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libRoadRunner: A high-performance SBML simulator
http://libroadrunner.org/
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Segmentation faults with roadrunner 1.4.23 in tellurium #424

Closed matthiaskoenig closed 6 years ago

matthiaskoenig commented 6 years ago

I get segmentation faults with the latest roadrunner on all python versions. I just tried to update the dependency for tellurium and tests fail.

https://travis-ci.org/sys-bio/tellurium/jobs/286390132 See branch roadrunner-update

tellurium/tests/sedml/test_omex.py .......................................................................*** Error in `/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7': double free or corruption (out): 0x00000000095f5160 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f518d23c7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f518d24537a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f518d24953c]
/home/mkoenig/git/tellurium/.tox/py27/local/lib/python2.7/site-packages/roadrunner/_roadrunner.so(_ZN2ls6MatrixIdED1Ev+0x1d)[0x7f516405fe9d]
/home/mkoenig/git/tellurium/.tox/py27/local/lib/python2.7/site-packages/roadrunner/_roadrunner.so(_ZN2rr14RoadRunnerImplD1Ev+0x350)[0x7f5164091180]
/home/mkoenig/git/tellurium/.tox/py27/local/lib/python2.7/site-packages/roadrunner/_roadrunner.so(_ZN2rr10RoadRunnerD1Ev+0x20)[0x7f516408ad50]
/home/mkoenig/git/tellurium/.tox/py27/local/lib/python2.7/site-packages/roadrunner/_roadrunner.so(_ZN2rr10RoadRunnerD0Ev+0x9)[0x7f516408ad79]
/home/mkoenig/git/tellurium/.tox/py27/local/lib/python2.7/site-packages/roadrunner/_roadrunner.so(+0x4f3c42)[0x7f5164005c42]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyObject_Call+0x43)[0x4b0cb3]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyObject_CallFunctionObjArgs+0x16a)[0x4b97fa]
/home/mkoenig/git/tellurium/.tox/py27/local/lib/python2.7/site-packages/roadrunner/_roadrunner.so(+0x4e4f98)[0x7f5163ff6f98]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7[0x4fd4e6]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7[0x4b5383]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalCodeEx+0x63c)[0x4c2b4c]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x68d1)[0x4ca8d1]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalCodeEx+0x255)[0x4c2765]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x6099)[0x4ca099]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalCodeEx+0x255)[0x4c2765]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x6099)[0x4ca099]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalCodeEx+0x255)[0x4c2765]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7[0x4de8b8]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyObject_Call+0x43)[0x4b0cb3]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x2ad1)[0x4c6ad1]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalCodeEx+0x255)[0x4c2765]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7[0x4de8b8]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyObject_Call+0x43)[0x4b0cb3]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7[0x4f492e]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyObject_Call+0x43)[0x4b0cb3]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7[0x553187]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyObject_Call+0x43)[0x4b0cb3]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x5faf)[0x4c9faf]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalCodeEx+0x255)[0x4c2765]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x68d1)[0x4ca8d1]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalCodeEx+0x255)[0x4c2765]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7[0x4de6fe]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyObject_Call+0x43)[0x4b0cb3]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x2ad1)[0x4c6ad1]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x5d8f)[0x4c9d8f]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalCodeEx+0x255)[0x4c2765]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7[0x4de6fe]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyObject_Call+0x43)[0x4b0cb3]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7[0x4f492e]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyObject_Call+0x43)[0x4b0cb3]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_CallObjectWithKeywords+0x30)[0x4ce5d0]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyInstance_New+0x84)[0x4e17e4]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyObject_Call+0x43)[0x4b0cb3]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x5faf)[0x4c9faf]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x5d8f)[0x4c9d8f]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x5d8f)[0x4c9d8f]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalCodeEx+0x255)[0x4c2765]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x68d1)[0x4ca8d1]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x5d8f)[0x4c9d8f]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalCodeEx+0x255)[0x4c2765]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7[0x4de8b8]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyObject_Call+0x43)[0x4b0cb3]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7[0x4f492e]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyObject_Call+0x43)[0x4b0cb3]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7[0x553187]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyObject_Call+0x43)[0x4b0cb3]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x2ad1)[0x4c6ad1]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalCodeEx+0x255)[0x4c2765]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalFrameEx+0x68d1)[0x4ca8d1]
/home/mkoenig/git/tellurium/.tox/py27/bin/python2.7(PyEval_EvalCodeEx+0x255)[0x4c2765]
======= Memory map: ========
00400000-006ea000 r-xp 00000000 00:2e 48366352                           /home/mkoenig/git/tellurium/.tox/py27/bin/python2.7
008e9000-008eb000 r--p 002e9000 00:2e 48366352                           /home/mkoenig/git/tellurium/.tox/py27/bin/python2.7
008eb000-00962000 rw-p 002eb000 00:2e 48366352                           /home/mkoenig/git/tellurium/.tox/py27/bin/python2.7
00962000-00985000 rw-p 00000000 00:00 0 
01ab9000-0dfab000 rw-p 00000000 00:00 0                                  [heap]
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7f5148021000-7f514c000000 ---p 00000000 00:00 0 
7f514fb03000-7f514fb1a000 r-xp 00000000 fd:00 40634781                   /lib/x86_64-linux-gnu/libresolv-2.23.so
7f514fb1a000-7f514fd1a000 ---p 00017000 fd:00 40634781                   /lib/x86_64-linux-gnu/libresolv-2.23.so
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7f514ff25000-7f514ff27000 r-xp 00000000 fd:00 40636922                   /lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2
7f514ff27000-7f5150126000 ---p 00002000 fd:00 40636922                   /lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2
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7f5153a2c000-7f515426c000 rw-p 00000000 00:00 0 
7f515426c000-7f515427f000 r-xp 00000000 00:2e 48502334                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/matplotlib/ttconv.so
7f515427f000-7f515447e000 ---p 00013000 00:2e 48502334                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/matplotlib/ttconv.so
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7f5156be8000-7f5156be9000 r--p 00001000 00:2e 48506844                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/markupsafe/_speedups.so
7f5156be9000-7f5156bea000 rw-p 00002000 00:2e 48506844                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/markupsafe/_speedups.so
7f5156bea000-7f5156c6a000 rw-p 00000000 00:00 0 
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7f5157138000-7f51585f4000 r-xp 00000000 00:2e 48506507                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/roadrunner/libroadrunner.so.1.4.23
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7f51587f3000-7f51588be000 rw-p 014bb000 00:2e 48506507                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/roadrunner/libroadrunner.so.1.4.23
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7f5158af3000-7f5158af4000 rw-p 0001d000 00:2e 48506512                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/roadrunner/libtelplugins_math.so
7f5158af4000-7f5158af5000 rw-p 00000000 00:00 0 
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7f5158d37000-7f5158dd7000 r-xp 00000000 00:2e 48506506                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/roadrunner/libtelplugins_c_api.so
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7f5158fd6000-7f5158fd9000 rw-p 0009f000 00:2e 48506506                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/roadrunner/libtelplugins_c_api.so
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7f5159224000-7f5159226000 rw-p 0001c000 00:2e 48373923                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/_nnls.so
7f5159226000-7f5159229000 r-xp 00000000 00:2e 48373891                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/_zeros.so
7f5159229000-7f5159428000 ---p 00003000 00:2e 48373891                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/_zeros.so
7f5159428000-7f5159429000 rw-p 00002000 00:2e 48373891                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/_zeros.so
7f5159429000-7f515944b000 r-xp 00000000 00:2e 48373944                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/_lsq/givens_elimination.so
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7f515964b000-7f515964e000 rw-p 00022000 00:2e 48373944                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/_lsq/givens_elimination.so
7f515964e000-7f515968e000 rw-p 00000000 00:00 0 
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7f51596b8000-7f51598b8000 ---p 0002a000 00:2e 48373894                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/_group_columns.so
7f51598b8000-7f51598bb000 rw-p 0002a000 00:2e 48373894                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/_group_columns.so
7f51598bb000-7f51598da000 r-xp 00000000 00:2e 48373924                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/_minpack.so
7f51598da000-7f5159ada000 ---p 0001f000 00:2e 48373924                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/_minpack.so
7f5159ada000-7f5159adb000 rw-p 0001f000 00:2e 48373924                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/_minpack.so
7f5159adb000-7f5159add000 rw-p 00031000 00:2e 48373924                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/_minpack.so
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7f5159cf4000-7f5159cf5000 rw-p 00017000 00:2e 48373916                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/_slsqp.so
7f5159cf5000-7f5159cf7000 rw-p 0002c000 00:2e 48373916                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/_slsqp.so
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7f5159f24000-7f515a123000 ---p 0000c000 00:2e 48373893                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/moduleTNC.so
7f515a123000-7f515a124000 rw-p 0000b000 00:2e 48373893                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/optimize/moduleTNC.so
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7f515a150000-7f515a350000 ---p 0002c000 00:2e 48373421                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/integrate/lsoda.so
7f515a350000-7f515a352000 rw-p 0002c000 00:2e 48373421                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/integrate/lsoda.so
7f515a352000-7f515a355000 rw-p 00046000 00:2e 48373421                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/integrate/lsoda.so
7f515a355000-7f515a370000 r-xp 00000000 00:2e 48373408                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/integrate/_dop.so
7f515a370000-7f515a570000 ---p 0001b000 00:2e 48373408                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/integrate/_dop.so
7f515a570000-7f515a572000 rw-p 0001b000 00:2e 48373408                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/integrate/_dop.so
7f515a572000-7f515a574000 rw-p 00037000 00:2e 48373408                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/integrate/_dop.so
7f515a574000-7f515a5a6000 r-xp 00000000 00:2e 48373424                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/integrate/vode.so
7f515a5a6000-7f515a7a6000 ---p 00032000 00:2e 48373424                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/integrate/vode.so
7f515a7a6000-7f515a7a8000 rw-p 00032000 00:2e 48373424                   /home/mkoenig/git/tellurium/.tox/py27/lib/python2.7/site-packages/scipy/integrate/vode.so
7f515a7a8000-7f515a7a9000 rw-p 00000000 00:00 0 ERROR: InvocationError: '/home/mkoenig/git/tellurium/.tox/py27/bin/pytest te
0u812 commented 6 years ago

This started happening in f842bfb. Reverting for now.

0u812 commented 6 years ago

I'm going to release 1.4.24 immediately to address the segfault issue

matthiaskoenig commented 6 years ago

Thanks, just pushed the dependency update to tellurium. Everything working now.

On Wed, Oct 11, 2017 at 10:00 PM, Kyle Medley notifications@github.com wrote:

I'm going to release 1.4.24 immediately to address the segfault issue

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