I'm at my wits end here -- I've spent the past six hours trying to debug
why I get the following output from h5ls:
$ h5ls test.h5/sleep1/
Events Dataset *ERROR*
notes Dataset {0/Inf}
(the file is at http://web.mit.edu/jonas/Public/test.h5 ). I've
double-checked to make sure i'm closing and flushing everything
correctly, to no avail. Running h5ls with --errors shows a stack trace
like follows:
[jonas@hamiltonian unittest]$ h5ls --errors test.h5/sleep1/
HDF5-DIAG: Error detected in HDF5 (1.8.1) thread 0:
#000: H5O.c line 242 in H5Oopen(): unable to open object
major: Symbol table
minor: Can't open object
#001: H5O.c line 1283 in H5O_open_name(): object not found
major: Symbol table
minor: Object not found
#002: H5Gloc.c line 468 in H5G_loc_find(): can't find object
major: Symbol table
minor: Object not found
#003: H5Gtraverse.c line 861 in H5G_traverse(): internal path
traversal failed
major: Symbol table
minor: Object not found
...
The problem is that I can apparently h5dump the file just fine. I
stumbled across this error when I was writing a h5ls tutorial for people
unfamiliar with the format.
Might anyone have seen this sort of error before, or be able to shed any
insight as to its origin?
Thanks,
...Eric
···
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Eric,
If the file was created by 1.6.* or earlier, try to run 1.6.7 version of h5repack and see if 1.8.1 h5ls still has a problem.
We are currently working on a bug with a similar error stack, and using h5repack was a workaround.
I cannot upload the file. Would it be possible for you to put it in my ftp directory
ftp.hdfgroup.uiuc.edu/pub/incoming/epourmal
Thank you!
Elena
···
On Aug 8, 2008, at 2:35 PM, Eric Jonas wrote:
I'm at my wits end here -- I've spent the past six hours trying to debug
why I get the following output from h5ls:
$ h5ls test.h5/sleep1/
Events Dataset *ERROR*
notes Dataset {0/Inf}
(the file is at http://web.mit.edu/jonas/Public/test.h5 ). I've
double-checked to make sure i'm closing and flushing everything
correctly, to no avail. Running h5ls with --errors shows a stack trace
like follows:
[jonas@hamiltonian unittest]$ h5ls --errors test.h5/sleep1/
HDF5-DIAG: Error detected in HDF5 (1.8.1) thread 0:
#000: H5O.c line 242 in H5Oopen(): unable to open object
major: Symbol table
minor: Can't open object
#001: H5O.c line 1283 in H5O_open_name(): object not found
major: Symbol table
minor: Object not found
#002: H5Gloc.c line 468 in H5G_loc_find(): can't find object
major: Symbol table
minor: Object not found
#003: H5Gtraverse.c line 861 in H5G_traverse(): internal path
traversal failed
major: Symbol table
minor: Object not found
...
The problem is that I can apparently h5dump the file just fine. I
stumbled across this error when I was writing a h5ls tutorial for people
unfamiliar with the format.
Might anyone have seen this sort of error before, or be able to shed any
insight as to its origin?
Thanks,
...Eric
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To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org.
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If the file was created by 1.6.* or earlier, try to run 1.6.7 version
of h5repack and see if 1.8.1 h5ls still has a problem.
The file was actually created with 1.8.1, unless I'm somehow linking
against the wrong libs. h5repack, alas, didn't seem to help.
I cannot upload the file. Would it be possible for you to put it in my
ftp directory
ftp.hdfgroup.uiuc.edu/pub/incoming/epourmal
Thank you!
Done, as jonas.test.h5. Thank you!
...Eric
···
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Eric,
Our released and development versions in SVN do not have this problem. But I can confirm the behavior with 1.8.1.
We just fixed a bug when compound datatype with an array datatype field had a wrong file format version number. "Events" dataset has this type, so I guess you encountered that bug.
The fix should be available in the next snapshot in both 1.8 and 1.9 versions. You can find snapshots under ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/
You may also check out the code from SVN
http://svn.hdfgorup.uiuc.edu/hdf5/trunk --- development branch
http://svn.hdfgorup.uiuc.edu/hdf5/branches/hdf5_1_8 -- released branch
Could you please send us a program that created the file? To our knowledge 1.8.1 shouldn't have this problem.
Thank you!
Elena
···
On Aug 8, 2008, at 4:28 PM, Eric Jonas wrote:
If the file was created by 1.6.* or earlier, try to run 1.6.7 version
of h5repack and see if 1.8.1 h5ls still has a problem.
The file was actually created with 1.8.1, unless I'm somehow linking
against the wrong libs. h5repack, alas, didn't seem to help.
I cannot upload the file. Would it be possible for you to put it in my
ftp directory
ftp.hdfgroup.uiuc.edu/pub/incoming/epourmal
Thank you!
Done, as jonas.test.h5. Thank you!
...Eric
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