Re: [ESPResSo-users] Errors with importing espressomd

[Michael Kuron]

Dear Le,

it seems like you compiled against Homebrew's Python but pypresso
executed Apple's Python. This happens if you left out the final step of
our Homebrew guide:

    ln -s /usr/local/bin/python2 /usr/local/bin/python

Regards,
Michael

On Do, 2017-10-12 at 18:01 +0200, Konrad Breitsprecher wrote:
> Hi Le, 
> 
> this may be the result of a unclean installation of the
> dependencies. 
> Maybe try a cleanup and reinstall with either homebrew or macports,
> as documented here.
> 
> Regards,
> Konrad
> 
> 2017-10-09 3:02 GMT+02:00 Le Qiao <address@hidden>:
> > Hi, 
> > 
> > I’m new to the espresso and having troubles importing espressomd
> > lib to start the simulation. I installed all the required
> > dependencies and there was no error in the build process. Any one
> > had the same issue before? Help!
> > 
> > Cheers
> > Le
> > 
> > $ ./pypresso 
> > Python 2.7.10 (default, Jul 15 2017, 17:16:57) 
> > [GCC 4.2.1 Compatible Apple LLVM 9.0.0 (clang-900.0.31)] on darwin
> > Type "help", "copyright", "credits" or "license" for more
> > information.
> > >>> import espressomd
> > [mbcx-MacBook-Pro: ] *** Process received signal ***
> > [mbcx-MacBook-Pro: ] Signal: Segmentation fault: 11 (11)
> > [mbcx-MacBook-Pro: ] Signal code: Address not mapped (1)
> > [mbcx-MacBook-Pro: ] Failing at address: 0x8
> > [mbcx-MacBook-Pro: ] [ 0] 0   libsystem_platform.dylib           
> > 0x00007fff7be3af5a _sigtramp + 26
> > [mbcx-MacBook-Pro: ] [ 1] 0   libsystem_c.dylib                  
> > 0x00007fff7bc4d600 _vasprintf + 370
> > [mbcx-MacBook-Pro: ] [ 2] 0   libboost_mpi-mt.dylib              
> > 0x00000001044fa809 _ZN5boost3mpi11environmentC2Eb + 73
> > [mbcx-MacBook-Pro: ] [ 3] 0   libEspressoCore.4.dylib            
> > 0x00000001046d8b37 _Z8mpi_initv + 167
> > [mbcx-MacBook-Pro: ] [ 4] 0   _init.so                           
> > 0x00000001042ab99a init_init + 970
> > [mbcx-MacBook-Pro: ] [ 5] 0   Python                             
> > 0x00007fff5ebe1a79 _PyImport_LoadDynamicModule + 150
> > [mbcx-MacBook-Pro: ] [ 6] 0   Python                             
> > 0x00007fff5ebe0816 PyImport_AppendInittab + 1797
> > [mbcx-MacBook-Pro: ] [ 7] 0   Python                             
> > 0x00007fff5ebe0402 PyImport_AppendInittab + 753
> > [mbcx-MacBook-Pro: ] [ 8] 0   Python                             
> > 0x00007fff5ebdf46a PyImport_ImportModuleLevel + 628
> > [mbcx-MacBook-Pro: ] [ 9] 0   Python                             
> > 0x00007fff5ebc5937 _PyBuiltin_Init + 1282
> > [mbcx-MacBook-Pro: ] [10] 0   Python                             
> > 0x00007fff5eb54581 PyObject_Call + 97
> > [mbcx-MacBook-Pro: ] [11] 0   Python                             
> > 0x00007fff5ebcfbfe PyEval_CallObjectWithKeywords + 159
> > [mbcx-MacBook-Pro: ] [12] 0   Python                             
> > 0x00007fff5ebcdc27 PyEval_EvalFrameEx + 14339
> > [mbcx-MacBook-Pro: ] [13] 0   Python                             
> > 0x00007fff5ebca232 PyEval_EvalCodeEx + 1551
> > [mbcx-MacBook-Pro: ] [14] 0   Python                             
> > 0x00007fff5ebc9c1d PyEval_EvalCode + 32
> > [mbcx-MacBook-Pro: ] [15] 0   Python                             
> > 0x00007fff5ebde012 PyImport_ExecCodeModuleEx + 212
> > [mbcx-MacBook-Pro: ] [16] 0   Python                             
> > 0x00007fff5ebe0d4c PyImport_AppendInittab + 3131
> > [mbcx-MacBook-Pro: ] [17] 0   Python                             
> > 0x00007fff5ebe0fe0 PyImport_AppendInittab + 3791
> > [mbcx-MacBook-Pro: ] [18] 0   Python                             
> > 0x00007fff5ebe0816 PyImport_AppendInittab + 1797
> > [mbcx-MacBook-Pro: ] [19] 0   Python                             
> > 0x00007fff5ebe0402 PyImport_AppendInittab + 753
> > [mbcx-MacBook-Pro: ] [20] 0   Python                             
> > 0x00007fff5ebdf431 PyImport_ImportModuleLevel + 571
> > [mbcx-MacBook-Pro: ] [21] 0   Python                             
> > 0x00007fff5ebc5937 _PyBuiltin_Init + 1282
> > [mbcx-MacBook-Pro: ] [22] 0   Python                             
> > 0x00007fff5eb54581 PyObject_Call + 97
> > [mbcx-MacBook-Pro: ] [23] 0   Python                             
> > 0x00007fff5ebcfbfe PyEval_CallObjectWithKeywords + 159
> > [mbcx-MacBook-Pro: ] [24] 0   Python                             
> > 0x00007fff5ebcdc27 PyEval_EvalFrameEx + 14339
> > [mbcx-MacBook-Pro: ] [25] 0   Python                             
> > 0x00007fff5ebca232 PyEval_EvalCodeEx + 1551
> > [mbcx-MacBook-Pro: ] [26] 0   Python                             
> > 0x00007fff5ebc9c1d PyEval_EvalCode + 32
> > [mbcx-MacBook-Pro: ] [27] 0   Python                             
> > 0x00007fff5ebe8ad1 PyParser_ASTFromFile + 287
> > [mbcx-MacBook-Pro: ] [28] 0   Python                             
> > 0x00007fff5ebe890e PyRun_InteractiveOneFlags + 344
> > [mbcx-MacBook-Pro: ] [29] 0   Python                             
> > 0x00007fff5ebe83b1 PyRun_InteractiveLoopFlags + 87
> > [mbcx-MacBook-Pro: ] *** End of error message ***
> > Segmentation fault: 11
> > 
> > 
> >