I'm seeing errors in our software when trying to delete attributes from HDF5 files just prior to replacing them with new values. I've "attached" one of the error messages to the end of this email. I'm not entirely sure what's going on, but I'm starting to think that the problem might be due to the fact that I'm deleting the attributes inside of an H5Ovisit callback function. My attempts to reproduce the problem without the H5Ovisit call have failed so far. Any suggestions as to what I might be doing wrong? I don't see anything in H5Ovisit that says not to use any particular HDF5 API inside the callback.
HDF5-DIAG: Error detected in HDF5 (1.8.7-pre1) thread 1:
#000: H5A.c line 2161 in H5Adelete_by_name(): unable to delete attribute
major: Attribute
minor: Can't delete message
#001: H5Oattribute.c line 1605 in H5O_attr_remove(): error deleting attribute
major: Attribute
minor: Can't delete message
#002: H5Omessage.c line 1313 in H5O_msg_iterate_real(): iterator function failed
major: Object header
minor: Unable to list node
#003: H5Oattribute.c line 1530 in H5O_attr_remove_cb(): unable to convert into null message
major: Object header
minor: Can't delete message
#004: H5Oalloc.c line 1219 in H5O_release_mesg(): unable to delete file space for object header message
major: Object header
minor: Can't delete message
#005: H5Omessage.c line 2088 in H5O_delete_mesg(): unable to delete file space for object header message
major: Object header
minor: Can't delete message
#006: H5Oshared.h line 243 in H5O_attr_shared_delete(): unable to decrement ref count for native message
major: Object header
minor: Unable to decrement reference count
#007: H5Oattr.c line 548 in H5O_attr_delete(): unable to adjust datatype link count
major: Attribute
minor: Bad object header link count
#008: H5Oshared.h line 237 in H5O_dtype_shared_delete(): unable to decrement ref count for shared message
major: Object header
minor: Unable to decrement reference count
#009: H5Oshared.c line 527 in H5O_shared_delete(): unable to adjust shared object link count
major: Object header
minor: Bad object header link count
#010: H5Oshared.c line 247 in H5O_shared_link_adj(): interfile hard links are not allowed
major: Links
minor: Unable to initialize object
I tried using an H5Ovisit call to make a list of the attributes to delete, which is then separately deleted using H5Adelete_by_name outside of the H5Ovisit callback, and the results were the same, so the problem I'm seeing doesn't appear to be due to the deletion inside the callback. That said, the loc_id I'm using in the delete call is the one provided to the callback (managed using H5Iinc_ref of course). It doesn't seem like that should be a problem, but I figured it should be mentioned just in case.
Anyway. Still stuck on this issue.
John Knutson wrote:
···
I'm seeing errors in our software when trying to delete attributes from HDF5 files just prior to replacing them with new values. I've "attached" one of the error messages to the end of this email. I'm not entirely sure what's going on, but I'm starting to think that the problem might be due to the fact that I'm deleting the attributes inside of an H5Ovisit callback function. My attempts to reproduce the problem without the H5Ovisit call have failed so far. Any suggestions as to what I might be doing wrong? I don't see anything in H5Ovisit that says not to use any particular HDF5 API inside the callback.
HDF5-DIAG: Error detected in HDF5 (1.8.7-pre1) thread 1:
#000: H5A.c line 2161 in H5Adelete_by_name(): unable to delete attribute
major: Attribute
minor: Can't delete message
#001: H5Oattribute.c line 1605 in H5O_attr_remove(): error deleting attribute
major: Attribute
minor: Can't delete message
#002: H5Omessage.c line 1313 in H5O_msg_iterate_real(): iterator function failed
major: Object header
minor: Unable to list node
#003: H5Oattribute.c line 1530 in H5O_attr_remove_cb(): unable to convert into null message
major: Object header
minor: Can't delete message
#004: H5Oalloc.c line 1219 in H5O_release_mesg(): unable to delete file space for object header message
major: Object header
minor: Can't delete message
#005: H5Omessage.c line 2088 in H5O_delete_mesg(): unable to delete file space for object header message
major: Object header
minor: Can't delete message
#006: H5Oshared.h line 243 in H5O_attr_shared_delete(): unable to decrement ref count for native message
major: Object header
minor: Unable to decrement reference count
#007: H5Oattr.c line 548 in H5O_attr_delete(): unable to adjust datatype link count
major: Attribute
minor: Bad object header link count
#008: H5Oshared.h line 237 in H5O_dtype_shared_delete(): unable to decrement ref count for shared message
major: Object header
minor: Unable to decrement reference count
#009: H5Oshared.c line 527 in H5O_shared_delete(): unable to adjust shared object link count
major: Object header
minor: Bad object header link count
#010: H5Oshared.c line 247 in H5O_shared_link_adj(): interfile hard links are not allowed
major: Links
minor: Unable to initialize object
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Hi John,
I tried using an H5Ovisit call to make a list of the attributes to delete, which is then separately deleted using H5Adelete_by_name outside of the H5Ovisit callback, and the results were the same, so the problem I'm seeing doesn't appear to be due to the deletion inside the callback. That said, the loc_id I'm using in the delete call is the one provided to the callback (managed using H5Iinc_ref of course). It doesn't seem like that should be a problem, but I figured it should be mentioned just in case.
Anyway. Still stuck on this issue.
Hmm, can you send some test code that show's the failure?
Quincey
···
On May 24, 2011, at 10:34 AM, John Knutson wrote:
John Knutson wrote:
I'm seeing errors in our software when trying to delete attributes from HDF5 files just prior to replacing them with new values. I've "attached" one of the error messages to the end of this email. I'm not entirely sure what's going on, but I'm starting to think that the problem might be due to the fact that I'm deleting the attributes inside of an H5Ovisit callback function. My attempts to reproduce the problem without the H5Ovisit call have failed so far. Any suggestions as to what I might be doing wrong? I don't see anything in H5Ovisit that says not to use any particular HDF5 API inside the callback.
HDF5-DIAG: Error detected in HDF5 (1.8.7-pre1) thread 1:
#000: H5A.c line 2161 in H5Adelete_by_name(): unable to delete attribute
major: Attribute
minor: Can't delete message
#001: H5Oattribute.c line 1605 in H5O_attr_remove(): error deleting attribute
major: Attribute
minor: Can't delete message
#002: H5Omessage.c line 1313 in H5O_msg_iterate_real(): iterator function failed
major: Object header
minor: Unable to list node
#003: H5Oattribute.c line 1530 in H5O_attr_remove_cb(): unable to convert into null message
major: Object header
minor: Can't delete message
#004: H5Oalloc.c line 1219 in H5O_release_mesg(): unable to delete file space for object header message
major: Object header
minor: Can't delete message
#005: H5Omessage.c line 2088 in H5O_delete_mesg(): unable to delete file space for object header message
major: Object header
minor: Can't delete message
#006: H5Oshared.h line 243 in H5O_attr_shared_delete(): unable to decrement ref count for native message
major: Object header
minor: Unable to decrement reference count
#007: H5Oattr.c line 548 in H5O_attr_delete(): unable to adjust datatype link count
major: Attribute
minor: Bad object header link count
#008: H5Oshared.h line 237 in H5O_dtype_shared_delete(): unable to decrement ref count for shared message
major: Object header
minor: Unable to decrement reference count
#009: H5Oshared.c line 527 in H5O_shared_delete(): unable to adjust shared object link count
major: Object header
minor: Bad object header link count
#010: H5Oshared.c line 247 in H5O_shared_link_adj(): interfile hard links are not allowed
major: Links
minor: Unable to initialize object
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Hi, Quincey,
I don't have a simple monolithic application that can be used to reproduce the problem, however I can email you directly the related code snippets where I'm seeing the problem, if that will help.
···
On a related note, I also tried replacing the H5Adelete_by_name call with an H5Dopen2 call followed by an H5Adelete call. Same results. Quincey Koziol wrote:
Hi John,
On May 24, 2011, at 10:34 AM, John Knutson wrote:
I tried using an H5Ovisit call to make a list of the attributes to delete, which is then separately deleted using H5Adelete_by_name outside of the H5Ovisit callback, and the results were the same, so the problem I'm seeing doesn't appear to be due to the deletion inside the callback. That said, the loc_id I'm using in the delete call is the one provided to the callback (managed using H5Iinc_ref of course). It doesn't seem like that should be a problem, but I figured it should be mentioned just in case.
Anyway. Still stuck on this issue.
Hmm, can you send some test code that show's the failure?
Quincey
John Knutson wrote:
I'm seeing errors in our software when trying to delete attributes from HDF5 files just prior to replacing them with new values. I've "attached" one of the error messages to the end of this email. I'm not entirely sure what's going on, but I'm starting to think that the problem might be due to the fact that I'm deleting the attributes inside of an H5Ovisit callback function. My attempts to reproduce the problem without the H5Ovisit call have failed so far. Any suggestions as to what I might be doing wrong? I don't see anything in H5Ovisit that says not to use any particular HDF5 API inside the callback.
HDF5-DIAG: Error detected in HDF5 (1.8.7-pre1) thread 1:
#000: H5A.c line 2161 in H5Adelete_by_name(): unable to delete attribute
major: Attribute
minor: Can't delete message
#001: H5Oattribute.c line 1605 in H5O_attr_remove(): error deleting attribute
major: Attribute
minor: Can't delete message
#002: H5Omessage.c line 1313 in H5O_msg_iterate_real(): iterator function failed
major: Object header
minor: Unable to list node
#003: H5Oattribute.c line 1530 in H5O_attr_remove_cb(): unable to convert into null message
major: Object header
minor: Can't delete message
#004: H5Oalloc.c line 1219 in H5O_release_mesg(): unable to delete file space for object header message
major: Object header
minor: Can't delete message
#005: H5Omessage.c line 2088 in H5O_delete_mesg(): unable to delete file space for object header message
major: Object header
minor: Can't delete message
#006: H5Oshared.h line 243 in H5O_attr_shared_delete(): unable to decrement ref count for native message
major: Object header
minor: Unable to decrement reference count
#007: H5Oattr.c line 548 in H5O_attr_delete(): unable to adjust datatype link count
major: Attribute
minor: Bad object header link count
#008: H5Oshared.h line 237 in H5O_dtype_shared_delete(): unable to decrement ref count for shared message
major: Object header
minor: Unable to decrement reference count
#009: H5Oshared.c line 527 in H5O_shared_delete(): unable to adjust shared object link count
major: Object header
minor: Bad object header link count
#010: H5Oshared.c line 247 in H5O_shared_link_adj(): interfile hard links are not allowed
major: Links
minor: Unable to initialize object
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Hi John,
Hi, Quincey,
I don't have a simple monolithic application that can be used to reproduce the problem, however I can email you directly the related code snippets where I'm seeing the problem, if that will help.
Yes, that should help.
On a related note, I also tried replacing the H5Adelete_by_name call with an H5Dopen2 call followed by an H5Adelete call. Same results.
:-(
Well, send us what you can and we can see what's going on.
Quincey
···
On May 24, 2011, at 1:31 PM, John Knutson wrote:
Quincey Koziol wrote:
Hi John,
On May 24, 2011, at 10:34 AM, John Knutson wrote:
I tried using an H5Ovisit call to make a list of the attributes to delete, which is then separately deleted using H5Adelete_by_name outside of the H5Ovisit callback, and the results were the same, so the problem I'm seeing doesn't appear to be due to the deletion inside the callback. That said, the loc_id I'm using in the delete call is the one provided to the callback (managed using H5Iinc_ref of course). It doesn't seem like that should be a problem, but I figured it should be mentioned just in case.
Anyway. Still stuck on this issue.
Hmm, can you send some test code that show's the failure?
Quincey
John Knutson wrote:
I'm seeing errors in our software when trying to delete attributes from HDF5 files just prior to replacing them with new values. I've "attached" one of the error messages to the end of this email. I'm not entirely sure what's going on, but I'm starting to think that the problem might be due to the fact that I'm deleting the attributes inside of an H5Ovisit callback function. My attempts to reproduce the problem without the H5Ovisit call have failed so far. Any suggestions as to what I might be doing wrong? I don't see anything in H5Ovisit that says not to use any particular HDF5 API inside the callback.
HDF5-DIAG: Error detected in HDF5 (1.8.7-pre1) thread 1:
#000: H5A.c line 2161 in H5Adelete_by_name(): unable to delete attribute
major: Attribute
minor: Can't delete message
#001: H5Oattribute.c line 1605 in H5O_attr_remove(): error deleting attribute
major: Attribute
minor: Can't delete message
#002: H5Omessage.c line 1313 in H5O_msg_iterate_real(): iterator function failed
major: Object header
minor: Unable to list node
#003: H5Oattribute.c line 1530 in H5O_attr_remove_cb(): unable to convert into null message
major: Object header
minor: Can't delete message
#004: H5Oalloc.c line 1219 in H5O_release_mesg(): unable to delete file space for object header message
major: Object header
minor: Can't delete message
#005: H5Omessage.c line 2088 in H5O_delete_mesg(): unable to delete file space for object header message
major: Object header
minor: Can't delete message
#006: H5Oshared.h line 243 in H5O_attr_shared_delete(): unable to decrement ref count for native message
major: Object header
minor: Unable to decrement reference count
#007: H5Oattr.c line 548 in H5O_attr_delete(): unable to adjust datatype link count
major: Attribute
minor: Bad object header link count
#008: H5Oshared.h line 237 in H5O_dtype_shared_delete(): unable to decrement ref count for shared message
major: Object header
minor: Unable to decrement reference count
#009: H5Oshared.c line 527 in H5O_shared_delete(): unable to adjust shared object link count
major: Object header
minor: Bad object header link count
#010: H5Oshared.c line 247 in H5O_shared_link_adj(): interfile hard links are not allowed
major: Links
minor: Unable to initialize object
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
