[Solved] PyRosetta segmentation fault in Linux

[Anonymous]

Hi,

PyRosetta is having a segmentation fault when trying to import a PDB file.

Tested with:

PyRosetta-Release1.1-r34960.linux.32Bit

Ubuntu Hardy Heron (8.04) fully patched – 32 bit – Python 2.5.2

Ubuntu Karmic Koala (9.10) fully patched – 32 bit – Python 2.5.4

There was an error message about the libboost-python library, so I installed the adjusted libboost-python lib (rosetta/libboost_python-gcc34-mt-1_38.so.1.38.0) according to Sergey’s message, and that was fine.

But then:

>source SetPyRosettaEnvironment.sh

>python ipython.py

In [1]: from rosetta import *

In [2]: my_pose = Pose()

In [3]: pose_from_pdb( my_pose, “test_in.pdb”)

Segmentation fault

I’ve tested this with various PDB files under both distributions. It always segfaults.

Did you have to install any gcc-3.4 libraries (these don’t come with Ubuntu 9.10 packages anymore) ?

I’m very impatient to start using this great piece of software in my research. Any clues are welcome.

Thanks,

Alex

[Anonymous]

after ‘from rosetta import *’ you have to use ‘init()’ to initialize a number of functions and parameters necessary to run PyRosetta.

[Anonymous]

Hi,

init() did work.

Thanks a lot. You made my day.

Alex

[Author]

Posts