After several hundred file saves (structure like %d/%d/rnorm with the first number timestep second iteration) I finally get:
HDF5-DIAG: Error detected in HDF5 (1.8.3) thread 0:
#000: H5G.c line 211 in H5Gcreate2(): unable to create group
major: Symbol table
minor: Unable to initialize object
#001: H5G.c line 266 in H5G_create_named(): unable to create and link to group
major: Symbol table
minor: Unable to initialize object
#002: H5L.c line 1639 in H5L_link_object(): unable to create new link to object
major: Links
minor: Unable to initialize object
#003: H5L.c line 1862 in H5L_create_real(): can't insert link
major: Symbol table
minor: Unable to insert object
#004: H5Gtraverse.c line 877 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#005: H5Gtraverse.c line 665 in H5G_traverse_real(): can't look up component
major: Symbol table
minor: Object not found
#006: H5Gobj.c line 1047 in H5G_obj_lookup(): can't locate object
major: Symbol table
minor: Object not found
#007: H5Gstab.c line 844 in H5G_stab_lookup(): unable to protect symbol table heap
major: Symbol table
minor: Protected metadata error
#008: H5HL.c line 360 in H5HL_protect(): unable to load heap
major: Heap
minor: Unable to load metadata into cache
#009: H5AC.c line 1978 in H5AC_protect(): H5C_protect() failed.
major: Object cache
minor: Unable to protect metadata
#010: H5C.c line 6202 in H5C_protect(): can't load entry
major: Object cache
minor: Unable to load metadata into cache
#011: H5C.c line 11038 in H5C_load_entry(): unable to load entry
major: Object cache
minor: Unable to load metadata into cache
#012: H5HLcache.c line 206 in H5HL_load(): bad heap signature
major: Heap
minor: Unable to load metadata into cache
There is enough space on the disk. Are there capacity limits in the tree structure? It broke at timestep 620, each timestep group contains on average 2-10 subgroups, each has a short double array of size 2-20. No compression was used. File was opened once, group creations and array writes were followed by flush. Any hints what happened are highly appreciated.
Regards,
Dominik
Thanks Quincey, will upgrade to 1.8.4 in any case.
However the crash just happened out of nowhere, with many successful runs before, so there is no way I can immediately tell if the upgrade helped.
Dominik
Quincey Koziol wrote:
···
Hi Dominik,
On Dec 14, 2009, at 1:41 AM, Dominik Szczerba wrote:
After several hundred file saves (structure like %d/%d/rnorm with the first number timestep second iteration) I finally get:
HDF5-DIAG: Error detected in HDF5 (1.8.3) thread 0:
#000: H5G.c line 211 in H5Gcreate2(): unable to create group
major: Symbol table
minor: Unable to initialize object
#001: H5G.c line 266 in H5G_create_named(): unable to create and link to group
major: Symbol table
minor: Unable to initialize object
#002: H5L.c line 1639 in H5L_link_object(): unable to create new link to object
major: Links
minor: Unable to initialize object
#003: H5L.c line 1862 in H5L_create_real(): can't insert link
major: Symbol table
minor: Unable to insert object
#004: H5Gtraverse.c line 877 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#005: H5Gtraverse.c line 665 in H5G_traverse_real(): can't look up component
major: Symbol table
minor: Object not found
#006: H5Gobj.c line 1047 in H5G_obj_lookup(): can't locate object
major: Symbol table
minor: Object not found
#007: H5Gstab.c line 844 in H5G_stab_lookup(): unable to protect symbol table heap
major: Symbol table
minor: Protected metadata error
#008: H5HL.c line 360 in H5HL_protect(): unable to load heap
major: Heap
minor: Unable to load metadata into cache
#009: H5AC.c line 1978 in H5AC_protect(): H5C_protect() failed.
major: Object cache
minor: Unable to protect metadata
#010: H5C.c line 6202 in H5C_protect(): can't load entry
major: Object cache
minor: Unable to load metadata into cache
#011: H5C.c line 11038 in H5C_load_entry(): unable to load entry
major: Object cache
minor: Unable to load metadata into cache
#012: H5HLcache.c line 206 in H5HL_load(): bad heap signature
major: Heap
minor: Unable to load metadata into cache
There is enough space on the disk. Are there capacity limits in the tree structure? It broke at timestep 620, each timestep group contains on average 2-10 subgroups, each has a short double array of size 2-20. No compression was used. File was opened once, group creations and array writes were followed by flush. Any hints what happened are highly appreciated.
There's no limits on the tree structure (we've created test files with 100's of thousands of links in a group). I can see from the error that it's having a problem loading the heap where the links are stored for the group, but I don't know what would cause that error - either the file is corrupted, there's a bug in your application or there's a bug in HDF5. I do notice that you are using the 1.8.3 release - is it possible to upgrade to the 1.8.4 release and see if that helps?
Quincey
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