How to fix the error "HDF5-DIAG: Error detected in HDF5"

HDF5 Library
1

Since I’m new to HDF5, I’m totally puzzled about this problem.
I had built the serial and parallel version in different files out of the root directory of hdf5.
So there’re 3 files in my directory, serial version, parallel version and the root directory obtained by tar -xf.
1

And I also had linked the correct libs, for it didn’t report regarding errors.
But i don’t know how to solve the problem as shown below:

The error report is following:

HDF5-DIAG: Error detected in HDF5 (1.8.18) MPI-process 0:
#000: …/…/hdf5-1_8_18/src/H5G.c line 468 in H5Gopen2(): unable to open group
major: Symbol table
minor: Can’t open object
#001: …/…/hdf5-1_8_18/src/H5Gint.c line 321 in H5G__open_name(): group not found
major: Symbol table
minor: Object not found
#002: …/…/hdf5-1_8_18/src/H5Gloc.c line 430 in H5G_loc_find(): can’t find object
major: Symbol table
minor: Object not found
#003: …/…/hdf5-1_8_18/src/H5Gtraverse.c line 863 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found

I also found the source code about the errors:

2
21054×116 6.02 KB

3
3926×114 6.6 KB

4
41289×111 6.99 KB

5
51371×134 10.9 KB

Sincerely thanks in advance!

2

I have same problem and could not understand how to fix it, are you have fixed it? I use the python package can open my file but use c++ can not. If you have fixed it could you explain the solving method detailed. I am the freshmen in this area. many thanks.

Error:
HDF5-DIAG: Error detected in HDF5 (1.12.3) thread 0:
#000: D:\a\hdf5\hdf5\hdfsrc\src\H5G.c line 509 in H5Gopen2(): unable to open group
major: Symbol table
minor: Can’t open object
#001: D:\a\hdf5\hdf5\hdfsrc\src\H5VLcallback.c line 4187 in H5VL_group_open(): group open failed
major: Virtual Object Layer
minor: Can’t open object
#002: D:\a\hdf5\hdf5\hdfsrc\src\H5VLcallback.c line 4154 in H5VL__group_open(): group open failed
major: Virtual Object Layer
minor: Can’t open object
#003: D:\a\hdf5\hdf5\hdfsrc\src\H5VLnative_group.c line 123 in H5VL__native_group_open(): unable to open group
major: Symbol table
minor: Can’t open object
#004: D:\a\hdf5\hdf5\hdfsrc\src\H5Gint.c line 269 in H5G__open_name(): group not found
major: Symbol table
minor: Object not found
#005: D:\a\hdf5\hdf5\hdfsrc\src\H5Gloc.c line 441 in H5G_loc_find(): can’t find object
major: Symbol table
minor: Object not found
#006: D:\a\hdf5\hdf5\hdfsrc\src\H5Gtraverse.c line 836 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#007: D:\a\hdf5\hdf5\hdfsrc\src\H5Gtraverse.c line 612 in H5G__traverse_real(): traversal operator failed
major: Symbol table
minor: Callback failed
#008: D:\a\hdf5\hdf5\hdfsrc\src\H5Gloc.c line 398 in H5G__loc_find_cb(): object ‘land_segments’ doesn’t exist
major: Symbol table
minor: Object not found

3

Hi @bingtao_chang,

Can you verify there is an HDF5 group in your file with the name “land_segments”?

One way to check is something like:

h5ls -r my-file.h5 | grep Group | grep land_segments

Aleksandar

1 Like
6

You are right, I made a foolish mistake. I used the wrong file, and it indeed does not contain this group. Thank you very much for your help.