Missing netCDF file extension in symbolic links

[Gabriel Antonius]

Dear devs,
I'm trying to run the example flow run_mgb2_phonons_nkpt_tsmear.py. However, the second work fails, because the symbolic links for the wavefunctions do not have the proper netCDF file extension. The work w0 completes without problems, but the task w1/t0 fails with the error message:

--- !ERROR
src_file: m_nctk.F90
src_line: 896
mpi_rank: 0
message: |
    nf90_open_par: /home/antonius/Projects/AbipyTests/Production/130-phonons/flow_mgb2_phonons_nkpt_tsmear/w1/t0/indata/in_WFK.nc - NetCDF library returned:  NetCDF:   Error initializing for parallel access

Indeed, the symbolic link created in flow_mgb2_phonons_nkpt_tsmear/w1/t0/indata/ is called in_WFK but points to the file flow_mgb2_phonons_nkpt_tsmear/w0/t0/outdata/out_WFK.nc. Thus, it is missing the .nc extension and abinit complains about it.

Is there a quick way to fix this?

[Matteo Giantomassi]

Hi,

To fix the problem, change the make_links method of the DfptTask class defined
in pymatgen.io.abinit.tasks to ensure that the link has the .nc extension
when the target is a netcdf file.

For the diff, see 9a69878

PS: In the next AbiPy relase, I will move all the workflow machinery from pymatgen.io.abinit to abipy.flowtk. This is the reason why I've fixed the bug in a specialized AbiPy branch. This bug fix won't be backported to pymatgen.

[Gabriel Antonius]

Thanks, Matteo! I installed the workflow_refactoring branch on my cluster and now the symbolic links are correct.
I should mention that the system administrators on this cluster installed a version of Abinit where iomode=3 is the default behavior, so I suppose it is important to specify this variable explicitly.