Re: [FEniCS-support] PETSc Pylab

Garth N. Wells Thu, 15 Jan 2015 05:00:04 -0800

On Thu, 15 Jan, 2015 at 12:47 PM, Jan Blechta<[email protected]> wrote:

Problem seems to be in libQt. Would it help switching the importorder?


import pylab
import dolfin

Or there's conflicting Qt lib, check that DOLFIN and pylab link to the
same:

 $ ldd /path/to/fenics/lib/libdolfin.so | grep -i qt
 $ # check pylab, don't know how

Or you could recompile dolfin without Qt (it's practically useless
dependecy, see plot-qt demo)

Jan: maybe you could propose on the mailing list to remove QT as anoptional dependency?


Garth

by configuring with
-DDOLFIN_ENABLE_QT:BOOL=OFF

Jan


On Thu, 15 Jan 2015 12:59:14 +0100
Steffen Wittek <[email protected]> wrote:

 the stacktrace:

 gdb -ex r -ex bt -args python -c "from dolfin import *; import pylab
 as py" [...]
 Reading symbols from python...(no debugging symbols found)...done.
 Starting program: /usr/bin/python -c from\ dolfin\ import\ \*\;\
 import\ pylab\ as\ py
 warning: Could not load shared library symbols for linux-vdso.so.1.
 Do you need "set solib-search-path" or "set sysroot"?
 [Thread debugging using libthread_db enabled]
 Using host libthread_db library "/usr/lib/libthread_db.so.1".
 [New Thread 0x7fffb46df700 (LWP 732)]

 Program received signal SIGSEGV, Segmentation fault.
 0x00007ffff74df73a in __strcmp_sse2_unaligned ()
 from /usr/lib/libc.so.6 #0  0x00007ffff74df73a in
 __strcmp_sse2_unaligned () from /usr/lib/libc.so.6 #1
 0x00007fffa9ce009f in QMetaType::registerNormalizedType(QByteArray
 const&, void (*)(void*), void* (*)(void const*), void (*)(void*),
 void* (*)(void*, void const*), int, QFlags<QMetaType::TypeFlag>,

QMetaObject const*) () ---Type <return> to continue, or q <return>to

 quit--- from /usr/lib/libQt5Core.so.5
 #2  0x00007fffaa0e91e1 in ?? ()
     from /usr/lib/python2.7/site-packages/PyQt5/QtCore.so
 #3  0x00007fffaa0e9280 in ?? ()
     from /usr/lib/python2.7/site-packages/PyQt5/QtCore.so
 #4  0x00007fffaa0e8de1 in ?? ()
     from /usr/lib/python2.7/site-packages/PyQt5/QtCore.so
 #5  0x00007ffff7b03917 in _PyImport_LoadDynamicModule ()
     from /usr/lib/libpython2.7.so.1.0
 #6  0x00007ffff7b019b1 in import_submodule () from
 /usr/lib/libpython2.7.so.1.0
 #7  0x00007ffff7b01ed6 in ensure_fromlist () from
 /usr/lib/libpython2.7.so.1.0
 #8  0x00007ffff7b02725 in PyImport_ImportModuleLevel ()
     from /usr/lib/libpython2.7.so.1.0
 #9  0x00007ffff7ae7ea8 in builtin___import__ ()
     from /usr/lib/libpython2.7.so.1.0
 #10 0x00007ffff7a588c3 in PyObject_Call ()
 from /usr/lib/libpython2.7.so.1.0 #11 0x00007ffff7ae9bb7 in
 PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.7.so.1.0
 #12 0x00007ffff7aecd78 in PyEval_EvalFrameEx ()
     from /usr/lib/libpython2.7.so.1.0
 #13 0x00007ffff7af0af0 in PyEval_EvalCodeEx ()
     from /usr/lib/libpython2.7.so.1.0
 #14 0x00007ffff7af0be9 in PyEval_EvalCode () from
 /usr/lib/libpython2.7.so.1.0
 ---Type <return> to continue, or q <return> to quit---
 #15 0x00007ffff7b00ac9 in PyImport_ExecCodeModuleEx ()
     from /usr/lib/libpython2.7.so.1.0
 #16 0x00007ffff7b00d43 in load_source_module ()
     from /usr/lib/libpython2.7.so.1.0
 #17 0x00007ffff7b019b1 in import_submodule () from
 /usr/lib/libpython2.7.so.1.0
 #18 0x00007ffff7b01c2f in load_next ()
 from /usr/lib/libpython2.7.so.1.0 #19 0x00007ffff7b02648 in
 PyImport_ImportModuleLevel () from /usr/lib/libpython2.7.so.1.0
 #20 0x00007ffff7ae7ea8 in builtin___import__ ()
     from /usr/lib/libpython2.7.so.1.0
 #21 0x00007ffff7a588c3 in PyObject_Call ()
 from /usr/lib/libpython2.7.so.1.0 #22 0x00007ffff7ae9bb7 in
 PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.7.so.1.0
 #23 0x00007ffff7aecd78 in PyEval_EvalFrameEx ()
     from /usr/lib/libpython2.7.so.1.0
 #24 0x00007ffff7af0af0 in PyEval_EvalCodeEx ()
     from /usr/lib/libpython2.7.so.1.0
 #25 0x00007ffff7af0be9 in PyEval_EvalCode () from
 /usr/lib/libpython2.7.so.1.0
 #26 0x00007ffff7b00ac9 in PyImport_ExecCodeModuleEx ()
     from /usr/lib/libpython2.7.so.1.0
 #27 0x00007ffff7b00d43 in load_source_module ()
     from /usr/lib/libpython2.7.so.1.0
 #28 0x00007ffff7b019b1 in import_submodule () from
 /usr/lib/libpython2.7.so.1.0
 ---Type <return> to continue, or q <return> to quit---
 #29 0x00007ffff7b01c2f in load_next ()
 from /usr/lib/libpython2.7.so.1.0 #30 0x00007ffff7b02648 in
 PyImport_ImportModuleLevel () from /usr/lib/libpython2.7.so.1.0
 #31 0x00007ffff7ae7ea8 in builtin___import__ ()
     from /usr/lib/libpython2.7.so.1.0
 #32 0x00007ffff7a588c3 in PyObject_Call ()
 from /usr/lib/libpython2.7.so.1.0 #33 0x00007ffff7ae9bb7 in
 PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.7.so.1.0
 #34 0x00007ffff7aecd78 in PyEval_EvalFrameEx ()
     from /usr/lib/libpython2.7.so.1.0
 #35 0x00007ffff7af0af0 in PyEval_EvalCodeEx ()
     from /usr/lib/libpython2.7.so.1.0
 #36 0x00007ffff7af0be9 in PyEval_EvalCode () from
 /usr/lib/libpython2.7.so.1.0
 #37 0x00007ffff7b00ac9 in PyImport_ExecCodeModuleEx ()
     from /usr/lib/libpython2.7.so.1.0
 #38 0x00007ffff7b00d43 in load_source_module ()
     from /usr/lib/libpython2.7.so.1.0
 #39 0x00007ffff7b019b1 in import_submodule () from
 /usr/lib/libpython2.7.so.1.0
 #40 0x00007ffff7b01c2f in load_next ()
 from /usr/lib/libpython2.7.so.1.0 #41 0x00007ffff7b02648 in
 PyImport_ImportModuleLevel () from /usr/lib/libpython2.7.so.1.0
 #42 0x00007ffff7ae7ea8 in builtin___import__ ()
     from /usr/lib/libpython2.7.so.1.0
 ---Type <return> to continue, or q <return> to quit---
 #43 0x00007ffff7a588c3 in PyObject_Call ()
 from /usr/lib/libpython2.7.so.1.0 #44 0x00007ffff7ae9bb7 in
 PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.7.so.1.0
 #45 0x00007ffff7aecd78 in PyEval_EvalFrameEx ()
     from /usr/lib/libpython2.7.so.1.0
 #46 0x00007ffff7af0af0 in PyEval_EvalCodeEx ()
     from /usr/lib/libpython2.7.so.1.0
 #47 0x00007ffff7af0be9 in PyEval_EvalCode () from
 /usr/lib/libpython2.7.so.1.0
 #48 0x00007ffff7b00ac9 in PyImport_ExecCodeModuleEx ()
     from /usr/lib/libpython2.7.so.1.0
 #49 0x00007ffff7b00d43 in load_source_module ()
     from /usr/lib/libpython2.7.so.1.0
 #50 0x00007ffff7b019b1 in import_submodule () from
 /usr/lib/libpython2.7.so.1.0
 #51 0x00007ffff7b01c2f in load_next ()
 from /usr/lib/libpython2.7.so.1.0 #52 0x00007ffff7b0260e in
 PyImport_ImportModuleLevel () from /usr/lib/libpython2.7.so.1.0
 #53 0x00007ffff7ae7ea8 in builtin___import__ ()
     from /usr/lib/libpython2.7.so.1.0
 #54 0x00007ffff7a588c3 in PyObject_Call ()
 from /usr/lib/libpython2.7.so.1.0 #55 0x00007ffff7ae9bb7 in
 PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.7.so.1.0
 #56 0x00007ffff7aecd78 in PyEval_EvalFrameEx ()
     from /usr/lib/libpython2.7.so.1.0
 ---Type <return> to continue, or q <return> to quit---
 #57 0x00007ffff7af0af0 in PyEval_EvalCodeEx ()
     from /usr/lib/libpython2.7.so.1.0
 #58 0x00007ffff7af0be9 in PyEval_EvalCode () from
 /usr/lib/libpython2.7.so.1.0
 #59 0x00007ffff7b00ac9 in PyImport_ExecCodeModuleEx ()
     from /usr/lib/libpython2.7.so.1.0
 #60 0x00007ffff7b00d43 in load_source_module ()
     from /usr/lib/libpython2.7.so.1.0
 #61 0x00007ffff7b019b1 in import_submodule () from
 /usr/lib/libpython2.7.so.1.0
 #62 0x00007ffff7b01c2f in load_next ()
 from /usr/lib/libpython2.7.so.1.0 #63 0x00007ffff7b02648 in
 PyImport_ImportModuleLevel () from /usr/lib/libpython2.7.so.1.0
 #64 0x00007ffff7ae7ea8 in builtin___import__ ()
     from /usr/lib/libpython2.7.so.1.0
 #65 0x00007ffff7aef7c4 in PyEval_EvalFrameEx ()
     from /usr/lib/libpython2.7.so.1.0
 #66 0x00007ffff7af0af0 in PyEval_EvalCodeEx ()
     from /usr/lib/libpython2.7.so.1.0
 #67 0x00007ffff7aeefe4 in PyEval_EvalFrameEx ()
     from /usr/lib/libpython2.7.so.1.0
 #68 0x00007ffff7af0af0 in PyEval_EvalCodeEx ()
     from /usr/lib/libpython2.7.so.1.0
 #69 0x00007ffff7af0be9 in PyEval_EvalCode () from
 /usr/lib/libpython2.7.so.1.0
 #70 0x00007ffff7b00ac9 in PyImport_ExecCodeModuleEx ()
 ---Type <return> to continue, or q <return> to quit---
     from /usr/lib/libpython2.7.so.1.0
 #71 0x00007ffff7b00d43 in load_source_module ()
     from /usr/lib/libpython2.7.so.1.0
 #72 0x00007ffff7b019b1 in import_submodule () from
 /usr/lib/libpython2.7.so.1.0
 #73 0x00007ffff7b01c2f in load_next ()
 from /usr/lib/libpython2.7.so.1.0 #74 0x00007ffff7b02648 in
 PyImport_ImportModuleLevel () from /usr/lib/libpython2.7.so.1.0
 #75 0x00007ffff7ae7ea8 in builtin___import__ ()
     from /usr/lib/libpython2.7.so.1.0
 #76 0x00007ffff7a588c3 in PyObject_Call ()
 from /usr/lib/libpython2.7.so.1.0 #77 0x00007ffff7ae9bb7 in
 PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.7.so.1.0
 #78 0x00007ffff7aecd78 in PyEval_EvalFrameEx ()
     from /usr/lib/libpython2.7.so.1.0
 #79 0x00007ffff7af0af0 in PyEval_EvalCodeEx ()
     from /usr/lib/libpython2.7.so.1.0
 #80 0x00007ffff7af0be9 in PyEval_EvalCode () from
 /usr/lib/libpython2.7.so.1.0
 #81 0x00007ffff7b00ac9 in PyImport_ExecCodeModuleEx ()
     from /usr/lib/libpython2.7.so.1.0
 #82 0x00007ffff7b00d43 in load_source_module ()
     from /usr/lib/libpython2.7.so.1.0
 #83 0x00007ffff7b019b1 in import_submodule () from
 /usr/lib/libpython2.7.so.1.0
 #84 0x00007ffff7b01c2f in load_next ()
 from /usr/lib/libpython2.7.so.1.0 ---Type <return> to continue, or q
 <return> to quit--- #85 0x00007ffff7b02648 in
 PyImport_ImportModuleLevel () from /usr/lib/libpython2.7.so.1.0
 #86 0x00007ffff7ae7ea8 in builtin___import__ ()
     from /usr/lib/libpython2.7.so.1.0
 #87 0x00007ffff7a588c3 in PyObject_Call ()
 from /usr/lib/libpython2.7.so.1.0 #88 0x00007ffff7ae9bb7 in
 PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.7.so.1.0
 #89 0x00007ffff7aecd78 in PyEval_EvalFrameEx ()
     from /usr/lib/libpython2.7.so.1.0
 #90 0x00007ffff7af0af0 in PyEval_EvalCodeEx ()
     from /usr/lib/libpython2.7.so.1.0
 #91 0x00007ffff7af0be9 in PyEval_EvalCode () from
 /usr/lib/libpython2.7.so.1.0
 #92 0x00007ffff7b00ac9 in PyImport_ExecCodeModuleEx ()
     from /usr/lib/libpython2.7.so.1.0
 #93 0x00007ffff7b00d43 in load_source_module ()
     from /usr/lib/libpython2.7.so.1.0
 #94 0x00007ffff7b019b1 in import_submodule () from
 /usr/lib/libpython2.7.so.1.0
 #95 0x00007ffff7b01c2f in load_next ()
 from /usr/lib/libpython2.7.so.1.0 #96 0x00007ffff7b0260e in
 PyImport_ImportModuleLevel () from /usr/lib/libpython2.7.so.1.0
 #97 0x00007ffff7ae7ea8 in builtin___import__ ()
     from /usr/lib/libpython2.7.so.1.0
 #98 0x00007ffff7a588c3 in PyObject_Call ()
 from /usr/lib/libpython2.7.so.1.0 ---Type <return> to continue, or q
 <return> to quit--- #99 0x00007ffff7ae9bb7 in
 PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.7.so.1.0
 #100 0x00007ffff7aecd78 in PyEval_EvalFrameEx ()
     from /usr/lib/libpython2.7.so.1.0
 #101 0x00007ffff7af0af0 in PyEval_EvalCodeEx ()
     from /usr/lib/libpython2.7.so.1.0
 #102 0x00007ffff7af0be9 in PyEval_EvalCode () from
 /usr/lib/libpython2.7.so.1.0
 #103 0x00007ffff7b0a10f in run_mod ()
 from /usr/lib/libpython2.7.so.1.0 #104 0x00007ffff7b0afd4 in
 PyRun_StringFlags () from /usr/lib/libpython2.7.so.1.0
 #105 0x00007ffff7b0c8eb in PyRun_SimpleStringFlags ()
     from /usr/lib/libpython2.7.so.1.0
 #106 0x00007ffff7b1d528 in Py_Main ()
 from /usr/lib/libpython2.7.so.1.0 #107 0x00007ffff746f040 in
 __libc_start_main () from /usr/lib/libc.so.6 #108 0x000000000040073e
 in _start ()

 Steffen
 On 01/15/15 09:30, Jan Blechta wrote:
 > On Wed, 14 Jan 2015 16:40:36 +0100
 > [email protected] wrote:
 >
 >> Hi,
 >>
 >> tried to solve this problem that had ocurred to me before. When
 >> loading dolfin and pylab at the same time I get a segmentation
 >> fault. A run in gdb gives this:
 >>

>> gdb -ex r -args python -c"from dolfin import *; import pylab aspy"

 >
 > Please, enclose also stacktrace
 >

> gdb -ex r -ex bt -args python -c"from dolfin import *; importpylab

 > as py"
 >
 > Jan
 >
 >> [...]

>> Reading symbols from python...(no debugging symbolsfound)...done.

 >> Starting program: /usr/bin/python -cfrom\ dolfin\ import\ \*\;\
 >> import\ pylab\ as\ py

>> warning: Could not load shared library symbols forlinux-vdso.so.1.

 >> Do you need "set solib-search-path" or "set sysroot"?
 >> [Thread debugging using libthread_db enabled]
 >> Using host libthread_db library "/usr/lib/libthread_db.so.1".
 >> [New Thread 0x7fffb46df700 (LWP 2418)]
 >>
 >> Program received signal SIGSEGV, Segmentation fault.
 >> 0x00007ffff74df9b2 in __strcmp_sse2_unaligned ()
 >> from /usr/lib/libc.so.6
 >>
 >> My dolfin is self-compiled (version 1.4.0+), python is of version
 >> 2.7 and the matplotlib is 1.4.2.
 >>
 >> Do you have any idea what could cause this problem?
 >> Thank you already in advance,
 >> Steffen
 >>
 >>
 >> _______________________________________________
 >> fenics-support mailing list
 >> [email protected]
 >> http://fenicsproject.org/mailman/listinfo/fenics-support
 >
 _______________________________________________
 fenics-support mailing list
 [email protected]
 http://fenicsproject.org/mailman/listinfo/fenics-support


_______________________________________________
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_______________________________________________
fenics-support mailing list
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Re: [FEniCS-support] PETSc Pylab

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