Newer numpy (f2py?) produces strange errors

[jmlorenzi]

Expected behavior

kmos models should be able to run after being compiled with any of the three backends. In addition running kmos bench should return output similar to

Using the [lat_int] backend.
1000000 steps took 1.23 seconds
Or 8.12e+05 steps/s

Actual behavior

When using numpy 1.13.3, models compile with no apparent errors, however when trying to run a model compiled with otf I get a Segmentation Fault. In addition, when running kmos bench on a model compiled with lat_int, the output looks like

Using the [???] backend.
1000000 steps took 1.24 seconds
Or 8.08e+05 steps/s

Notice the question marks instead of the backend name. This does not happen with the local_smart backend.

Steps to reproduce the issue

1. Update numpy to ver 1.13.3
2. Pick your favorite otf-enabled model, recompile it with kmos export -b otf
3. Run kmos bench on the model folder

2a. Pick your favorite "default backend" kmos model, compile it with kmos export -b lat_int
3b. Run kmos bench on the model folder

System information

kmos version: 0.3.21
Linux Debian Jessie

Downgrading to numpy 1.8.2 solves the issue. Before I investigate this, it would be nice is somebody could try to reproduce this issue, to make sure is not something wrong with my installation.

[mseibt]

I was able to reproduce this issue. However both run and bench produce a SegFault for me.

I used numpy 1.11.0 which works fine and numpy 1.13.3 which does not.

[jmlorenzi]

Hi Michael,

Thanks a lot for reproducing this. Yes, the SegFault seems to occur as soon as you try to import kmos.run. I will try to take a look into this next week.

[wulx]

Hi Juan,
SegFault happends when gfortran-7 is used, and it disappears after I update alternatives to gfortran-6.
My OS is the latest Ubuntu 17.10. After hundreds of tries, I found that sudo apt install python-ase works for me while pip install ... makes tons of trouble.

The details are displayed as follows.

mc@mc-server:~/AlOnSi/AlOnSi_otf$ ase info
platform        Linux-4.13.0-16-generic-x86_64-with-Ubuntu-17.10-artful
python-3.6.3    /usr/bin/python3
ase-3.14.1      /usr/lib/python3/dist-packages/ase/
numpy-1.12.1    /usr/lib/python3/dist-packages/numpy/
scipy-0.18.1    /usr/lib/python3/dist-packages/scipy/
mc@mc-server:~/AlOnSi/AlOnSi_otf$ kmos --version
0.3.21
mc@mc-server:~/AlOnSi/AlOnSi_otf$ gfortran --version
GNU Fortran (Ubuntu 6.4.0-8ubuntu1) 6.4.0 20171010
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.