ImportError: no module named graph_tool.all

Rampo · December 11, 2013, 12:46am

Hello,

I am new to graph-tool. So, I installed it on Mac OS X using the command
sudo port install py-graph-tool. Installation was complete and I went on to
run my python code.

This is what I got:

Traceback (most recent call last):
File "SIR.py", line 1, in <module>
from graph_tool.all import *
ImportError: No module named graph_tool.all

The piece of code that created this so called error:

from graph_tool.all import *
from random import *
import smallworld

I figured that after installing py-graph-tool, it should work. What I
already tried is adding this line to .profile:

export PYTHONPATH=/usr/local/lib/python2.7/site-packages/

However, no success.
Please, help me out here.

Regards

Rampo · December 11, 2013, 12:49am

I tried installing py-graph-tool again. This is what I after running, sudo
port install py-graph-tool, again:

---> Computing dependencies for py-graph-tool
---> Cleaning py-graph-tool
---> Scanning binaries for linking errors: 100.0%
---> No broken files found.

tiago · December 11, 2013, 8:18am

It seems that you are not invoking the version of python which belongs
to macports, but rather the system's version, which does not know
anything about the modules installed by macports.

Make sure to call the correct python interpreter, which probably is
something like: /usr/local/bin/python2.7

Cheers,
Tiago

Rampo · December 11, 2013, 9:02am

So, I figured in order to call the Macports python version you have to use:

/opt/local/bin/python2.7

However I get this error now using /opt/local/bin/python2.7 SIR.py:

Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6

Rampo · December 11, 2013, 9:21am

Some additional info from the report:

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000

Application Specific Information:
abort() called

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff8f5fc866 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff8c16035c pthread_kill + 92
2 libsystem_c.dylib 0x00007fff8c4f9bba abort + 125
3 org.python.python 0x0000000114247ec1 Py_FatalError + 49
4 org.python.python 0x0000000114247411 PyThreadState_Get + 28
5 org.python.python 0x0000000114244476 Py_InitModule4_64 + 58
6 libboost_python.dylib 0x0000000113fb1ef8
boost::python::detail::init_module(char const*, void (*)()) + 40
7 org.python.python 0x000000010d5add86
_PyImport_LoadDynamicModule + 150
8 org.python.python 0x000000010d5ada87 import_submodule + 279
9 org.python.python 0x000000010d5ad854 ensure_fromlist + 532
10 org.python.python 0x000000010d5ab573
PyImport_ImportModuleLevel + 1347
11 org.python.python 0x000000010d58b304 builtin___import__ +
132
12 org.python.python 0x000000010d4ff665 PyObject_Call + 101
13 org.python.python 0x000000010d593763 PyEval_EvalFrameEx +
13683
14 org.python.python 0x000000010d590076 PyEval_EvalCodeEx +
1734
15 org.python.python 0x000000010d58f9a6 PyEval_EvalCode + 54
16 org.python.python 0x000000010d5b775d PyRun_StringFlags +
125
17 org.python.python 0x000000010d594985 PyEval_EvalFrameEx +
18325
18 org.python.python 0x000000010d590076 PyEval_EvalCodeEx +
1734
19 org.python.python 0x000000010d596f36 fast_function + 294
20 org.python.python 0x000000010d59328b PyEval_EvalFrameEx +
12443
21 org.python.python 0x000000010d590076 PyEval_EvalCodeEx +
1734
22 org.python.python 0x000000010d58f9a6 PyEval_EvalCode + 54
23 org.python.python 0x000000010d5a9f57
PyImport_ExecCodeModuleEx + 247
24 org.python.python 0x000000010d5ace77 load_source_module +
935
25 org.python.python 0x000000010d5ad16a load_package + 298
26 org.python.python 0x000000010d5ada87 import_submodule + 279
27 org.python.python 0x000000010d5ad51f load_next + 271
28 org.python.python 0x000000010d5ab4b1
PyImport_ImportModuleLevel + 1153
29 org.python.python 0x000000010d58b304 builtin___import__ +
132
30 org.python.python 0x000000010d4ff665 PyObject_Call + 101
31 org.python.python 0x000000010d593763 PyEval_EvalFrameEx +
13683
32 org.python.python 0x000000010d590076 PyEval_EvalCodeEx +
1734
33 org.python.python 0x000000010d58f9a6 PyEval_EvalCode + 54
34 org.python.python 0x000000010d5b7611 PyRun_FileExFlags +
161
35 org.python.python 0x000000010d5b715e
PyRun_SimpleFileExFlags + 718
36 org.python.python 0x000000010d5cb002 Py_Main + 3314
37 libdyld.dylib 0x00007fff967335fd start + 1

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000 rbx: 0x00007fff79527310 rcx: 0x00007fff52711708
rdx: 0x0000000000000000
  rdi: 0x0000000000000d07 rsi: 0x0000000000000006 rbp: 0x00007fff52711730
rsp: 0x00007fff52711708
   r8: 0x0000000000000040 r9: 0x00007fff52711700 r10: 0x0000000008000000
r11: 0x0000000000000206
  r12: 0x0000000000000000 r13: 0x000000010f44ba60 r14: 0x0000000000000006
r15: 0x00000000000003f5
  rip: 0x00007fff8f5fc866 rfl: 0x0000000000000206 cr2: 0x0000000114280d5c

Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133

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External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by all processes on this machine:
    task_for_pid: 330445
    thread_create: 2
    thread_set_state: 0

tiago · December 11, 2013, 10:26am

This looks like a library linking incompatibility issue. Please submit a
bug report to the macports project at:

http://trac.macports.org/wiki/Tickets

They should be able to help you with this.

Cheers,
Tiago