Accelerator Modeling » Synergia2

reproduce by:

build the libffgsvopenmp-ql branch
go to examples/fodo
synergia fodo.py
syndiagplot diagnostics.h5 x_std

Results in:

HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 0:
  #000: H5D.c line 334 in H5Dopen2(): not found
    major: Dataset
    minor: Object not found
  #001: H5Gloc.c line 430 in H5G_loc_find(): can't find object
    major: Symbol table
    minor: Object not found
  #002: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
    major: Symbol table
    minor: Object not found
  #003: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed
    major: Symbol table
    minor: Callback failed
  #004: H5Gloc.c line 385 in H5G_loc_find_cb(): object 'std_storage_order' doesn't exist
    major: Symbol table
    minor: Object not found
Traceback (most recent call last):
  File "/home/egstern/syn2-libfftest/install/lib/synergia_tools/diag_plot.py", line 203, in <module>
    do_plots(options, plotparams)
  File "/home/egstern/syn2-libfftest/install/lib/synergia_tools/diag_plot.py", line 194, in do_plots
    do_plot(inputfile, options, plotparams, multiple_files)
  File "/home/egstern/syn2-libfftest/install/lib/synergia_tools/diag_plot.py", line 162, in do_plot
    ymaster = hdf5_read_any(f, params.y_attr)
  File "/home/egstern/syn2-libfftest/install/lib/synergia_tools/diag_plot.py", line 145, in hdf5_read_any
    return hdf5_file.read_array2d(member)
RuntimeError: unidentifiable C++ exception

In this branch, the ordering of the particle array has been switched to fortran order for vectorization which apparently causes hdf5 trouble. I can successfully read the data with tables python module.