Comments (5)
scottransom
commented on September 4, 2024
1
Yes. And I don't understand it at all. I can reproduce it with Anaconda, but cannot reproduce it with either Python2 or Python3 in a virtual environment, which is what I've been using recently.
from presto.
matteobachetti
commented on September 4, 2024
Running on GDB:
(gdb) run
Starting program: /home/mbachett/anaconda/envs/py27/bin/python /home/mbachett/pulsar_software/presto/python/ffdot_example.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Warning: '/home/mbachett/pulsar_software/presto//lib/fftw_wisdom.txt' is not up-to-date.
You should run 'makewisdom'. See $PRESTO/INSTALL.
*** Error in `/home/mbachett/anaconda/envs/py27/bin/python': double free or corruption (out): 0x0000000001068500 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x77725)[0x7ffff6d5e725]
/lib/x86_64-linux-gnu/libc.so.6(+0x7ff4a)[0x7ffff6d66f4a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7ffff6d6aabc]
/home/mbachett/pulsar_software/presto/lib/python/_presto.so(+0x10a09)[0x7fffecda3a09]
/home/mbachett/anaconda/envs/py27/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x8942)[0x7ffff7ada5a2]
/home/mbachett/anaconda/envs/py27/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x89e)[0x7ffff7adb1ce]
/home/mbachett/anaconda/envs/py27/bin/../lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x8596)[0x7ffff7ada1f6]
/home/mbachett/anaconda/envs/py27/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x89e)[0x7ffff7adb1ce]
/home/mbachett/anaconda/envs/py27/bin/../lib/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x7ffff7adb2e2]
/home/mbachett/anaconda/envs/py27/bin/../lib/libpython2.7.so.1.0(PyRun_FileExFlags+0xb0)[0x7ffff7afb960]
/home/mbachett/anaconda/envs/py27/bin/../lib/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0xef)[0x7ffff7afbb3f]
/home/mbachett/anaconda/envs/py27/bin/../lib/libpython2.7.so.1.0(Py_Main+0xca4)[0x7ffff7b11484]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7ffff6d07830]
/home/mbachett/anaconda/envs/py27/bin/python[0x400649]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:03 12587525 /home/mbachett/anaconda/envs/py27/bin/python2.7
00600000-00601000 rw-p 00000000 08:03 12587525 /home/mbachett/anaconda/envs/py27/bin/python2.7
00601000-010ea000 rw-p 00000000 00:00 0 [heap]
7fffdc000000-7fffdc021000 rw-p 00000000 00:00 0
7fffdc021000-7fffe0000000 ---p 00000000 00:00 0
7fffe0115000-7fffe1b17000 rw-p 00000000 00:00 0
7fffe1b17000-7fffe3c24000 r-xp 00000000 08:03 11673449 /home/mbachett/anaconda/envs/py27/lib/libmkl_avx.so
7fffe3c24000-7fffe3e24000 ---p 0210d000 08:03 11673449 /home/mbachett/anaconda/envs/py27/lib/libmkl_avx.so
7fffe3e24000-7fffe3e29000 r--p 0210d000 08:03 11673449 /home/mbachett/anaconda/envs/py27/lib/libmkl_avx.so
(...)
Program received signal SIGABRT, Aborted.
0x00007ffff6d1c418 in __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:54
54 ../sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb) where
#0 0x00007ffff6d1c418 in __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:54
#1 0x00007ffff6d1e01a in __GI_abort () at abort.c:89
#2 0x00007ffff6d5e72a in __libc_message (do_abort=do_abort@entry=2, fmt=fmt@entry=0x7ffff6e776b0 "*** Error in `%s': %s: 0x%s ***\n") at ../sysdeps/posix/libc_fatal.c:175
#3 0x00007ffff6d66f4a in malloc_printerr (ar_ptr=<optimized out>, ptr=<optimized out>, str=0x7ffff6e777c0 "double free or corruption (out)", action=3) at malloc.c:5007
#4 _int_free (av=<optimized out>, p=<optimized out>, have_lock=0) at malloc.c:3868
#5 0x00007ffff6d6aabc in __GI___libc_free (mem=<optimized out>) at malloc.c:2969
#6 0x00007fffecda3a09 in _wrap_corr_rz_plane (self=<optimized out>, args=<optimized out>) at presto_src/presto_wrap.c:18528
#7 0x00007ffff7ada5a2 in call_function (oparg=<optimized out>, pp_stack=0x7fffffffce78) at Python/ceval.c:4350
#8 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2987
#9 0x00007ffff7adb1ce in PyEval_EvalCodeEx (co=0x7fffed9b57b0, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=7, kws=0x7ffff7f30b90,
kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3582
#10 0x00007ffff7ada1f6 in fast_function (nk=<optimized out>, na=7, n=<optimized out>, pp_stack=0x7fffffffd098, func=0x7fffe3e9e7d0) at Python/ceval.c:4445
#11 call_function (oparg=<optimized out>, pp_stack=0x7fffffffd098) at Python/ceval.c:4370
#12 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2987
#13 0x00007ffff7adb1ce in PyEval_EvalCodeEx (co=0x7ffff7ed2eb0, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=0, kws=0x0, kwcount=0,
defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3582
#14 0x00007ffff7adb2e2 in PyEval_EvalCode (co=<optimized out>, globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:669
#15 0x00007ffff7afb960 in run_mod (arena=0x6b78c0, flags=0x7fffffffd390, locals=0x7ffff7f6d168, globals=0x7ffff7f6d168, filename=<optimized out>, mod=0x6cbac8)
at Python/pythonrun.c:1376
#16 PyRun_FileExFlags (fp=0x66c310, filename=<optimized out>, start=<optimized out>, globals=0x7ffff7f6d168, locals=0x7ffff7f6d168, closeit=1, flags=0x7fffffffd390)
at Python/pythonrun.c:1362
#17 0x00007ffff7afbb3f in PyRun_SimpleFileExFlags (fp=0x66c310, filename=0x7fffffffd95b "/home/mbachett/pulsar_software/presto/python/ffdot_example.py",
closeit=1, flags=0x7fffffffd390) at Python/pythonrun.c:948
#18 0x00007ffff7b11484 in Py_Main (argc=<optimized out>, argv=<optimized out>) at Modules/main.c:645
#19 0x00007ffff6d07830 in __libc_start_main (main=0x400710 <main>, argc=2, argv=0x7fffffffd4b8, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>,
stack_end=0x7fffffffd4a8) at ../csu/libc-start.c:291
#20 0x0000000000400649 in _start ()
(gdb) bt
#0 0x00007ffff6d1c418 in __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:54
#1 0x00007ffff6d1e01a in __GI_abort () at abort.c:89
#2 0x00007ffff6d5e72a in __libc_message (do_abort=do_abort@entry=2, fmt=fmt@entry=0x7ffff6e776b0 "*** Error in `%s': %s: 0x%s ***\n") at ../sysdeps/posix/libc_fatal.c:175
#3 0x00007ffff6d66f4a in malloc_printerr (ar_ptr=<optimized out>, ptr=<optimized out>, str=0x7ffff6e777c0 "double free or corruption (out)", action=3) at malloc.c:5007
#4 _int_free (av=<optimized out>, p=<optimized out>, have_lock=0) at malloc.c:3868
#5 0x00007ffff6d6aabc in __GI___libc_free (mem=<optimized out>) at malloc.c:2969
#6 0x00007fffecda3a09 in _wrap_corr_rz_plane (self=<optimized out>, args=<optimized out>) at presto_src/presto_wrap.c:18528
#7 0x00007ffff7ada5a2 in call_function (oparg=<optimized out>, pp_stack=0x7fffffffce78) at Python/ceval.c:4350
#8 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2987
#9 0x00007ffff7adb1ce in PyEval_EvalCodeEx (co=0x7fffed9b57b0, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=7, kws=0x7ffff7f30b90,
kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3582
#10 0x00007ffff7ada1f6 in fast_function (nk=<optimized out>, na=7, n=<optimized out>, pp_stack=0x7fffffffd098, func=0x7fffe3e9e7d0) at Python/ceval.c:4445
#11 call_function (oparg=<optimized out>, pp_stack=0x7fffffffd098) at Python/ceval.c:4370
#12 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2987
#13 0x00007ffff7adb1ce in PyEval_EvalCodeEx (co=0x7ffff7ed2eb0, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=0, kws=0x0, kwcount=0,
defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3582
#14 0x00007ffff7adb2e2 in PyEval_EvalCode (co=<optimized out>, globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:669
#15 0x00007ffff7afb960 in run_mod (arena=0x6b78c0, flags=0x7fffffffd390, locals=0x7ffff7f6d168, globals=0x7ffff7f6d168, filename=<optimized out>, mod=0x6cbac8)
at Python/pythonrun.c:1376
#16 PyRun_FileExFlags (fp=0x66c310, filename=<optimized out>, start=<optimized out>, globals=0x7ffff7f6d168, locals=0x7ffff7f6d168, closeit=1, flags=0x7fffffffd390)
at Python/pythonrun.c:1362
#17 0x00007ffff7afbb3f in PyRun_SimpleFileExFlags (fp=0x66c310, filename=0x7fffffffd95b "/home/mbachett/pulsar_software/presto/python/ffdot_example.py",
closeit=1, flags=0x7fffffffd390) at Python/pythonrun.c:948
#18 0x00007ffff7b11484 in Py_Main (argc=<optimized out>, argv=<optimized out>) at Modules/main.c:645
#19 0x00007ffff6d07830 in __libc_start_main (main=0x400710 <main>, argc=2, argv=0x7fffffffd4b8, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>,
stack_end=0x7fffffffd4a8) at ../csu/libc-start.c:291
#20 0x0000000000400649 in _start ()
from presto.
matteobachetti
commented on September 4, 2024
Looking at
#6 0x00007fffecda3a09 in _wrap_corr_rz_plane (self=<optimized out>, args=<optimized out>) at presto_src/presto_wrap.c:18528
it seems that it originates from some of the automatic code that SWIG is throwing out, so it would probably be interesting to see if the problem is reproduced in the new SWIG branch.
@scottransom
from presto.
emmacarli
commented on September 4, 2024
Is this issue still relevant? I am experiencing similar problems.
from presto.
scottransom
commented on September 4, 2024
Note that there is some evidence that it is related to the import_array(); call that is required by the Numpy C-API. This is on my list of things to try to figure out soon if I can find some time.
from presto.
Related Issues (20)
- makezaplist.py: No module named presto HOT 15
- AttributeError: 'NoneType' object has no attribute 'groups' HOT 4
- Who's using the classic branch? HOT 4
- Problem doing ACCEL_sift - sifting:candlist_from_candfile HOT 4
- Docker on ARM: build results in "Error: Old-style type declaration REAL*10 not supported at (1)" HOT 4
- docker build fails on arm64 system
- Errors in running "test_presto_python" HOT 15
- Issue with sigproc keyword signed HOT 3
- Issue Installing PRESTO Python Packages in Python3.9 on RHEL 8 HOT 8
- Import Error on single_pulse_search.py HOT 1
- Undefined reference error during installation HOT 15
- accelsearch frequency range HOT 4
- Using prepsubband for only a fraction of a dataset HOT 3
- Build issue with pulsestack.py HOT 2
- `rfifind` and OpenMP HOT 4
- Separating `FFTFIT` into a separate Python package? HOT 2
- Automated documentation for `PRESTO`? HOT 2
- Packaging `PRESTO` for multiple OSes? HOT 3
- ld: cannot find -lfftw3f: No such file or directory HOT 2
- undefined symbol: _gfortran_st_close HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from presto.