Error in `python': double free or corruption (out) #138

icankeep · 2021-12-14T13:35:55Z

$ python
Python 3.6.13 | packaged by conda-forge | (default, Sep 23 2021, 07:56:31) 
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from cylp.cy import CyClpSimplex
>>> s = CyClpSimplex()
*** Error in `python': double free or corruption (out): 0x000056182c3083f0 ***
======= Backtrace: =========
/usr/lib64/libc.so.6(+0x81679)[0x7f26c37c4679]
/conda/envs/notebook/lib/libstdc++.so.6(_ZNSs6assignERKSs+0x41)[0x7f26c2b209a5]
/conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyClpSimplex.cpython-36m-x86_64-linux-gnu.so(_ZN11IClpSimplexC2EP7_objectPFiPvEPFiS2_iE+0xd4)[0x7f26b8a4fc64]
/conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyClpSimplex.cpython-36m-x86_64-linux-gnu.so(+0x67d05)[0x7f26b8a93d05]
python(+0xf9ed6)[0x56182aba0ed6]
python(_PyObject_FastCallKeywords+0x193)[0x56182abfc443]
python(+0x155e65)[0x56182abfce65]
python(_PyEval_EvalFrameDefault+0x53c)[0x56182ac4b7bc]
python(+0xe9a95)[0x56182ab90a95]
python(PyEval_EvalCodeEx+0x39)[0x56182ab91f29]
python(PyEval_EvalCode+0x1b)[0x56182ac6387b]
python(+0x2239b3)[0x56182acca9b3]
python(+0xc7473)[0x56182ab6e473]
python(PyRun_InteractiveLoopFlags+0xed)[0x56182ab6ed75]
python(+0xc7e14)[0x56182ab6ee14]
python(Py_Main+0x6a7)[0x56182acd0d67]
python(main+0xe7)[0x56182ab73d17]
/usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f26c3765505]
python(+0x1ab83d)[0x56182ac5283d]
======= Memory map: ========
56182aaa7000-56182aafe000 r--p 00000000 fd:08 1330795                    /conda/envs/notebook/bin/python3.6
56182aafe000-56182acd5000 r-xp 00057000 fd:08 1330795                    /conda/envs/notebook/bin/python3.6
56182acd5000-56182ad7b000 r--p 0022e000 fd:08 1330795                    /conda/envs/notebook/bin/python3.6
56182ad7c000-56182ad7f000 r--p 002d4000 fd:08 1330795                    /conda/envs/notebook/bin/python3.6
56182ad7f000-56182ade2000 rw-p 002d7000 fd:08 1330795                    /conda/envs/notebook/bin/python3.6
56182ade2000-56182ae13000 rw-p 00000000 00:00 0 
56182bd27000-56182c325000 rw-p 00000000 00:00 0                          [heap]
7f2690000000-7f2690021000 rw-p 00000000 00:00 0 
7f2690021000-7f2694000000 ---p 00000000 00:00 0 
7f2697a9c000-7f2697aa0000 r--p 00000000 fd:08 1457209                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyDantzigPivot.cpython-36m-x86_64-linux-gnu.so
7f2697aa0000-7f2697aab000 r-xp 00004000 fd:08 1457209                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyDantzigPivot.cpython-36m-x86_64-linux-gnu.so
7f2697aab000-7f2697aad000 r--p 0000f000 fd:08 1457209                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyDantzigPivot.cpython-36m-x86_64-linux-gnu.so
7f2697aad000-7f2697aae000 ---p 00011000 fd:08 1457209                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyDantzigPivot.cpython-36m-x86_64-linux-gnu.so
7f2697aae000-7f2697aaf000 r--p 00011000 fd:08 1457209                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyDantzigPivot.cpython-36m-x86_64-linux-gnu.so
7f2697aaf000-7f2697ab0000 rw-p 00012000 fd:08 1457209                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyDantzigPivot.cpython-36m-x86_64-linux-gnu.so
7f2697ab0000-7f2697ab1000 rw-p 00000000 00:00 0 
7f2697ab1000-7f2697ab6000 r--p 00000000 fd:08 1457206                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyCoinMpsIO.cpython-36m-x86_64-linux-gnu.so
7f2697ab6000-7f2697ac0000 r-xp 00005000 fd:08 1457206                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyCoinMpsIO.cpython-36m-x86_64-linux-gnu.so
7f2697ac0000-7f2697ac3000 r--p 0000f000 fd:08 1457206                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyCoinMpsIO.cpython-36m-x86_64-linux-gnu.so
7f2697ac3000-7f2697ac4000 ---p 00012000 fd:08 1457206                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyCoinMpsIO.cpython-36m-x86_64-linux-gnu.so
7f2697ac4000-7f2697ac5000 r--p 00012000 fd:08 1457206                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyCoinMpsIO.cpython-36m-x86_64-linux-gnu.so
7f2697ac5000-7f2697ac7000 rw-p 00013000 fd:08 1457206                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyCoinMpsIO.cpython-36m-x86_64-linux-gnu.so
7f2697ac7000-7f2697acb000 r--p 00000000 fd:08 1457210                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyDualPivotPythonBase.cpython-36m-x86_64-linux-gnu.so
7f2697acb000-7f2697ad4000 r-xp 00004000 fd:08 1457210                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyDualPivotPythonBase.cpython-36m-x86_64-linux-gnu.so
7f2697ad4000-7f2697ad7000 r--p 0000d000 fd:08 1457210                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyDualPivotPythonBase.cpython-36m-x86_64-linux-gnu.so
7f2697ad7000-7f2697ad8000 r--p 0000f000 fd:08 1457210                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyDualPivotPythonBase.cpython-36m-x86_64-linux-gnu.so
7f2697ad8000-7f2697ad9000 rw-p 00010000 fd:08 1457210                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyDualPivotPythonBase.cpython-36m-x86_64-linux-gnu.so
7f2697ad9000-7f2697add000 r--p 00000000 fd:08 1457214                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyPivotPythonBase.cpython-36m-x86_64-linux-gnu.so
7f2697add000-7f2697ae4000 r-xp 00004000 fd:08 1457214                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyPivotPythonBase.cpython-36m-x86_64-linux-gnu.so
7f2697ae4000-7f2697ae6000 r--p 0000b000 fd:08 1457214                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyPivotPythonBase.cpython-36m-x86_64-linux-gnu.so
7f2697ae6000-7f2697ae7000 r--p 0000c000 fd:08 1457214                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyPivotPythonBase.cpython-36m-x86_64-linux-gnu.so
7f2697ae7000-7f2697ae8000 rw-p 0000d000 fd:08 1457214                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyPivotPythonBase.cpython-36m-x86_64-linux-gnu.so
7f2697ae8000-7f2697aec000 r--p 00000000 fd:08 1457213                    /conda/envs/notebook/lib/python3.6/site-packages/cylp/cy/CyPEPivot.cpython-36m-x86_64-linux-gnu.soAborted (core dumped)

icankeep · 2021-12-14T13:37:25Z

python3.6

conda install coin-or-cbc
pip install cylp
python

from cylp.cy import CyClpSimplex
s = CyClpSimplex()

then error:
Error in `python': double free or corruption (out)

tkralphs · 2021-12-14T15:41:07Z

This looks related to this comment in #137, but I can't seem to replicate. It could also be related to #105. Can you see if installing 875d5d5 fixes it?

icankeep · 2021-12-15T09:36:15Z

I tried to install it locally with this commit version, but still the same problem

git clone [email protected]:coin-or/CyLP.git
git checkout  875d5d5
cd CyLP
python setup.py install

cafunechen · 2021-12-15T09:54:00Z

I tried to install it locally with this commit version, but still the same problem
git clone [email protected]:coin-or/CyLP.git
git checkout  875d5d5
cd CyLP
python setup.py install

oh， I didn't expect someone to have the same problem as me. If you solve it, can you tell me？ thanks！！ that’s my problem #137

cafunechen · 2021-12-15T10:04:19Z

and the different is ,when i build git checkout 875d5d5 ,the error cames different

from cylp.cy import CyClpSimplex


Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "~/CyLP/cylp/cy/__init__.py", line 1, in <module>
    from .CyCoinIndexedVector import CyCoinIndexedVector
ModuleNotFoundError: No module named 'cylp.cy.CyCoinIndexedVector'

and my step is

git clone -n  https://github.com/coin-or/CyLP.git
cd Cylp
git checkout  875d5d5ad07cd1b4b53d3715e4aa29164a025e9
python setup.py install

icankeep · 2021-12-15T12:01:20Z

Traceback (most recent call last):
File "", line 1, in
File "~/CyLP/cylp/cy/init.py", line 1, in
from .CyCoinIndexedVector import CyCoinIndexedVector
ModuleNotFoundError: No module named 'cylp.cy.CyCoinIndexedVector'

git clone -n  https://github.com/coin-or/CyLP.git
cd Cylp
git checkout  875d5d5ad07cd1b4b53d3715e4aa29164a025e9
python setup.py install

# Need to add this step
cd cylp/cy
python

>> from cylp.cy import CyClpSimplex
>> s = CyClpSimplex()

cafunechen · 2021-12-15T12:16:01Z

s = CyClpSimplex()

ok, i get the same error~

tkralphs · 2021-12-15T15:18:16Z

# Need to add this step
cd cylp/cy
python

I don't understand this. Are you saying it only happens if you are in this directory? In general, for Python 3, you should not be in the directory containing the source when you work with the package because relative imports don't work correctly. In any case, I can't replicate any of this. Can you give some more details, such as what distro and version you're using, etc.

tkralphs · 2021-12-15T15:56:09Z

OK, I now tried running CyLP through valgrind and I do see some memory errors---they're just not causing a crash in my case (strangely). So I will try to debug this.

tkralphs · 2021-12-21T20:34:38Z

I haven't really been able to uncover anything. The memory errors I see seem to be internal to Python (using uninitialized value kind of stuff, which are not always consequential errors). So I guess I will need some help in replicating this after all. It looks a bit strange to me.

tkralphs · 2021-12-22T03:07:44Z

If anyone who is seeing this issue can build CyLP with debugging symbols and run through valgrind, that would be super helpful. Even better, build Cbc from source with debugging symbols. I think just doing python setup.py build --debug should work for building CyLP with debugging symbols. For Cbc, follow the instructions here, adding the flag --enable-debug in the build step.

UPDATE: After building the Cbc source, you need to set the environment variable COIN_INSTALL_DIR in order to tell CyLP to link to your custom-built version. Alternatively, what I eventually dis was just to copy the libraries into the lib directory of my conda virtual environment.

cafunechen · 2021-12-22T03:24:24Z

which version should i build Cylp? the 875d5d5 or the latest ?

tkralphs · 2021-12-22T16:58:32Z

which version should i build Cylp? the 875d5d5 or the latest ?

I guess that building the latest would give us the most information. But the best would be to build both in different virtual environments.

YankeeTsao mentioned this issue Dec 22, 2021

Error in `python': double free or corruption (out) #140

Closed

mgrover1 mentioned this issue Mar 28, 2022

BUG: Error when using CyLP ARM-DOE/pyart#1022

Open

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Error in `python': double free or corruption (out) #138

Error in `python': double free or corruption (out) #138

icankeep commented Dec 14, 2021

icankeep commented Dec 14, 2021

tkralphs commented Dec 14, 2021

icankeep commented Dec 15, 2021

cafunechen commented Dec 15, 2021

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tkralphs commented Dec 22, 2021

Error in `python': double free or corruption (out) #138

Error in `python': double free or corruption (out) #138

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icankeep commented Dec 14, 2021

icankeep commented Dec 14, 2021

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