Segmentation fault (core dumped) during all tests

[camattelaer]

Hi all

I've been trying to get SSTMap running today, but every possible way of installing resulted in a segfault during exection of the gist.calculate_grid_quantities() command.

I followed even the tip of checking out the all_conda branch, creating env from the .yml and installing again... ([https://github.com//issues/121#issuecomment-1659484166])

output of quick_test:
Testing: amber Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 0.09 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 0.00 seconds Done. Initializing ... Total time running __init__: 1.12 seconds System information: Parameter file: /home/camattelaer/Downloads/sstmap_test_suite/platforms/amber/testcase.prmtop Trajectory: /home/camattelaer/Downloads/sstmap_test_suite/platforms/amber/md100ps.nc Frames: 100, Total Atoms: 3026, Waters: 1001, Solute Atoms: 23 Grid information: GIST grid center: 18.030 17.173 17.058 GIST grid dimensions: 48 48 48 GIST grid spacing: 0.500 A^3 Segmentation fault (core dumped)0.0% Done.

output of test_water_models:
Testing: tip3p Initializing ... Obtaining non-bonded parameters for the system ... Total time running generate_nonbonded_params: 0.33 seconds Done. Assigning hydrogen bond types ... Total time running assign_hb_types: 0.01 seconds Done. Initializing ... Total time running __init__: 0.55 seconds System information: Parameter file: /home/camattelaer/Downloads/sstmap_test_suite/water_models/tip3p/tip3p.prmtop Trajectory: /home/camattelaer/Downloads/sstmap_test_suite/water_models/tip3p/md100ps.nc Frames: 100, Total Atoms: 7743, Waters: 2581, Solute Atoms: 0 Grid information: GIST grid center: 22.506 22.156 21.516 GIST grid dimensions: 20 20 20 GIST grid spacing: 0.500 A^3 Segmentation fault (core dumped)0.0% Done.

Any help on resolving this issue would greatly be appreciated.

Kind regards

Charles-Alexandre

[camattelaer]

ok, so i apparently had an old alias python=python3 in my .bashrc which was throwing every conda env off.

My apologies, everything seems to be running fine.

Getting some Arrays are not almost equal to 3 decimals output but most of the tests report PASSED.