#26 Long select's causes core dump

v1.6.0.0
closed-works-for-me
7
2013-03-29
2003-05-01
Anonymous
No

Using pymol 0.86 and a large select causes a core dump. The command is:
pymol -c -q -x /db/pdb//pdb1bg1.ent -d "select A/139/ or A/140/ or A/141/ or A/142/ or A/143/ or A/144/ or A/145/ or A/146/ or A/147/ or A/148/ or A/149/ or A/150/ or A/151/ or A/152/ or A/153/ or A/154/ or A/155/ or A/156/ or A/157/ or A/158/ or A/159/ or A/160/ or A/161/ or A/162/ or A/163/ or A/164/ or A/165/ or A/166/ or A/167/ or A/168/ or A/169/ or A/170/ or A/171/ or A/172/ or A/173/ or A/174/ or A/175/ or A/176/ or A/177/ or A/178/ or A/179/ or A/180/ or A/199/ or A/200/ or A/201/ or A/202/ or A/203/ or A/204/ or A/205/ or A/206/ or A/207/ or A/208/ or A/209/ or A/210/ or A/211/ or A/212/ or A/213/ or A/214/ or A/215/ or A/216/ or A/217/ or A/218/ or A/219/ or A/220/ or A/221/ or A/222/ or A/223/ or A/224/ or A/225/ or A/226/ or A/227/ or A/228/ or A/229/ or A/230/ or A/231/ or A/232/ or A/233/ or A/234/ or A/235/ or A/236/ or A/237/ or A/239/ or A/240/ or A/241/ or A/242/ or A/243/ or A/244/ or A/245/ or A/246/ or A/247/ or A/248/ or A/249/ or A/250/ or A/251/ or A/261/ or A/262/ or A/263/ or A/264/ or A/265/ or A/266/ or A/267/ or A/268/ or A/269/ or A/270/ or A/271/ or A/272/ or A/273/ or A/274/ or A/275/ or A/276/ or A/277/ or A/278/ or A/279/ or A/280/ or A/281/ or A/282/ or A/283/ or A/284/ or A/285/ or A/286/ or A/287/ or A/288/ or A/289/ or A/290/ or A/302/ or A/303/ or A/304/ or A/305/ or A/306/ or A/307/ or A/308/ or A/309/ or A/310/ or A/311/ or A/312/ or A/313/ or A/314/ or A/315/ or A/316/ or A/317/ or A/318/ or A/319/ or A/320/ or A/356/ or A/357/ or A/358/ or A/371/ or A/372/ or A/373/ or A/426/ or A/427/ or A/428/ or A/432/ or A/433/ or A/434/ or A/467/ or A/468/ or A/469/ or A/470/ or A/471/ or A/472/ or A/473/ or A/474/ or A/475/ or A/476/ or A/477/ or A/478/ or A/479/ or A/480/ or A/481/ or A/482/ or A/483/ or A/492/ or A/493/ or A/494/ or A/501/ or A/502/ or A/503/ or A/504/ or A/505/ or A/506/ or A/507/ or A/508/ or A/509/ or A/510/ or A/511/ or A/512/ or A/513/ or A/514/ or A/515/ or A/522/ or A/523/ or A/524/ or A/525/ or A/526/ or A/527/ or A/528/ or A/529/ or A/530/ or A/531/ or A/532/ or A/533/ or A/546/ or A/547/ or A/548/ or A/549/ or A/561/ or A/562/ or A/563/ or A/564/ or A/565/ or A/566/ or A/567/ or A/568/ or A/569/ or A/570/ or A/571/ or A/572/ or A/573/ or A/574/ or A/578/ or A/579/ or A/580/ or A/581/ or A/593/ or A/594/ or A/595/ or A/642/ or A/643/ or A/644/ or A/645/ or A/650/ or A/651/ or A/652/ or A/653/ or A/684/ or A/685/ or A/686/"

Run on PDB structure 1bg1

Discussion

  • Warren L. DeLano

    • labels: --> Stability and Performance
    • priority: 5 --> 7
    • assigned_to: nobody --> wdelano
     
  • Warren L. DeLano

    PyMOL selections cannot be infinitely long. However, pymol shouldn't core dump, but version 1.2 still does...

     
  • cowsandmilk

    cowsandmilk - 2011-05-27

    this still occurs on 1.4.1 .

    *** stack smashing detected ***: /usr/bin/python terminated
    ======= Backtrace: =========
    /lib64/libc.so.6(__fortify_fail+0x37)[0x7f8ba19c5e97]
    /lib64/libc.so.6(__fortify_fail+0x0)[0x7f8ba19c5e60]
    /usr/lib64/python2.7/site-packages/pymol/_cmd.so(+0xe0fae)[0x7f8b9fdf3fae]
    /usr/lib64/python2.7/site-packages/pymol/_cmd.so(+0x2c296e)[0x7f8b9ffd596e]
    /usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x1333)[0x7f8ba257dd93]
    /usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x150)[0x7f8ba2583a90]
    /usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xe5c)[0x7f8ba257d8bc]
    /usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x309)[0x7f8ba2583c49]
    /usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xe5c)[0x7f8ba257d8bc]
    /usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x150)[0x7f8ba2583a90]
    /usr/lib64/libpython2.7.so.1.0(+0xa3f0c)[0x7f8ba2567f0c]
    /usr/lib64/libpython2.7.so.1.0(PyObject_Call+0x52)[0x7f8ba2563592]
    /usr/lib64/libpython2.7.so.1.0(+0xcb302)[0x7f8ba258f302]
    /usr/lib64/libpython2.7.so.1.0(PyObject_CallMethod+0xdd)[0x7f8ba258f4dd]
    /usr/lib64/python2.7/site-packages/pymol/_cmd.so(+0x2fb1a3)[0x7f8ba000e1a3]
    /usr/lib64/python2.7/site-packages/pymol/_cmd.so(+0x2fbfda)[0x7f8ba000efda]
    /usr/lib64/python2.7/site-packages/pymol/_cmd.so(was_main+0x305)[0x7f8ba0010a05]
    /usr/lib64/python2.7/site-packages/pymol/_cmd.so(+0x2c274c)[0x7f8b9ffd574c]
    /usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x1333)[0x7f8ba257dd93]
    /usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x150)[0x7f8ba2583a90]
    /usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xe5c)[0x7f8ba257d8bc]
    /usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x309)[0x7f8ba2583c49]
    /usr/lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x7f8ba25b2592]
    /usr/lib64/libpython2.7.so.1.0(+0xfcc61)[0x7f8ba25c0c61]
    /usr/lib64/libpython2.7.so.1.0(PyRun_FileExFlags+0x84)[0x7f8ba25c1074]
    /usr/lib64/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0x189)[0x7f8ba25c17c9]
    /usr/lib64/libpython2.7.so.1.0(Py_Main+0x36c)[0x7f8ba25cb1bc]
    /lib64/libc.so.6(__libc_start_main+0xfd)[0x7f8ba18fabfd]
    /usr/bin/python[0x4006e9]

     
  • Thomas Holder

    Thomas Holder - 2013-03-29
    • status: open --> closed-works-for-me
    • assigned_to: Warren L. DeLano --> Thomas Holder
    • milestone: --> v1.6.0.0
     
  • Thomas Holder

    Thomas Holder - 2013-03-29

    tested with 1.6 alpha on Mac and Linux

     

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