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Bug #12177

Hdf_file class fails on reading diagnostics in the libffgsvopenmp-ql branch

Added by Eric Stern over 3 years ago. Updated over 3 years ago.

Status:
Remission
Priority:
Normal
Assignee:
-
Start date:
04/06/2016
Due date:
% Done:

0%

Estimated time:
Duration:

Description

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.

History

#1 Updated by Eric Stern over 3 years ago

  • Status changed from New to Remission

The synergia tools in the devel branch is able to read these files, so the problem is in the file reading code in the libff branch. I'm putting this into remission so there won't be problems when the libff branch gets merged into the main branch.



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