Include 
-I/mnt/1TB/var/tmp/portage/dev-lang/python-3.3.2-r2/work/x86_64-pc-linux-gnu -c 
/mnt/1TB/var/tmp/portage/dev-lang/python-3.3.2-r2/work/Python-3.3.2/Modules/xxlimited.c
 -o 
build/temp.linux-x86_64-3.3-pydebug/mnt/1TB/var/tmp/portage/dev-lang/python-3.3.2-r2/work/Python-3.3.2/Modules/xxlimited.o
In file included from 
/mnt/1TB/var/tmp/portage/dev-lang/python-3.3.2-r2/work/Python-3.3.2/Include/Python.h:68:0,
 from 
/mnt/1TB/var/tmp/portage/dev-lang/python-3.3.2-r2/work/Python-3.3.2/Modules/xxlimited.c:17:
/mnt/1TB/var/tmp/portage/dev-lang/python-3.3.2-r2/work/Python-3.3.2/Include/object.h:65:2:
 error: #error Py_LIMITED_API is incompatible with Py_DEBUG, Py_TRACE_REFS, and 
Py_REF_DEBUG


I think make should ignore this error unless you fix xxlimited.c sources.

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files: build.log
messages: 196534
nosy: mmokrejs
priority: normal
severity: normal
status: open
title: python-3.3.2-r2: Modules/xxlimited.c:17:error: #error Py_LIMITED_API is 
incompatible with Py_DEBUG, Py_TRACE_REFS, and Py_REF_DEBUG
type: compile error
versions: Python 3.3
Added file: http://bugs.python.org/file31520/build.log

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[issue18884] python-2.7.5-r3: 40 bytes in 1 blocks are definitely lost

2013-08-30 Thread Martin Mokrejs

New submission from Martin Mokrejs:

It is not important why I had in this moment matplotlib not in sync with python 
itself whcih was configure using --with-pydebug ... but here I just want to 
show that maybe you do not test for memleaks using valgrind on import errors 
(maybe include such testcase into you tests).
Anyway, here is what I got:


==14007== Memcheck, a memory error detector
==14007== Copyright (C) 2002-2012, and GNU GPL'd, by Julian Seward et al.
==14007== Using Valgrind-3.8.1 and LibVEX; rerun with -h for copyright info
==14007== Command: /usr/bin/python2.7 blah.py
==14007== 
Traceback (most recent call last):
  File blah.py, line 288, in module
import pylab
  File /usr/lib64/python2.7/site-packages/pylab.py, line 1, in module
from matplotlib.pylab import *
  File /usr/lib64/python2.7/site-packages/matplotlib/pylab.py, line 222, in 
module
from matplotlib import mpl  # pulls in most modules
  File /usr/lib64/python2.7/site-packages/matplotlib/mpl.py, line 1, in 
module
from matplotlib import artist
  File /usr/lib64/python2.7/site-packages/matplotlib/artist.py, line 7, in 
module
from transforms import Bbox, IdentityTransform, TransformedBbox, \
  File /usr/lib64/python2.7/site-packages/matplotlib/transforms.py, line 35, 
in module
from matplotlib._path import (affine_transform, 
count_bboxes_overlapping_bbox,
ImportError: /usr/lib64/python2.7/site-packages/matplotlib/_path.so: undefined 
symbol: _PyMem_DebugFree
[100070 refs]
==14007== 
==14007== HEAP SUMMARY:
==14007== in use at exit: 6,303,492 bytes in 31,921 blocks
==14007==   total heap usage: 1,266,299 allocs, 1,234,378 frees, 179,304,947 
bytes allocated
==14007== 
==14007== 40 bytes in 1 blocks are definitely lost in loss record 167 of 3,515
==14007==at 0x4C2C63B: malloc (vg_replace_malloc.c:270)
==14007==by 0x4EF1E8C: PyMem_Malloc (object.c:2343)
==14007==by 0x10064848: initialize_builtin_datetime_metadata 
(arraytypes.c.src:3953)
==14007==by 0x100719E2: set_typeinfo (arraytypes.c.src:4047)
==14007==by 0x1016354E: initmultiarray (multiarraymodule.c:4057)
==14007==by 0x4FB2661: _PyImport_LoadDynamicModule (importdl.c:53)
==14007==by 0x4FAE3A7: load_module (import.c:1915)
==14007==by 0x4FB07C1: import_submodule (import.c:2700)
==14007==by 0x4FAFCC6: load_next (import.c:2515)
==14007==by 0x4FAED8B: import_module_level (import.c:2224)
==14007==by 0x4FAF320: PyImport_ImportModuleLevel (import.c:2288)
==14007==by 0x4F78862: builtin___import__ (bltinmodule.c:49)

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components: Interpreter Core
messages: 196538
nosy: mmokrejs
priority: normal
severity: normal
status: open
title: python-2.7.5-r3: 40 bytes in 1 blocks are definitely lost
versions: Python 2.7

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[issue18883] python-3.3.2-r2: Modules/xxlimited.c:17:error: #error Py_LIMITED_API is incompatible with Py_DEBUG, Py_TRACE_REFS, and Py_REF_DEBUG

2013-08-30 Thread Martin Mokrejs

Martin Mokrejs added the comment:

See for what I did to Gentoo: http://bugs.python.org/issue18843#msg196520

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[issue18883] python-3.3.2-r2: Modules/xxlimited.c:17:error: #error Py_LIMITED_API is incompatible with Py_DEBUG, Py_TRACE_REFS, and Py_REF_DEBUG

2013-08-30 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Uh. I don't understand. So did you want to say I should not run configure 
--with-pydebug in python 3.3 or what? I am fine if you fix the Makefile not to 
exit on this particular file. I am missing something.

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[issue18859] README.valgrind should mention --with-valgrind

2013-08-30 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Moreover, it should explain what that really does. One could think of several 
answers or even their combinations what this configure flag will really do:

a) python will run itself under valgrind, don't bother ever doing it yourself
b) you don't have to bother with uncommenting the lines in valgrind.supp
c) make install will install the valgrind.supp but you have to edit it on 
your own
d) you may use valgrind but don't use other tool replacing malloc(), like 
electric fence, DUMA, etc. You should be quite verbose how (in)compatible is 
this with other tools.

Or some combination of them?

valgrind docs say it won't work if a binary lacks debug symbols (wasn't 
compiled with -g). Initially I got mislead I though I have to convert my 
blah.py to blah.c using cython, compile that with gcc -ggdb blah.c and then I 
may run valgrind on the binary.

In the end, I don't understand why everybody has to remove the comment symbols 
from the valgrind-python.supp file at all. Why isn't that by default enabled?



I also suggest you mention right in the file other handy information because 
people quite likely get on this path while chasing memory corruption issues, 
maybe broken hardware:

1. Mention that python uses 256kB chunks by default.
2. Mention there exists --without-pymalloc as Tim explained me in 
http://bugs.python.org/issue18843#msg196492
3. Explain how to interpret those stacktraces one could get: 
http://bugs.python.org/issue18843#msg196481

Thank you!

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[issue18883] python-3.3.2-r2: Modules/xxlimited.c:17:error: #error Py_LIMITED_API is incompatible with Py_DEBUG, Py_TRACE_REFS, and Py_REF_DEBUG

2013-08-30 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Hmm, but I did not add -DPy_LIMITED_API=1. Python 2.7.5 can be compiled using 
same configuration. Going back to the build.log file I see:

configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu 
--mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share 
--sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --with-fpectl 
--enable-shared --disable-ipv6 --with-threads --infodir=${prefix}/share/info 
--mandir=${prefix}/share/man --with-computed-gotos --with-dbmliborder=gdbm 
--with-libc= --enable-loadable-sqlite-extensions --with-system-expat 
--with-system-ffi --with-pydebug --without-pymalloc --with-valgrind


I specified only --with-pydebug --without-pymalloc --with-valgrind. So where 
does the limited API come from? Bug in configure.ac?

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[issue18883] python-3.3.2-r2: Modules/xxlimited.c:17:error: #error Py_LIMITED_API is incompatible with Py_DEBUG, Py_TRACE_REFS, and Py_REF_DEBUG

2013-08-30 Thread Martin Mokrejs

Martin Mokrejs added the comment:

So I conclude that you want to say that some of the configure flags is wrong? 
Which? I can surely report that at Gentoo. I still think Makefile should be 
changed so that it make does not even try to compile xxlimited.c if 
-DPy_LIMITED_API=1 is in CFLAGS regardless how that happened.

http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/dev-lang/python/

Look into the python-3.3.2-r2.ebuild file for what it does, and how does differ 
from 3.7.5-r2.ebuild which can be compiled fine through emerge abd thsoe 3 
configure arguments I requested.

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[issue18884] python-2.7.5-r3: 40 bytes in 1 blocks are definitely lost

2013-08-30 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Why do you think so? My point is that this happens when import fails. But 
python is at fault and should handle import errors.

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[issue18884] python-2.7.5-r3: 40 bytes in 1 blocks are definitely lost

2013-08-30 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Of course I did recompile matplotlib to use the recompiled python with debug 
ABI. I just don't understand why if something is not leaded why a memleak has 
to happen.

Anyway, now my application using the recompiled matplotlib baffled this through 
valgrind as well. An there was no ImportError: ;-)


==17489== 40 bytes in 1 blocks are definitely lost in loss record 718 of 5,487
==17489==at 0x4C2C63B: malloc (vg_replace_malloc.c:270)
==17489==by 0x4EF1E8C: PyMem_Malloc (object.c:2343)
==17489==by 0x10064848: initialize_builtin_datetime_metadata 
(arraytypes.c.src:3953)
==17489==by 0x100719E2: set_typeinfo (arraytypes.c.src:4047)
==17489==by 0x1016354E: initmultiarray (multiarraymodule.c:4057)
==17489==by 0x4FB2661: _PyImport_LoadDynamicModule (importdl.c:53)
==17489==by 0x4FAE3A7: load_module (import.c:1915)
==17489==by 0x4FB07C1: import_submodule (import.c:2700)
==17489==by 0x4FAFCC6: load_next (import.c:2515)
==17489==by 0x4FAED8B: import_module_level (import.c:2224)
==17489==by 0x4FAF320: PyImport_ImportModuleLevel (import.c:2288)
==17489==by 0x4F78862: builtin___import__ (bltinmodule.c:49)


This is probably because I also added --without-pymalloc as you wanted.

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[issue18884] python-2.7.5-r3: 40 bytes in 1 blocks are definitely lost

2013-08-30 Thread Martin Mokrejs

Changes by Martin Mokrejs mmokr...@users.sourceforge.net:


Added file: 
http://bugs.python.org/file31523/valgrind_python275_without-pymalloc.txt

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-30 Thread Martin Mokrejs

Martin Mokrejs added the comment:

I think it would be of tremendous help if python reported the physical memory 
address though do not know how much work is that for you. I already said that, 
I wonder why memtest86+ could not find an error, I even tried other tools for 
that. Could --with-pydebug immediately after writing those pad bytes try to 
read them back, just to make sure they are readable? Theoretically one could 
catch the wrong bit of memory immediately.

It is random, I think CPU must be fully loaded for a long while, plus something 
unknown has to kick in. Maybe that has to heat up the memory modules to cause 
the failure. My motherboard is already 3rd but doubt it is at fault, except 
that the SandyBridge chip is bad by design. Was replaced few days ago with CPU 
cooler (was the main reason for technician to come). I take that replacing 
motherboard was a nice offer from Dell. I would instead think that maybe CPU is 
heating too much.

BIOS is weird. ACPI and PCIe ASPM are exploiting Linux kernel hotplug support 
and PCI developers are puzzled. I experience that SandyBridge resets e.g. its 
USB2.0 controller if there was a hotplug even on some of its other root ports 
(express card was inserted/ejected). But in overall I don't think it is a bad 
deal and it works. These exceptional glitches are I think a software error or 
BIOS error. It just wouldn't be running all the days and nights. No, it is not 
overheated, at least not now with the replaced cooler.

I can put in other memory module (with which I bought the laptop from Dell). 
Other than that, hmm ... I could take out the hard drive and attach it to some 
other computer, boot from Live-DVD ... the problem is I need a lot of RAM for 
some of my stuff and it would have to be relatively same CPU type (I compiled 
binaries with avx). Yes, the emerge crash definitely was another case, I could 
hope to get that happen on even 1GB RAM machine, sure. I just don't have a 
testcase for that to trigger. I tried to stitch something but no, I probably 
coded something not going in the right direction. If you would have the time to 
stitch down some test for me to execute with the garbage collector calls, it 
would be probably the best.

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-29 Thread Martin Mokrejs

Martin Mokrejs added the comment:

I wanted to move away from the --with-pydebug to a normal python and I failed 
with:

# emerge dev-lang/python:2.7

 * IMPORTANT: 11 news items need reading for repository 'gentoo'.
 * Use eselect news to read news items.

Calculating dependencies... done!
Debug memory block at address p=0xa7f5900: API 'o'
80 bytes originally requested
The 7 pad bytes at p-7 are not all FORBIDDENBYTE (0xfb):
at p-7: 0xfb
at p-6: 0xfb
at p-5: 0xfa *** OUCH
at p-4: 0xfb
at p-3: 0xfb
at p-2: 0xfb
at p-1: 0xfb
Because memory is corrupted at the start, the count of bytes requested
   may be bogus, and checking the trailing pad bytes may segfault.
The 8 pad bytes at tail=0xa7f5950 are FORBIDDENBYTE, as expected.
The block was made by call #21242094 to debug malloc/realloc.
Data at p: 73 00 00 00 79 00 00 00 ... 67 00 00 00 00 00 00 00
Fatal Python error: bad leading pad byte
Aborted (core dumped)
#

Great. So, what can we gather now from this? It got overwritten within few 
dozens of seconds at most since I started emerge. It is in a different memory 
region (so no memory module HW bug). I am attaching the resolved stacktrace 
just in case ...

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-29 Thread Martin Mokrejs

Martin Mokrejs added the comment:

One more note. At that time I had running my application which at that time was 
parsing an XML file using xml.parsers.expat! That is being run in my pipeline 
before I render figures (the initially reported crash case). So, 
matplotlib/numpy is ruled out.

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-29 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Sorry, I should explain a bit more. Gentoo Linux uses a tool named emerge to 
handle packages. It is written in python. So, by that command I initiated 
re-compilation of python itself but it crashed quickly. At that moment emerge 
called the python available on the system at that time which was configured 
using --with-pydebug.


Meanwhile I went to install DUMA http://duma.sourceforge.net/ and started to 
re-run emerge.

# emerge duma
# export LD_PRELOAD=/usr/lib64/libduma.so.0.0.0
# sysctl -w vm.max_map_count=100
# emerge dev-lang/python:2.7 


Thanks for your analysis, will try to stitch something.

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-29 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Thanks, will recompile without pymalloc.

I don't understand why always is only 1 bit different. Could that be 
overwritten by another use process or do you believe it must be the python or 
some of the modules imported into it on runtime?

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-29 Thread Martin Mokrejs

Martin Mokrejs added the comment:

That is why I asked if other process can interfere. So, they are isolated on 
Linux, good. ;-) The crash in #msg196481 is just the emerge written in python, 
at the start it is resolving some graph of package dependencies ... once it 
resolves order of packages and prints a lot of output. so, it did not get to 
that before it crashed. In sum with what you said, my application running as 
another process should not interfere with the emerge process, so it turns out 
that was irrelevant comment from my side. ;)

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-29 Thread Martin Mokrejs

Martin Mokrejs added the comment:

http://www.gentoo.org/proj/en/portage/index.xml
http://dev.gentoo.org/~zmedico/portage/archives

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-27 Thread Martin Mokrejs

Martin Mokrejs added the comment:

I took a crack from another angle. I converted my application using cython and 
then used gcc. Finally, ran valgrind over the binary. It is not finished yet 
but already spotted plenty of hints.

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Added file: 
http://bugs.python.org/file31490/python2.7_through_cython_valgrind.txt

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[issue18850] xml.etree.ElementTree accepts control chars.

2013-08-27 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Incidentally I read today 
http://blastedbio.blogspot.co.uk/2012/05/blast-tabular-missing-descriptions.html
 mentioning ^A being used. Maybe that would stop working?

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-27 Thread Martin Mokrejs

Martin Mokrejs added the comment:

No, I did not know that. Thanks, I did now.

quote
  * Uncomment Py_USING_MEMORY_DEBUGGER in Objects/obmalloc.c,
then rebuild Python
  * Uncomment the lines in Misc/valgrind-python.supp that
suppress the warnings for PyObject_Free and PyObject_Realloc

/quote

Why isn't there a configure switch for this? :(

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-27 Thread Martin Mokrejs

Martin Mokrejs added the comment:

I was just checking whether configure picked up my --with-pymalloc and 
incidentally saw:

  --with-valgrind Enable Valgrind support

maybe Misc/README.valgrind needs revision and should explain what that does as 
well? ;-)

It should also explain what is one supposed to do with 
Misc/valgrind-python.supp. It becomes clear once one goes to edit that file, 
true. ;-)

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-26 Thread Martin Mokrejs

New submission from Martin Mokrejs:

Hi,
  it happened to me that using faulthandler and python compiled with 
--with-pydebug and C*FLAGS=-ggdb I got this stacktrace (will attach longer 
version as a file):


(gdb) where
#0  0x7f0e3af8aacb in raise () from /lib64/libpthread.so.0
#1  0x7f0e3a0b05f6 in faulthandler_fatal_error (signum=6) at 
faulthandler.c:321
#2  signal handler called
#3  0x7f0e3ac061f5 in raise () from /lib64/libc.so.6
#4  0x7f0e3ac0766b in abort () from /lib64/libc.so.6
#5  0x7f0e3b327828 in Py_FatalError (msg=0x7f0e3b373232 bad leading pad 
byte) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Python/pythonrun.c:1689
#6  0x7f0e3b257dc8 in _PyObject_DebugCheckAddressApi (api=111 'o', 
p=0x449e6900) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Objects/obmalloc.c:1591
#7  0x7f0e3b257a6c in _PyObject_DebugFreeApi (api=111 'o', p=0x449e6900) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Objects/obmalloc.c:1478
#8  0x7f0e3b257913 in _PyObject_DebugFree (p=0x449e6900) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Objects/obmalloc.c:1422
#9  0x7f0e3b34319a in PyObject_GC_Del (op=0x449e6920) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Modules/gcmodule.c:1561
#10 0x7f0e3b275ef7 in tupledealloc (op=0x449e6920) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Objects/tupleobject.c:235
#11 0x7f0e3b255bac in _Py_Dealloc (op=(True,)) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Objects/object.c:2262
#12 0x7f0e3b246d77 in dict_dealloc (mp=0x449b5d80) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Objects/dictobject.c:1010
#13 0x7f0e3b255bac in _Py_Dealloc (op=
{'_label': unknown at remote 0x449dd4b8, '_facecolors_original': (float 
at remote 0xb65dd38, float at remote 0x5034630, float at remote 
0xb3c6af8), '_transform': unknown at remote 0x449e6b50, 'figure': 
Figure(_label='', _transform=None, figure=None, _axobservers=[], images=[], 
texts=[], _hold=True, artists=[], _agg_filter=None, patch=Rectangle(_label='', 
_transform=BboxTransformTo(_invalid=2, _inverted=Affine2D(_invalid=0, 
_inverted=None, _mtx=numpy.ndarray at remote 0xd5bc6ec0, _shorthand_name='', 
_parents=WeakValueDictionary(_remove=function at remote 0xbf7d060, data={}) 
at remote 0x129fbdf8) at remote 0xd5bb0300, 
_boxout=TransformedBbox(_invalid=2, _transform=Affine2D(_invalid=2, 
_inverted=None, _mtx=numpy.ndarray at remote 0xd5bad540, _shorthand_name='', 
_parents=WeakValueDictionary(_remove=function at remote 0xc166450, 
data={741848704: KeyedRef at remote 0x40290a80, 405520480: KeyedRef at 
remote 0x29e86b10, 322803328: KeyedRef at remote 0x29e
 86570, 3585872752: KeyedRef ...(truncated)) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Objects/object.c:2262
#14 0x7f0e3b27ad3d in subtype_dealloc (
self=PathCollection(_label=unknown at remote 0x449dd4b8, 
_facecolors_original=(float at remote 0xb65dd38, float at remote 0x5034630, 
float at remote 0xb3c6af8), _transform=unknown at remote 0x449e6b50, 
figure=Figure(_label='', _transform=None, figure=None, _axobservers=[], 
images=[], texts=[], _hold=True, artists=[], _agg_filter=None, 
patch=Rectangle(_label='', _transform=BboxTransformTo(_invalid=2, 
_inverted=Affine2D(_invalid=0, _inverted=None, _mtx=numpy.ndarray at remote 
0xd5bc6ec0, _shorthand_name='', 
_parents=WeakValueDictionary(_remove=function at remote 0xbf7d060, data={}) 
at remote 0x129fbdf8) at remote 0xd5bb0300, 
_boxout=TransformedBbox(_invalid=2, _transform=Affine2D(_invalid=2, 
_inverted=None, _mtx=numpy.ndarray at remote 0xd5bad540, _shorthand_name='', 
_parents=WeakValueDictionary(_remove=function at remote 0xc166450, 
data={741848704: KeyedRef at remote 0x40290a80, 405520480: KeyedRef at 
remote 0x29e86b10, 322803328: KeyedRef at remo
 te 0x29e86570, 3585872752: KeyedR...(truncated)) at 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Objects/typeobject.c:1015
#15 0x7f0e3b255bac in _Py_Dealloc (
op=PathCollection(_label=unknown at remote 0x449dd4b8, 
_facecolors_original=(float at remote 0xb65dd38, float at remote 0x5034630, 
float at remote 0xb3c6af8), _transform=unknown at remote 0x449e6b50, 
figure=Figure(_label='', _transform=None, figure=None, _axobservers=[], 
images=[], texts=[], _hold=True, artists=[], _agg_filter=None, 
patch=Rectangle(_label='', _transform=BboxTransformTo(_invalid=2, 
_inverted=Affine2D(_invalid=0, _inverted=None, _mtx=numpy.ndarray at remote 
0xd5bc6ec0, _shorthand_name='', 
_parents=WeakValueDictionary(_remove=function at remote 0xbf7d060, data={}) 
at remote 0x129fbdf8) at remote 0xd5bb0300, 
_boxout=TransformedBbox(_invalid=2, _transform=Affine2D(_invalid=2, 
_inverted=None, _mtx=numpy.ndarray at remote 0xd5bad540, _shorthand_name='', 
_parents=WeakValueDictionary

[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-26 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Should have included from the head of gdb output:

Program terminated with signal 6, Aborted.

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-26 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Would you please guide me what gdb commands I should issue for you? Thank you. 
BTW, I ran memtest86+ few days ago, although this is non-ECC memory I think HW 
is fine.

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-26 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Grr, forgot to look into a file where I recorded STDERR.


Debug memory block at address p=0x449e6900: API 'o'
80 bytes originally requested
The 7 pad bytes at p-7 are not all FORBIDDENBYTE (0xfb):
at p-7: 0xfb
at p-6: 0xfb
at p-5: 0xfa *** OUCH
at p-4: 0xfb
at p-3: 0xfb
at p-2: 0xfb
at p-1: 0xfb
Because memory is corrupted at the start, the count of bytes requested
   may be bogus, and checking the trailing pad bytes may segfault.
The 8 pad bytes at tail=0x449e6950 are FORBIDDENBYTE, as expected.
The block was made by call #8155854715 to debug malloc/realloc.
Data at p: 00 00 00 00 00 00 00 00 ... 20 af 5b 3b 0e 7f 00 00
Fatal Python error: bad leading pad byte
Fatal Python error: Aborted

Current thread 0x7f0e3b7ec700:
  File /usr/lib64/python2.7/site-packages/matplotlib/axes.py, line 932 in cla
  File /usr/lib64/python2.7/site-packages/matplotlib/figure.py, line 906 in 
clf
  File /usr/lib64/python2.7/site-packages/matplotlib/figure.py, line 926 in 
clear
  File blah.py, line 12513 in draw_hist2d_plot

In that function I call:
del(_series)
del(_ax1)
_figure.clear() # 12513

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-26 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Thank you for explanation what is going on. I called matplotlibs drawing 
function to include 49308 dots and corresponding legend items with their 
colors. That's all I can say. I am not a native English speaker so I don't know 
what 'rogue extension modules' means.

Do you think it is a matplotlib or numpy issue which were in the stacktrace? Or 
a memory module error?

I am running analyses which take weeks. Will python give me a clear 
warning/error when the object counter overflows?

So what should I do now? I am clue-less right now.

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[issue18845] 2.7.5-r2: Fatal Python error: Segmentation fault

2013-08-26 Thread Martin Mokrejs

New submission from Martin Mokrejs:

While running my app testsuite I have another one which crashed.

Fatal Python error: Segmentation fault

Current thread 0x7fe8d3527700:
  File /usr/lib64/python2.7/site-packages/matplotlib/transforms.py, line 2370 
in get_matrix
  File /usr/lib64/python2.7/site-packages/matplotlib/transforms.py, line 2203 
in get_affine
  File /usr/lib64/python2.7/site-packages/matplotlib/transforms.py, line 2175 
in transform_affine
  File /usr/lib64/python2.7/site-packages/matplotlib/transforms.py, line 1238 
in transform
  File /usr/lib64/python2.7/site-packages/matplotlib/transforms.py, line 1030 
in get_points
  File /usr/lib64/python2.7/site-packages/matplotlib/transforms.py, line 277 
in __array__
  File /usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py, 
line 110 in draw_path_collection
  File /usr/lib64/python2.7/site-packages/matplotlib/collections.py, line 259 
in draw
  File /usr/lib64/python2.7/site-packages/matplotlib/artist.py, line 54 in 
draw_wrapper
  File /usr/lib64/python2.7/site-packages/matplotlib/collections.py, line 695 
in draw
  File /usr/lib64/python2.7/site-packages/matplotlib/artist.py, line 54 in 
draw_wrapper
  File /usr/lib64/python2.7/site-packages/matplotlib/axes.py, line 2086 in 
draw
  File /usr/lib64/python2.7/site-packages/matplotlib/artist.py, line 54 in 
draw_wrapper
  File /usr/lib64/python2.7/site-packages/matplotlib/figure.py, line 1006 in 
draw
  File /usr/lib64/python2.7/site-packages/matplotlib/artist.py, line 54 in 
draw_wrapper
  File /usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py, 
line 440 in draw
  File /usr/lib64/python2.7/site-packages/matplotlib/backends/backend_agg.py, 
line 492 in print_png
  File /usr/lib64/python2.7/site-packages/matplotlib/backend_bases.py, line 
2096 in print_figure
  File /usr/lib64/python2.7/site-packages/matplotlib/figure.py, line 1370 in 
savefig

  I wanted to draw 55620 dots in a scatter plot, each with a legend and its 
associated color. Actually only 100 color are used and multiple adjacent dots 
in the series have same color as necessary.


Is this a matplotlib or a python error?

--
files: matplotlib_crash_1676__SRR091640_shortened.txt
messages: 196239
nosy: mmokrejs
priority: normal
severity: normal
status: open
title: 2.7.5-r2: Fatal Python error: Segmentation fault
type: crash
versions: Python 2.7
Added file: 
http://bugs.python.org/file31478/matplotlib_crash_1676__SRR091640_shortened.txt

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[issue18843] Py_FatalError (msg=0x7f0e3b373232 bad leading pad byte) at Python-2.7.5/Python/pythonrun.c:1689

2013-08-26 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Yes, I have rebuilt all python modules but even gdb exited on startup due to 
python ABI change. I am using Gentoo Linux 
(https://bugs.gentoo.org/show_bug.cgi?id=482348) and unless python-updater 
forgot to include some package in the listing of those needed to be recompiled, 
I am sane. And becuase gdb could not even start up I *hope* those no recompiled 
yet would NOT work AT ALL.

Thanks for clarification, I thought that I might reach some internal number 
(the serial number as you say) in python and run out of some internal counters 
on objects. Actually, I hit these issues because I wondered why some of my 
application tests fail. Although all tests crunch a really lot of data they 
merely do the same in the end: draw charts using matplotlib which uses numpy. I 
have huge lists which I recently converted to generators (if possible) and now 
I even use imap(), izip(), ifilter() from itertools. One of the crashed tests 
has 153 levels in gdb stacktrace and few lines from the very top/outer already 
had the izip() objects. But the tests which crashed are not so huge like 
others, maybe take just 1/10 of the size of others, so I wonder why these 
failed.

I think some crashes are related to me deleting explictly a huge list in my 
code even before leaving a function. Or maybe returning such lists between 
child/parent functions?

Could valgring or something else help to find who is overwriting data of 
others? But I don't have experience with using it.

I think this _figure.clear() crash could be manifestation of python deleting a 
wrong object/pointer. Some ugly for loops over lists took ... don't know how 
much but in total even 26GB of RAM was reserved by the process (most of it also 
as residual memory requirement). With itertools() I got down 10x.

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[issue17234] python-2.7.3-r3: crash in visit_decref()

2013-08-25 Thread Martin Mokrejs

Martin Mokrejs added the comment:

Hi Ramchandra and Christian,
  I am using numpy, matplotlib, expat/cElementTree, doing a lot of os.Popen 
calls. But I think the problem is taht I have huge lists and when I do not need 
them I do del(_mylist) in the code ASAP. That probably causes a lot of churn.

  Here is one stacktrace I just got with the faulthandler installed. It does 
not show in the trace any 3rd-party module so can I conclude it is a core 
python bug? Just recompiling with -ggdb so eventually will have better 
stacktraces.




  Does this help? I don't have the gdb stacktrace as I recompiled the binary 
now again ... :(

Fatal Python error: 
/mnt/1TB/var/tmp/portage/dev-lang/python-2.7.5-r2/work/Python-2.7.5/Objects/dictobject.c:1009
 object at 0x40c0a60 has negative ref count -1
Fatal Python error: Aborted

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[issue17234] python-2.7.3-r3: crash in visit_decref()

2013-02-19 Thread Martin Mokrejs

New submission from Martin Mokrejs:

Hi,
  I do see relatively often a crash in python. Here is one stacktrace from my 
Gentoo Linux running 3.7.4 kernel:

(gdb) where
#0  0x7f624f340f08 in visit_decref () from /usr/lib64/libpython2.7.so.1.0
#1  0x7f624f2a455a in list_traverse () from /usr/lib64/libpython2.7.so.1.0
#2  0x7f624f3412c7 in collect () from /usr/lib64/libpython2.7.so.1.0
#3  0x7f624f341f11 in _PyObject_GC_Malloc () from 
/usr/lib64/libpython2.7.so.1.0
#4  0x7f624f2cdd59 in PyType_GenericAlloc () from 
/usr/lib64/libpython2.7.so.1.0
#5  0x7f624f2d09c3 in type_call () from /usr/lib64/libpython2.7.so.1.0
#6  0x7f624f27bdc3 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0
#7  0x7f624f310d76 in PyEval_EvalFrameEx () from 
/usr/lib64/libpython2.7.so.1.0
#8  0x7f624f31285e in PyEval_EvalFrameEx () from 
/usr/lib64/libpython2.7.so.1.0
#9  0x7f624f313905 in PyEval_EvalCodeEx () from 
/usr/lib64/libpython2.7.so.1.0
#10 0x7f624f313a32 in PyEval_EvalCode () from /usr/lib64/libpython2.7.so.1.0
#11 0x7f624f32d97c in run_mod () from /usr/lib64/libpython2.7.so.1.0
#12 0x7f624f32e53d in PyRun_StringFlags () from 
/usr/lib64/libpython2.7.so.1.0
#13 0x7f624f30a44e in builtin_eval () from /usr/lib64/libpython2.7.so.1.0
#14 0x7f624f312456 in PyEval_EvalFrameEx () from 
/usr/lib64/libpython2.7.so.1.0
#15 0x7f624f313905 in PyEval_EvalCodeEx () from 
/usr/lib64/libpython2.7.so.1.0
#16 0x7f624f2a104c in function_call () from /usr/lib64/libpython2.7.so.1.0
#17 0x7f624f27bdc3 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0
#18 0x7f624f28a82f in instancemethod_call () from 
/usr/lib64/libpython2.7.so.1.0
#19 0x7f624f27bdc3 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0
#20 0x7f624f30c9b7 in PyEval_CallObjectWithKeywords () from 
/usr/lib64/libpython2.7.so.1.0
#21 0x7f624612f807 in call_with_frame.isra.9 () from 
/usr/lib64/python2.7/lib-dynload/pyexpat.so
#22 0x7f6246132080 in my_StartElementHandler () from 
/usr/lib64/python2.7/lib-dynload/pyexpat.so
#23 0x7f6245ed0fb0 in doContent () from /usr/lib64/libexpat.so.1
#24 0x7f6245ed21b4 in contentProcessor () from /usr/lib64/libexpat.so.1
#25 0x7f6245ecce2a in XML_ParseBuffer () from /usr/lib64/libexpat.so.1
#26 0x7f6246132d5b in xmlparse_Parse () from 
/usr/lib64/python2.7/lib-dynload/pyexpat.so
#27 0x7f624f312456 in PyEval_EvalFrameEx () from 
/usr/lib64/libpython2.7.so.1.0
#28 0x7f624f296379 in gen_send_ex.isra.1 () from 
/usr/lib64/libpython2.7.so.1.0
#29 0x7f624f2ce40f in wrap_next () from /usr/lib64/libpython2.7.so.1.0
#30 0x7f624f27bdc3 in PyObject_Call () from /usr/lib64/libpython2.7.so.1.0
#31 0x7f624f310d76 in PyEval_EvalFrameEx () from 
/usr/lib64/libpython2.7.so.1.0
#32 0x7f624f31285e in PyEval_EvalFrameEx () from 
/usr/lib64/libpython2.7.so.1.0
#33 0x7f624f31285e in PyEval_EvalFrameEx () from 
/usr/lib64/libpython2.7.so.1.0
#34 0x7f624f31285e in PyEval_EvalFrameEx () from 
/usr/lib64/libpython2.7.so.1.0
#35 0x7f624f31285e in PyEval_EvalFrameEx () from 
/usr/lib64/libpython2.7.so.1.0
#36 0x7f624f313905 in PyEval_EvalCodeEx () from 
/usr/lib64/libpython2.7.so.1.0
#37 0x7f624f313a32 in PyEval_EvalCode () from /usr/lib64/libpython2.7.so.1.0
#38 0x7f624f32d97c in run_mod () from /usr/lib64/libpython2.7.so.1.0
#39 0x7f624f32e750 in PyRun_FileExFlags () from 
/usr/lib64/libpython2.7.so.1.0
#40 0x7f624f32f1cf in PyRun_SimpleFileExFlags () from 
/usr/lib64/libpython2.7.so.1.0
#41 0x7f624f3407e2 in Py_Main () from /usr/lib64/libpython2.7.so.1.0
#42 0x7f624ec8f91d in __libc_start_main () from /lib64/libc.so.6
#43 0x0040094d in _start ()
(gdb)

--
messages: 182371
nosy: mmokrejs
priority: normal
severity: normal
status: open
title: python-2.7.3-r3: crash in visit_decref()
type: crash
versions: Python 2.7

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[issue17207] string format precision misbehaving

2013-02-14 Thread Martin Mokrejs

New submission from Martin Mokrejs:

Hi,
  I don't know if this is related to issue8040 or not. I find the 2.7 string 
formatting behavior inconsistent. I found out sometimes I have to divide my 
number by 100 so that the percentage values get printed correctly. Somehow, 
when a percent sign appears in the formatting definition python magically 
multiplies the number by 100. But sometimes not. This is not specified in 
http://docs.python.org/2/library/stdtypes.html#string-formatting so I really do 
not like this whole thing, sorry to say that.

Some examples, which should have been posted in the Library reference doc above.

$ python
Python 2.7.3 (default, Dec 19 2012, 00:02:12) 
[GCC 4.6.3] on linux2
Type help, copyright, credits or license for more information.
 %s % 12.77
'12.77'
 %s % '{:.2%}'.format(12.77)
'1276.67%'
 %s % '{:.2%}'.format(float(12.77))
'1276.67%'

 %s % ( '{:.4%}'.format(12.77) )
'1276.6667%'
 %s % ( '{:.4}'.format(12.77) )
'12.77'
 %s % ( '{:.2}'.format(12.77) )
'1.3e+01'
 %s%% % ( '{:.2}'.format(12.77) )
'1.3e+01%'
 %s%% % ( '{:.2}'.format('12.77') )
'12%'
 %s%% % ( '{:.4}'.format(float(12.77)) )
'12.77%'


 %s % ( '{:.2%}'.format(1/10) )
'0.00%'
 %s % ( '{:.2%}'.format(1/10.0) )
'10.00%'
 %s % ( '{:.2%}'.format(1/10.0 * 100) )
'1000.00%'
 %s % ( '{:.2%}'.format((1/10.0) * 100) )
'1000.00%'

 %s % ( '{:.2}'.format((1/10.0) * 100) )
'1e+01'
 %s % ( '{:.2%}'.format((1/10.0) * 100) )
'1000.00%'



1) Would somebody please document the behavior?

2) Would somebody explain how can I print 12.67% (I want precision of 2 places 
after the decimal dot).

3) Why sometimes using float() fixes the behavior (likely converting int() to 
float()?

4) But why does the scientific exponential notation sometimes come out?



5) Finally, it would be nice if the python 2.7 docs contained how to format 
floats to 2 places after the dot using the old syntax:

float=%f % (12.77)

I would like to get just 12.77 out. I can use round() but that is not what I 
am asking for. I want to change just the formatting of the output:

 round(12.77, 2)
12.77
 


Thank you

--
components: ctypes
messages: 182125
nosy: mmokrejs
priority: normal
severity: normal
status: open
title: string format precision misbehaving
type: behavior
versions: Python 2.7

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[issue15416] 3 * [] gives a list of 3 cross-referenced lists, a[1]='blah' writes in to ALL three!

2013-01-03 Thread Martin Mokrejs

Martin Mokrejs added the comment:

For the sake of internet archives, the following could be included in the FAQ 
you referred to:

http://www.scipy.org/Cookbook/BuildingArrays

 import numpy as np
 a=np.array(5*[False],bool)
 a
array([False, False, False, False, False], dtype=bool)
 a[4]=1
 a
array([False, False, False, False,  True], dtype=bool)


But thanks for the link, it helped me at that time.

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[issue15416] 3 * [] gives a list of 3 cross-referenced lists, a[1]='blash

2012-07-21 Thread Martin Mokrejs

New submission from Martin Mokrejs mmokr...@users.sourceforge.net:

Hi,
  I thought that I can easily create a list of, say 3, nested lists:

$ python
Python 2.7.3 (default, May 17 2012, 21:10:41) 
[GCC 4.5.3] on linux2
Type help, copyright, credits or license for more information.
 3 * [[]]
[[], [], []]
 a=3 * [[]]
 a[0]
[]
 a[1].append('sdds')
 a
[['sdds'], ['sdds'], ['sdds']]
 a[0].append('xxx')
 a
[['sdds', 'xxx'], ['sdds', 'xxx'], ['sdds', 'xxx']]


The below works as expected.

 a=[[], [], []]
 a
[[], [], []]
 a[0]
[]
 a[1]
[]
 a[1].append('sdds')
 a[0].append('xxx')
 a
[['xxx'], ['sdds'], []]



Of course, I want to do like:

a = len(b) * [] # to get a list of individual hashes
c = len(b) * [0] # to get a list of indvidual counters

--
components: None
messages: 166081
nosy: mmokrejs
priority: normal
severity: normal
status: open
title: 3 * [] gives a list of 3 cross-referenced lists, a[1]='blash
type: behavior
versions: Python 2.7

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[issue15416] 3 * [] gives a list of 3 cross-referenced lists, a[1]='blah' writes in to ALL three!

2012-07-21 Thread Martin Mokrejs

Changes by Martin Mokrejs mmokr...@users.sourceforge.net:


--
title: 3 * [] gives a list of 3 cross-referenced lists, a[1]='blash - 3 * [] 
gives a list of 3 cross-referenced lists, a[1]='blah' writes in to ALL three!

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[issue4925] Improve error message of subprocess

2009-01-12 Thread Martin Mokrejs

New submission from Martin Mokrejs mmokr...@users.sourceforge.net:

I think the following error output unsatisfactory as it does not give me
any hint what file was not found:

$ fetch_quals.py blah.txt 
Traceback (most recent call last):
  File /home/mmokrejs/bin/fetch_quals.py, line 15, in module
_p1 = subprocess.Popen(['query_tracedb', 'retrieve', 'quality',
_id], stdin=subprocess.PIPE, stdout=subprocess.PIPE)
  File /usr/lib/python2.5/subprocess.py, line 594, in __init__
errread, errwrite)
  File /usr/lib/python2.5/subprocess.py, line 1091, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
$

I know now that I had to specify full path tot he binary or include
shell=True argument but anyway, please improve the error message.

--
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messages: 79684
nosy: mmokrejs
severity: normal
status: open
title: Improve error message of subprocess
type: behavior
versions: Python 2.5

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[issue3264] Use -lcrypto instead of -lcrypt on Solaris 2.6 when available

2008-07-03 Thread Martin Mokrejs

Martin Mokrejs [EMAIL PROTECTED] added the comment:

# ar tv /usr/lib/libcrypt.a
rw-rw-r-- 0/1   1296 Jul 16 05:57 1997 crypt.o
rw-rw-r-- 0/1   4996 Jul 16 05:57 1997 cryptio.o
rw-rw-r-- 0/1   1508 Jul 16 05:57 1997 des_encrypt.o
rw-rw-r-- 0/1   5356 Jul 16 05:58 1997 des_crypt.o
# ls -la /usr/lib/libcrypt.so
ls: cannot access /usr/lib/libcrypt.so: No such file or directory
#

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[issue3265] Python-2.5.2/Modules/_ctypes/malloc_closure.c:70: error: `MAP_ANONYMOUS' undeclared

2008-07-03 Thread Martin Mokrejs

Martin Mokrejs [EMAIL PROTECTED] added the comment:

A Goggle search gives between many others:
http://gcc.gnu.org/ml/gcc/2000-09/msg00054.html
http://www.ravenbrook.com/project/mps/master/design/vmso/
http://developers.sun.com/solaris/articles/read_mmap.html

Added file: http://bugs.python.org/file10799/mmap.2

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[issue3265] Python-2.5.2/Modules/_ctypes/malloc_closure.c:70: error: `MAP_ANONYMOUS' undeclared

2008-07-03 Thread Martin Mokrejs

Martin Mokrejs [EMAIL PROTECTED] added the comment:

http://unix.derkeiler.com/Newsgroups/comp.unix.solaris/2004-07/0256.html
http://source.winehq.org/source/libs/wine/mmap.c

I will stop posting URLs. ;-)

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[issue3264] Use -lcrypto instead of -lcrypt on Solaris 2.6 when available

2008-07-03 Thread Martin Mokrejs

Martin Mokrejs [EMAIL PROTECTED] added the comment:

# ar x /usr/lib/libcrypt.a;nm -g des_crypt.o
 U ___errno
033c T _des_crypt
0274 T _des_encrypt
 U _des_encrypt1
01b0 T _des_setkey
 U _mutex_lock
 U _mutex_unlock
 U _thr_getspecific
 U _thr_keycreate
 U _thr_setspecific
033c W des_crypt
0274 W des_encrypt
01b0 W des_setkey
 U free
 U malloc
#

The installation is actually very fresh, as I re-installed the
machine some year ago but it was turned off since few days. With
whatever last aggregate patches were available on dying Solaris
web pages.

# gcc -v
Reading specs from /usr/local/lib/gcc/sparc-sun-solaris2.6/3.4.2/specs
Configured with: ../configure --with-as=/usr/ccs/bin/as
--with-ld=/usr/ccs/bin/ld --disable-nls --disable-libgcj
--enable-languages=c,c++
Thread model: posix
gcc version 3.4.2
#

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[issue3266] Python-2.5.2/Modules/mmapmodule.c:915: error: `O_RDWR' undeclared

2008-07-03 Thread Martin Mokrejs

Martin Mokrejs [EMAIL PROTECTED] added the comment:

So adding these two lines helped:

# diff /usr/scratch/Python-2.5.2/Modules/mmapmodule.c.ori
/usr/scratch/Python-2.5.2/Modules/mmapmodule.c
36a37
 #include sys/types.h
38a40
 #include fcntl.h
#

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[issue3265] Python-2.5.2/Modules/_ctypes/malloc_closure.c:70: error: `MAP_ANONYMOUS' undeclared

2008-07-03 Thread Martin Mokrejs

Martin Mokrejs [EMAIL PROTECTED] added the comment:

Thanks, but I can only help with testing. :(

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[issue3264] Use -lcrypto instead of -lcrypt on Solaris 2.6 when available

2008-07-03 Thread Martin Mokrejs

Martin Mokrejs [EMAIL PROTECTED] added the comment:

Could it be the name clashing problem between -lcrypt and -lcrypto?

bash-3.00# ar x /usr/lib/libcrypt.a;nm -g des_crypt.o
 U ___errno
033c T _des_crypt
0274 T _des_encrypt
 U _des_encrypt1
01b0 T _des_setkey
 U _mutex_lock
 U _mutex_unlock
 U _thr_getspecific
 U _thr_keycreate
 U _thr_setspecific
033c W des_crypt
0274 W des_encrypt
01b0 W des_setkey
 U free
 U malloc
bash-3.00# ar x /usr/local/lib/libcrypto.a;nm -g des_crypt.o
 U ___errno
033c T _des_crypt
0274 T _des_encrypt
 U _des_encrypt1
01b0 T _des_setkey
 U _mutex_lock
 U _mutex_unlock
 U _thr_getspecific
 U _thr_keycreate
 U _thr_setspecific
033c W des_crypt
0274 W des_encrypt
01b0 W des_setkey
 U free
 U malloc
bash-3.00#

There used to be name clashes between -lcrypt from KTH-KRB/HEIMDAL
with those from openssl -lcrypto in the past. I think that was
fixed around/in openssl-2.7 and heimdal-1.0. The clashes caused
openssh dying when compiled with kerberos4 support because the
functions of same names expected in some way different data.
I am sure you would Goggle it out.

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[issue3264] Use -lcrypto instead of -lcrypt on Solaris 2.6 when available

2008-07-03 Thread Martin Mokrejs

Martin Mokrejs [EMAIL PROTECTED] added the comment:

You say did always work?

http://mail.python.org/pipermail/python-list/2002-December/177479.html

Maybe the reason why in ruby they forced to -shared flag
because it was possible to link only with the shared library?
I do not know from which package to get the shared version. :(
http://blade.nagaokaut.ac.jp/cgi-bin/scat.rb/ruby/ruby-list/33517

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[issue3264] Use -lcrypto instead of -lcrypt on Solaris 2.6 when available

2008-07-03 Thread Martin Mokrejs

Martin Mokrejs [EMAIL PROTECTED] added the comment:

Confirming the enabling line 216 like below helped. Thanks. Maybe change
Resolution?

204 # Socket module helper for SSL support; you must comment out the
other
205 # socket line above, and possibly edit the SSL variable:
206 #SSL=/usr/local/ssl
207 #_ssl _ssl.c \
208 #   -DUSE_SSL -I$(SSL)/include -I$(SSL)/include/openssl \
209 #   -L$(SSL)/lib -lssl -lcrypto
210 
211 # The crypt module is now disabled by default because it breaks
builds
212 # on many systems (where -lcrypt is needed), e.g. Linux (I believe).
213 #
214 # First, look at Setup.config; configure may have set this for you.
215 
216 crypt cryptmodule.c # -lcrypt   # crypt(3); needs -lcrypt on
some systems

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[issue3235] Improve subprocess module usage

2008-07-02 Thread Martin Mokrejs

Martin Mokrejs [EMAIL PROTECTED] added the comment:

Georg, but would you please improve the docs explaining what communicate
really does? The syntax is nice but I don't see how can I use poll()
described in the same above to use that. Providing Examples section
would be the best. Of course I don't mind if the examples come from Doug
Hellman or not, as mentioned in msg68956. ;-) Or how about placing a
link to that page
(http://blog.doughellmann.com/2007/07/pymotw-subprocess.html)?

Please reopen unless better docs are available. I don't care about 2.6
either, sorry.

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[issue3264] Use -lcrypto instead of -lcrypt on Solaris 2.6 when available

2008-07-02 Thread Martin Mokrejs

New submission from Martin Mokrejs [EMAIL PROTECTED]:

Hi,
  although the issues libraries to be created with -fpic are known I
still do believe ./config could do something here:

building 'crypt' extension
gcc -shared -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes
build/temp.solaris-2.6-sun4u-2.5/usr/scratch/Python-2.5.2/Modules/cryptmodule.o
-L/usr/local/lib -lcrypt -o build/lib.solaris-2.6-sun4u-2.5/crypt.so
Text relocation remains referenced
against symbol  offset  in file
_des_setkey 0x4 /usr/lib/libcrypt.a(crypt.o)
_des_encrypt0x10/usr/lib/libcrypt.a(crypt.o)
_des_crypt  0x1c/usr/lib/libcrypt.a(crypt.o)
unknown   0x4
/usr/lib/libcrypt.a(des_crypt.o)
unknown   0x8
/usr/lib/libcrypt.a(des_crypt.o)
...
ld: fatal: relocations remain against allocatable but non-writable sections
collect2: ld returned 1 exit status
# gcc -shared -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes
build/temp.solaris-2.6-sun4u-2.5/usr/scratch/Python-2.5.2/Modules/cryptmodule.o
-L/usr/local/lib -lcrypto -o build/lib.solaris-2.6-sun4u-2.5/crypt.so
#

--
components: Build
messages: 69144
nosy: mmokrejs
severity: normal
status: open
title: Use -lcrypto instead of -lcrypt on Solaris 2.6 when available
versions: Python 2.5

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[issue3265] Python-2.5.2/Modules/_ctypes/malloc_closure.c:70: error: `MAP_ANONYMOUS' undeclared

2008-07-02 Thread Martin Mokrejs

New submission from Martin Mokrejs [EMAIL PROTECTED]:

Hi,
  when building on Solaris 2.6 with gcc I get the following error:

building '_ctypes' extension
gcc -shared -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -I. -I/usr/scratch/Python-2.5.2/./Include
-Ibuild/temp.solaris-2.6-sun4u-2.5/libffi/include
-Ibuild/temp.solaris-2.6-sun4u-2.5/libffi
-I/usr/scratch/Python-2.5.2/Modules/_ctypes/libffi/src -I. -IInclude
-I./Include -I/usr/local/include -I/usr/scratch/Python-2.5.2/Include
-I/usr/scratch/Python-2.5.2 -c
/usr/scratch/Python-2.5.2/Modules/_ctypes/_ctypes.c -o
build/temp.solaris-2.6-sun4u-2.5/usr/scratch/Python-2.5.2/Modules/_ctypes/_ctypes.o
gcc -shared -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -I. -I/usr/scratch/Python-2.5.2/./Include
-Ibuild/temp.solaris-2.6-sun4u-2.5/libffi/include
-Ibuild/temp.solaris-2.6-sun4u-2.5/libffi
-I/usr/scratch/Python-2.5.2/Modules/_ctypes/libffi/src -I. -IInclude
-I./Include -I/usr/local/include -I/usr/scratch/Python-2.5.2/Include
-I/usr/scratch/Python-2.5.2 -c
/usr/scratch/Python-2.5.2/Modules/_ctypes/callbacks.c -o
build/temp.solaris-2.6-sun4u-2.5/usr/scratch/Python-2.5.2/Modules/_ctypes/callbacks.o
gcc -shared -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -I. -I/usr/scratch/Python-2.5.2/./Include
-Ibuild/temp.solaris-2.6-sun4u-2.5/libffi/include
-Ibuild/temp.solaris-2.6-sun4u-2.5/libffi
-I/usr/scratch/Python-2.5.2/Modules/_ctypes/libffi/src -I. -IInclude
-I./Include -I/usr/local/include -I/usr/scratch/Python-2.5.2/Include
-I/usr/scratch/Python-2.5.2 -c
/usr/scratch/Python-2.5.2/Modules/_ctypes/callproc.c -o
build/temp.solaris-2.6-sun4u-2.5/usr/scratch/Python-2.5.2/Modules/_ctypes/callproc.o
/usr/scratch/Python-2.5.2/Modules/_ctypes/callproc.c: In function
`_CallProc':
/usr/scratch/Python-2.5.2/Modules/_ctypes/callproc.c:921: warning:
implicit declaration of function `alloca'
gcc -shared -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -I. -I/usr/scratch/Python-2.5.2/./Include
-Ibuild/temp.solaris-2.6-sun4u-2.5/libffi/include
-Ibuild/temp.solaris-2.6-sun4u-2.5/libffi
-I/usr/scratch/Python-2.5.2/Modules/_ctypes/libffi/src -I. -IInclude
-I./Include -I/usr/local/include -I/usr/scratch/Python-2.5.2/Include
-I/usr/scratch/Python-2.5.2 -c
/usr/scratch/Python-2.5.2/Modules/_ctypes/stgdict.c -o
build/temp.solaris-2.6-sun4u-2.5/usr/scratch/Python-2.5.2/Modules/_ctypes/stgdict.o
gcc -shared -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -I. -I/usr/scratch/Python-2.5.2/./Include
-Ibuild/temp.solaris-2.6-sun4u-2.5/libffi/include
-Ibuild/temp.solaris-2.6-sun4u-2.5/libffi
-I/usr/scratch/Python-2.5.2/Modules/_ctypes/libffi/src -I. -IInclude
-I./Include -I/usr/local/include -I/usr/scratch/Python-2.5.2/Include
-I/usr/scratch/Python-2.5.2 -c
/usr/scratch/Python-2.5.2/Modules/_ctypes/cfield.c -o
build/temp.solaris-2.6-sun4u-2.5/usr/scratch/Python-2.5.2/Modules/_ctypes/cfield.o
gcc -shared -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -I. -I/usr/scratch/Python-2.5.2/./Include
-Ibuild/temp.solaris-2.6-sun4u-2.5/libffi/include
-Ibuild/temp.solaris-2.6-sun4u-2.5/libffi
-I/usr/scratch/Python-2.5.2/Modules/_ctypes/libffi/src -I. -IInclude
-I./Include -I/usr/local/include -I/usr/scratch/Python-2.5.2/Include
-I/usr/scratch/Python-2.5.2 -c
/usr/scratch/Python-2.5.2/Modules/_ctypes/malloc_closure.c -o
build/temp.solaris-2.6-sun4u-2.5/usr/scratch/Python-2.5.2/Modules/_ctypes/malloc_closure.o
/usr/scratch/Python-2.5.2/Modules/_ctypes/malloc_closure.c: In function
`more_core':
/usr/scratch/Python-2.5.2/Modules/_ctypes/malloc_closure.c:70: error:
`MAP_ANONYMOUS' undeclared (first use in this function)
/usr/scratch/Python-2.5.2/Modules/_ctypes/malloc_closure.c:70: error:
(Each undeclared identifier is reported only once
/usr/scratch/Python-2.5.2/Modules/_ctypes/malloc_closure.c:70: error:
for each function it appears in.)
building '_ctypes_test' extension
gcc -shared -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -I. -I/usr/scratch/Python-2.5.2/./Include -I.
-IInclude -I./Include -I/usr/local/include
-I/usr/scratch/Python-2.5.2/Include -I/usr/scratch/Python-2.5.2 -c
/usr/scratch/Python-2.5.2/Modules/_ctypes/_ctypes_test.c -o
build/temp.solaris-2.6-sun4u-2.5/usr/scratch/Python-2.5.2/Modules/_ctypes/_ctypes_test.o
gcc -shared -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes
build/temp.solaris-2.6-sun4u-2.5/usr/scratch/Python-2.5.2/Modules/_ctypes/_ctypes_test.o
-L/usr/local/lib -o build/lib.solaris-2.6-sun4u-2.5/_ctypes_test.so


Let me add that I see -fPIC in the top-level Makefile but do not know
why -static is not in the same variable as well. Anyway, it is not
a shared library problem I think as I already recompiled my bzip2,
openssl and ncurses libs with -shared -fpic. ;-)

--
messages: 69152
nosy: mmokrejs
severity: normal
status: open
title: Python

[issue3266] Python-2.5.2/Modules/mmapmodule.c:915: error: `O_RDWR' undeclared

2008-07-02 Thread Martin Mokrejs

New submission from Martin Mokrejs [EMAIL PROTECTED]:

Some typo in the sources showing up on Solaris 2.6 only?

building 'mmap' extension
gcc -shared -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -I. -I/usr/scratch/Python-2.5.2/./Include -I.
-IInclude -I./Include -I/usr/local/include
-I/usr/scratch/Python-2.5.2/Include -I/usr/scratch/Python-2.5.2 -c
/usr/scratch/Python-2.5.2/Modules/mmapmodule.c -o
build/temp.solaris-2.6-sun4u-2.5/usr/scratch/Python-2.5.2/Modules/mmapmodule.o
/usr/scratch/Python-2.5.2/Modules/mmapmodule.c: In function
`new_mmap_object':
/usr/scratch/Python-2.5.2/Modules/mmapmodule.c:915: warning: implicit
declaration of function `open'
/usr/scratch/Python-2.5.2/Modules/mmapmodule.c:915: error: `O_RDWR'
undeclared (first use in this function)
/usr/scratch/Python-2.5.2/Modules/mmapmodule.c:915: error: (Each
undeclared identifier is reported only once
/usr/scratch/Python-2.5.2/Modules/mmapmodule.c:915: error: for each
function it appears in.)

--
components: Build
messages: 69153
nosy: mmokrejs
severity: normal
status: open
title: Python-2.5.2/Modules/mmapmodule.c:915: error: `O_RDWR' undeclared
versions: Python 2.5

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[issue3234] subprocess.py strips last character when raising an AttributeError

2008-06-29 Thread Martin Mokrejs

New submission from Martin Mokrejs [EMAIL PROTECTED]:

I try to get working pipe emulation using Popen. I try to pass StringIO
object to p1.stdin of the first process and I got the following:

  File /usr/lib/python2.5/subprocess.py, line 587, in __init__
errread, errwrite) = self._get_handles(stdin, stdout, stderr)

  File /usr/lib/python2.5/subprocess.py, line 932, in _get_handles
p2cread = stdin.fileno()

AttributeError: 'cStringIO.StringI' object has no attribute 'fileno'

Aside from the fact I would hope that cStringIO could provide
self.fileno() I believe the error message should have been:

AttributeError: 'cStringIO.StringIO' object has no attribute 'fileno'

--
components: Library (Lib)
messages: 68942
nosy: mmokrejs
severity: normal
status: open
title: subprocess.py strips last character when raising an AttributeError
type: crash
versions: Python 2.5

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[issue3235] Improve subprocess module usage

2008-06-29 Thread Martin Mokrejs

New submission from Martin Mokrejs [EMAIL PROTECTED]:

Although I do appreciate that you try to improve python it is not clear
to me from http://docs.python.org/lib/module-subprocess.html:

1. Why the old functions have been deprecated
2. I can pipe together two processes. But how can I use pipe to feed the
first process of the two? The example at
http://docs.python.org/lib/node535.html is not sufficient. Show how to
bind together cat(1) and tr(1). Cat should read from STDIN and pass the
same to STDOUT, being read by tr(1).
3. Nowhere is explained what this magic really does:
   output = p2.communicate()[0]
   I figured out the result is e.g. a string of '\n' separated lines.
   What is not clear whether at this very moment the processes get
   started and whether one can still write on input to them. It seems
   not, the p1.stdin has to be already populated with data.
Thanks.

--
assignee: georg.brandl
components: Documentation
messages: 68943
nosy: georg.brandl, mmokrejs
severity: normal
status: open
title: Improve subprocess module usage
type: resource usage
versions: Python 2.5

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[issue3235] Improve subprocess module usage

2008-06-29 Thread Martin Mokrejs

Martin Mokrejs [EMAIL PROTECTED] added the comment:

Please link to http://www.python.org/dev/peps/pep-0324/ from the docs
webpage at least.

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