Runtime error trying open SMILEI HDF5

[kevinCassou]

Dear openPMD developers,

We are trying to shift to openPMD-viewer for post-processing of SMILEI PIC code data output.
Following the doc we tried

series = io.Series(path,io.Access.read_only)

and we got :

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-53-76e6870bcf32> in <module>
----> 1 series = io.Series(path,io.Access.read_only)

RuntimeError: [setAttribute] Value for string attribute 'name' must not be empty!

It looks from the openPMD standard technical files that it should not be a problem. Main differences (from documentation based on WARP ) that SMILEI PIC code generates one HDF5 for fields and one for tracked particles with all the timesteps inside;

Then looking to the HDF5 structure of PIC data SMILEI : TrackParticles_species.h5 and Fields0.h5. The structure seems to respect openPMD standard.

• For particles data/timestep/particles/species/.... . In the metadata we have the name=attribute is empty :

/ (96)
    Group size = 1
    Number of attributes = 11
        basePath = /data/%T/
        date = 2022-02-12 20:32:23 +�
        iterationEncoding = groupBased
        iterationFormat = /data/%T/
        meshesPath = no_meshes
        name = 
        openPMD = 1.0.0
        openPMDextension = 0
        particlesPath = particles/
        software = Smilei
        softwareVersion = ??-??

• For the fields it looks less similar as there is not sub repertory fields but again data/timestep/El_mode_0 ...* . In the metadata we have also name=attribute empty :

/ (96)
    Group size = 2
    Number of attributes = 11
        basePath = /data/%T/
        date = 2022-02-12 20:32:23 +�
        iterationEncoding = groupBased
        iterationFormat = /data/%T/
        meshesPath = 
        name = 
        openPMD = 1.0.0
        openPMDextension = 0
        particlesPath = no_particles
        software = Smilei
        softwareVersion = ??-??

Some minor adjustement might be required on SMILEI could you guide us on it ? or is that a bug with empty attributes on openpmd-api ?

Software Environment:

• version of openPMD-api: openpmd-api 0.14.4 nompi_py37hf1a3fc2_101 conda-forge
• installed openPMD-api via: [conda-forge]

[franzpoeschel]

Hello,
this issue is known and has been recently fixed. If you want to try the dev branch, then I expect things should work.

Background: We don't support writing empty strings due to corner cases in HDF5. Checking for empty strings accidentally leaked into reading due to shared code.

[ax3l]

Fixed in the 0.14.5 release.
Thank you for the detailed report and please let us know if you encounter any other errors in the future @kevinCassou 👍