Graceful Error Handling in Particle Patches

[ax3l]

Describe the bug We recently introduced more graceful error handling when we encounter incomplete data. I found another data set, which we use in openPMD-updater, that only contains structure but no real data in it.

In this data set, particlePatches cause read errors in openPMD-ls.

To Reproduce Download the file structure.h5 from https://github.com/openPMD/openPMD-example-datasets/pull/22 / https://github.com/openPMD/openPMD-example-datasets/blob/draft/structure.h5

$ openpmd-ls structure.h5 
openPMD series: structure
openPMD standard: 1.1.0
openPMD extensions: 1

data author: Axel Huebl <a.huebl@hzdr.de>
data created: 2018-02-20 12:42:57 +0100
data backend: HDF5
generating machine: ax3l
generating software: openPMD Example Script (version: 1.1.0.1)
generating software dependencies: python@2.7.13;numpy@1.13.3;hdf5@1.8.18;h5py@2.7.1

number of iterations: 1 (groupBased)
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 0:
  #000: H5A.c line 454 in H5Aopen(): unable to open attribute: 'unitDimension'
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 124 in H5VL__native_attr_open(): unable to open attribute: 'unitDimension'
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 422 in H5A__open(): unable to load attribute info from object header for attribute: 'unitDimension'
    major: Attribute
    minor: Can't open object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: 'unitDimension'
    major: Attribute
    minor: Object not found
  all iterations: [AbstractIOHandlerImpl] IO Task READ_ATT failed with exception. Clearing IO queue and passing on the exception.
Cannot read patch record 'extent' due to read error and will skip it:Read Error in backend HDF5
Object type:    Attribute
Error type: NotFound
Further description:    [HDF5] Internal error: Failed to open HDF5 attribute 'unitDimension' (/data/0/particles/electrons/particlePatches/extent/) during attribute read
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 0:
  #000: H5A.c line 454 in H5Aopen(): unable to open attribute: 'unitDimension'
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 124 in H5VL__native_attr_open(): unable to open attribute: 'unitDimension'
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 422 in H5A__open(): unable to load attribute info from object header for attribute: 'unitDimension'
    major: Attribute
    minor: Can't open object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: 'unitDimension'
    major: Attribute
    minor: Object not found
[AbstractIOHandlerImpl] IO Task READ_ATT failed with exception. Clearing IO queue and passing on the exception.
Cannot read patch record 'offset' due to read error and will skip it:Read Error in backend HDF5
Object type:    Attribute
Error type: NotFound
Further description:    [HDF5] Internal error: Failed to open HDF5 attribute 'unitDimension' (/data/0/particles/electrons/particlePatches/offset/) during attribute read
0 

number of meshes: 3
  all meshes:
    B
    E
    rho

number of particle species: 1
  all particle species:
    electrons

Expected behavior Should as it does for the other missing data gracefully skip

Software Environment

• version of openPMD-api: 0.15.2
• installed openPMD-api via: conda-forge
• operating system: Ubuntu 22.04
• machine: no
• name and version of Python implementation: 3.11.6
• version of HDF5: 1.14.2
• version of ADIOS2: N/A
• name and version of MPI: N/A

Additional context @s-sajid-ali and me are working on 2.0 updates for https://github.com/openPMD/openPMD-updater and moved the little example file in it to https://github.com/openPMD/openPMD-example-datasets via https://github.com/openPMD/openPMD-example-datasets/pull/22

[ax3l]

X-ref: #1439 pt. 3

[ax3l]

The problem is actually that particle patches are not openPMD records https://github.com/openPMD/openPMD-standard/blob/latest/STANDARD.md#sub-group-for-each-particle-species Update: they are records, in a sub-group.

But the API seems to currently parse it as such, looking for unitDimension on extent, offset, etc.

[ax3l]

Fix coming for particle patches example from openPMD-validator via https://github.com/openPMD/openPMD-validator/pull/75 and https://github.com/openPMD/openPMD-example-datasets/pull/23