Hi Faith, I would suggest to try to install kwant via conda. With: conda install -c conda-forge kwant Best, Bas On 27 Feb 2017, 11:55 +0100, Fatih Dogan , wrote:

Hello,

I have installed the latest version of kwant on a CentOS system that I do not have root access. So I installed it on my home directory. When I run the test file, i get the following seg fault.

python3 -c 'import kwant; kwant.test(verbose=2)' /lib/python3.6/site-packages/kwant-unknown-py3.6-linux-x86_64.egg/kwant/solvers/default.py:18: RuntimeWarning: MUMPS is not available, SciPy built-in solver will be used as a fallback. Performance can be very poor in this case.   "Performance can be very poor in this case.", RuntimeWarning) kwant.graph.tests.test_core.test_empty ... ok kwant.graph.tests.test_core.test_num_nodes ... ok .... kwant.tests.test_lattice.test_neighbors ... ok kwant.tests.test_lattice.test_shape ... ok kwant.tests.test_lattice.test_wire ... ok kwant.tests.test_lattice.test_translational_symmetry ... Segmentation fault

Where I skipped a lot of lines, they were ok for most, skipped when related to MUMPS. I am not that familiar with python or kwant to know what this error means. Can someone help?

Thanks

Fatih

Thank you for the replies. I do not have Anaconda installed. It appears to be a major software (400MB size). System has python 2.6 installed. So I began with installing python 3.6. I installed pip and all dependencies (Scipy etc) on my home folder. For Kwant, the only change I made to the tar.gz is to change build.conf to include lapack library i compiled using gcc. [lapack] libraries = lapack refblas library_dirs = . extra_link_args = -Wl -lgfortran # I hope this helps. Regards, Fatih

Hello, Thank you very much. miniconda worked. I had to manually remove everything from my account and install from scratch, but i got it to work (for testing at least). The only skip I got was: kwant.solvers.tests.test_sparse.test_umfpack_del ... SKIP which i wont bother to check for now. Please expect more questions as i dig into kwant more. Thanks again. Fatih On Mon, Feb 27, 2017 at 4:26 PM, Joseph Weston wrote:

Hi,

...

I do not have Anaconda installed. It appears to be a major software (400MB size).

Indeed Anaconda is a large package. There is, however, a stripped down version called Miniconda [1], which installs just the "conda" tool and a version of Python (rather than the whole scientific Python stack). The Miniconda installer is a more reasonable size (40MB). The advantage of using conda over, say, pip is that there are conda packages for most non-python dependencies required for scientific computing, which means that there are fewer problems when it comes to linking, as conda knows about the whole software stack.

...

[lapack] libraries = lapack refblas library_dirs = . extra_link_args = -Wl -lgfortran

I am almost certain that this is a linking issue, e.g. Kwant is linked against some version of BLAS and LAPACK is linked against another, or something like that. Without being able to exactly reproduce your setup I probably won't be able to say any more than that.

I would strongly suggest using conda; this will probably get you set up the fastest.

Regards,

Joe

[1]: https://conda.io/miniconda.html