Hi,
I am suffering from pymol startup error. It gets terminated with the
following error messages:
PyMOL(TM) Molecular Graphics System, Version 1.5.0.3.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
PyMOL is user-supported open-source software. Although some versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.
More information can be found at "http://www.pymol.org";.
Enter "help" for a list of commands.
Enter "help <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 2.0 or greater. Shaders available.
*** buffer overflow detected ***: /usr/bin/python terminated
======= Backtrace: =========
/lib64/libc.so.6(__fortify_fail+0x37)[0x7f30e5ee8277]
/lib64/libc.so.6(+0xfc350)[0x7f30e5ee6350]
/lib64/libc.so.6(+0xfb7d9)[0x7f30e5ee57d9]
/lib64/libc.so.6(_IO_default_xsputn+0x89)[0x7f30e5e623d9]
/lib64/libc.so.6(_IO_vfprintf+0x48a3)[0x7f30e5e35473]
/lib64/libc.so.6(__vsprintf_chk+0x97)[0x7f30e5ee5877]
/lib64/libc.so.6(__sprintf_chk+0x7d)[0x7f30e5ee57bd]
/usr/lib64/python2.7/site-packages/pymol/_cmd.so(CShaderMgr_ReadShaderFromDisk+0x2f3)[0x7f30e46ca8d3]
/usr/lib64/python2.7/site-packages/pymol/_cmd.so(CShaderPrg_NewFromFile+0x2e)[0x7f30e46cb71e]
/usr/lib64/python2.7/site-packages/pymol/_cmd.so(ShaderMgrConfig+0xa9)[0x7f30e46cb849]
/usr/lib64/python2.7/site-packages/pymol/_cmd.so(was_main+0x13e)[0x7f30e49bb8ce]
/usr/lib64/python2.7/site-packages/pymol/_cmd.so(+0x34b5c1)[0x7f30e497e5c1]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x113a)[0x7f30e646611a]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x143)[0x7f30e646b303]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0xd27)[0x7f30e6465d07]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x403)[0x7f30e646b5c3]
/usr/lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x7f30e64998b2]
/usr/lib64/libpython2.7.so.1.0(+0xf3d91)[0x7f30e64a6d91]
/usr/lib64/libpython2.7.so.1.0(PyRun_FileExFlags+0x86)[0x7f30e64a7156]
/usr/lib64/libpython2.7.so.1.0(PyRun_SimpleFileExFlags+0x17d)[0x7f30e64a7a2d]
/usr/lib64/libpython2.7.so.1.0(Py_Main+0x3ad)[0x7f30e64b122d]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f30e5e0ba15]
/usr/bin/python[0x400791]
======= Memory map: ========
00400000-00401000 r-xp 00000000 09:06 1181836
/usr/bin/python2.7
00600000-00601000 r--p 00000000 09:06 1181836
/usr/bin/python2.7
00601000-00602000 rw-p 00001000 09:06 1181836
/usr/bin/python2.7
00e65000-01a25000 rw-p 00000000 00:00 0
[heap]
404f9000-40596000 rw-p 00000000 00:00 0
41954000-41956000 r-xs 00000000 09:08 19
/tmp/gleT7vZR (deleted)
7f30dd223000-7f30dd423000 rw-s 7661eb000 00:05 593
/dev/nvidia0
7f30dd423000-7f30dd623000 rw-s 59aad7000 00:05 593
/dev/nvidia0
7f30dd623000-7f30dd823000 rw-s 6072fa000 00:05 593
/dev/nvidia0
7f30dd823000-7f30dd923000 rw-s 506579000 00:05 593
/dev/nvidia0
7f30dd923000-7f30dd92a000 rw-s 5176ff000 00:05 593
/dev/nvidia0
7f30dd92a000-7f30dd94a000 rw-s d0060000 00:05 593
/dev/nvidia0
7f30dd94a000-7f30dd98a000 rw-s 574b37000 00:05 593
/dev/nvidia0
7f30dd98a000-7f30dd9aa000 rw-s 56bbd3000 00:05 593
/dev/nvidia0
7f30dd9aa000-7f30dd9ea000 rw-s 6d1e49000 00:05 593
/dev/nvidia0
7f30dd9ea000-7f30ddaa2000 rw-p 00000000 00:00 0
7f30ddaa2000-7f30ddaa5000 r-xp 00000000 09:06 1058995
/usr/lib64/python2.7/lib-dynload/fcntl.so
7f30ddaa5000-7f30ddca4000 ---p 00003000 09:06 1058995
/usr/lib64/python2.7/lib-dynload/fcntl.so
7f30ddca4000-7f30ddca5000 r--p 00002000 09:06 1058995
/usr/lib64/python2.7/lib-dynload/fcntl.so
7f30ddca5000-7f30ddca6000 rw-p 00003000 09:06 1058995
/usr/lib64/python2.7/lib-dynload/fcntl.so
7f30ddca6000-7f30ddcc1000 r-xp 00000000 09:06 1059009
/usr/lib64/python2.7/lib-dynload/_io.so
7f30ddcc1000-7f30ddec1000 ---p 0001b000 09:06 1059009
/usr/lib64/python2.7/lib-dynload/_io.so
7f30ddec1000-7f30ddec2000 r--p 0001b000 09:06 1059009
/usr/lib64/python2.7/lib-dynload/_io.so
7f30ddec2000-7f30ddecb000 rw-p 0001c000 09:06 1059009
/usr/lib64/python2.7/lib-dynload/_io.so
7f30ddecb000-7f30ddecf000 r-xp 00000000 09:06 1059019
/usr/lib64/python2.7/lib-dynload/zlib.so
7f30ddecf000-7f30de0ce000 ---p 00004000 09:06 1059019
/usr/lib64/python2.7/lib-dynload/zlib.so
7f30de0ce000-7f30de0cf000 r--p 00003000 09:06 1059019
/usr/lib64/python2.7/lib-dynload/zlib.so
7f30de0cf000-7f30de0d1000 rw-p 00004000 09:06 1059019
/usr/lib64/python2.7/lib-dynload/zlib.so
7f30de0d1000-7f30de253000 rw-p 00000000 00:00 0
7f30de253000-7f30de25b000 r-xp 00000000 09:06 1058997
/usr/lib64/python2.7/lib-dynload/operator.so
7f30de25b000-7f30de45a000 ---p 00008000 09:06 1058997
/usr/lib64/python2.7/lib-dynload/operator.so
7f30de45a000-7f30de45b000 r--p 00007000 09:06 1058997
/usr/lib64/python2.7/lib-dynload/operator.so
7f30de45b000-7f30de45d000 rw-p 00008000 09:06 1058997
/usr/lib64/python2.7/lib-dynload/operator.so
7f30de45d000-7f30de460000 r-xp 00000000 09:06 1058990
/usr/lib64/python2.7/lib-dynload/_random.so
7f30de460000-7f30de65f000 ---p 00003000 09:06 1058990
/usr/lib64/python2.7/lib-dynload/_random.so
7f30de65f000-7f30de660000 r--p 00002000 09:06 1058990
/usr/lib64/python2.7/lib-dynload/_random.so
7f30de660000-7f30de661000 rw-p 00003000 09:06 1058990
/usr/lib64/python2.7/lib-dynload/_random.so
7f30de661000-7f30de80b000 r-xp 00000000 09:05 237
/lib64/libcrypto.so.1.0.0
7f30de80b000-7f30dea0a000 ---p 001aa000 09:05 237
/lib64/libcrypto.so.1.0.0
7f30dea0a000-7f30dea25000 r--p 001a9000 09:05 237
/lib64/libcrypto.so.1.0.0
7f30dea25000-7f30dea30000 rw-p 001c4000 09:05 237
/lib64/libcrypto.so.1.0.0
7f30dea30000-7f30dea34000 rw-p 00000000 00:00 0
7f30dea34000-7f30dea94000 r-xp 00000000 09:05 478
/lib64/libssl.so.1.0.0
7f30dea94000-7f30dec93000 ---p 00060000 09:05 478
/lib64/libssl.so.1.0.0
7f30dec93000-7f30dec97000 r--p 0005f000 09:05 478
/lib64/libssl.so.1.0.0
7f30dec97000-7f30dec9d000 rw-p 00063000 09:05 478
/lib64/libssl.so.1.0.0
7f30dec9d000-7f30dec9e000 rw-p 00000000 00:00 0
7f30dec9e000-7f30deca1000 r-xp 00000000 09:06 1057834
/usr/lib64/python2.7/lib-dynload/_hashlib.so
7f30deca1000-7f30deea0000 ---p 00003000 09:06 1057834
/usr/lib64/python2.7/lib-dynload/_hashlib.so
7f30deea0000-7f30deea1000 r--p 00002000 09:06 1057834
/usr/lib64/python2.7/lib-dynload/_hashlib.so
7f30deea1000-7f30deea2000 rw-p 00003000 09:06 1057834
/usr/lib64/python2.7/lib-dynload/_hashlib.so
7f30deea2000-7f30deeb4000 r-xp 00000000 09:06 1058979
/usr/lib64/python2.7/lib-dynload/cPickle.so
7f30deeb4000-7f30df0b3000 ---p 00012000 09:06 1058979
/usr/lib64/python2.7/lib-dynload/cPickle.so
7f30df0b3000-7f30df0b4000 r--p 00011000 09:06 1058979
/usr/lib64/python2.7/lib-dynload/cPickle.so
7f30df0b4000-7f30df0b5000 rw-p 00012000 09:06 1058979
/usr/lib64/python2.7/lib-dynload/cPickle.so
7f30df0b5000-7f30df0b9000 r-xp 00000000 09:06 1058999
/usr/lib64/python2.7/lib-dynload/cStringIO.so
7f30df0b9000-7f30df2b8000 ---p 00004000 09:06 1058999
/usr/lib64/python2.7/lib-dynload/cStringIO.so
7f30df2b8000-7f30df2b9000 r--p 00003000 09:06 1058999
/usr/lib64/python2.7/lib-dynload/cStringIO.so
7f30df2b9000-7f30df2bb000 rw-p 00004000 09:06 1058999
/usr/lib64/python2.7/lib-dynload/cStringIO.so
7f30df2bb000-7f30df2bf000 r-xp 00000000 09:06 1058998
/usr/lib64/python2.7/lib-dynload/binascii.so
7f30df2bf000-7f30df4bf000 ---p 00004000 09:06 1058998
/usr/lib64/python2.7/lib-dynload/binascii.so
7f30df4bf000-7f30df4c0000 r--p 00004000 09:06 1058998
/usr/lib64/python2.7/lib-dynload/binascii.so
7f30df4c0000-7f30df4c1000 rw-p 00005000 09:06 1058998
/usr/lib64/python2.7/lib-dynload/binascii.so
7f30df4c1000-7f30df4c8000 r-xp 00000000 09:06 1058978
/usr/lib64/python2.7/lib-dynload/_struct.so
7f30df4c8000-7f30df6c7000 ---p 00007000 09:06 1058978
/usr/lib64/python2.7/lib-dynload/_struct.so
7f30df6c7000-7f30df6c8000 r--p 00006000 09:06 1058978
/usr/lib64/python2.7/lib-dynload/_struct.so
7f30df6c8000-7f30df6ca000 rw-p 00007000 09:06 1058978
/usr/lib64/python2.7/lib-dynload/_struct.so
7f30df6ca000-7f30df6cd000 r-xp 00000000 09:06 1052760
/usr/lib64/libXau.so.6.0.0
7f30df6cd000-7f30df8cc000 ---p 00003000 09:06 1052760
/usr/lib64/libXau.so.6.0.0
7f30df8cc000-7f30df8cd000 r--p 00002000 09:06 1052760
/usr/lib64/libXau.so.6.0.0
7f30df8cd000-7f30df8ce000 rw-p 00003000 09:06 1052760
/usr/lib64/libXau.so.6.0.0
7f30df8ce000-7f30df8d7000 r-xp 00000000 09:06 1059458
/usr/lib64/libXrender.so.1.3.0
7f30df8d7000-7f30dfad6000 ---p 00009000 09:06 1059458
/usr/lib64/libXrender.so.1.3.0
7f30dfad6000-7f30dfad7000 r--p 00008000 09:06 1059458
/usr/lib64/libXrender.so.1.3.0
7f30dfad7000-7f30dfad8000 rw-p 00009000 09:06 1059458
/usr/lib64/libXrender.so.1.3.0
7f30dfad8000-7f30dfaf6000 r-xp 00000000 09:06 1062118
/usr/lib64/libxcb.so.1.1.0
7f30dfaf6000-7f30dfcf6000 ---p 0001e000 09:06 1062118
/usr/lib64/libxcb.so.1.1.0
7f30dfcf6000-7f30dfcf7000 r--p 0001e000 09:06 1062118
/usr/lib64/libxcb.so.1.1.0
7f30dfcf7000-7f30dfcf8000 rw-p 0001f000 09:06 1062118
/usr/lib64/libxcb.so.1.1.0
7f30dfcf8000-7f30dfd0d000 r-xp 00000000 09:05 286
/lib64/libz.so.1.2.7
7f30dfd0d000-7f30dff0c000 ---p 00015000 09:05 286
/lib64/libz.so.1.2.7
7f30dff0c000-7f30dff0d000 r--p 00014000 09:05 286
/lib64/libz.so.1.2.7
7f30dff0d000-7f30dff0e000 rw-p 00015000 09:05 286
/lib64/libz.so.1.2.7
7f30dff0e000-7f30dff13000 r-xp 00000000 09:06 1054532
/usr/lib64/libXxf86vm.so.1.0.0
7f30dff13000-7f30e0112000 ---p 00005000 09:06 1054532
/usr/lib64/libXxf86vm.so.1.0.0
7f30e0112000-7f30e0113000 r--p 00004000 09:06 1054532
/usr/lib64/libXxf86vm.so.1.0.0
7f30e0113000-7f30e0114000 rw-p 00005000 09:06 1054532
/usr/lib64/libXxf86vm.so.1.0.0
7f30e0114000-7f30e011d000 r-xp 00000000 09:06 1060694
/usr/lib64/libXrandr.so.2.2.0/usr/bin/pymol: line 2: 22569
Aborted /usr/bin/python
/usr/lib64/python2.7/site-packages/pymol/__init__.py "$@"
Can anybody help me out of this problem? I will highly appreciate.
Thanks,
KK
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