Hello,
When I am using PUGHIOHDF5 to output h5 files I see this error. Things seem OK with CarpetIOHDF5. Can I use PUGH, or I need to use Carpet? The output for h5ls is:Cactus\ Parameters Group Global\ Attributes Group WAVETOY::phi\ timelevel\ 0\ at\ iteration\ 0 Dataset {20, 20, 20} etc...
The h5 data written by CarpetIoHdf5 looks chunked. Is there a way to combine it? Or I need to ask support from VisIt to do this?
One more thing: when hdf5 is build on the fly with the HDF5 thorn I see a lot of warnings like: H5*.c:*: warning:etc..... I don't see this when I use an externally installed hdf5 library.
Maria
________________________________________ From: Erik Schnetter [schnetter@cct.lsu.edu] Sent: Thursday, February 03, 2011 10:40 AM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: [Users] VisIt could not read from the file
Maria
These errors look severs. Were there other errors or warnings, e.g. during startup? Is there e.g. a version mismatch between different HDF5 libraries, or was there an error while writing this file? Can you h5ls or h5dump this file?
-erik
On Thu, Feb 3, 2011 at 10:09 AM, Babiuc-Hamilton, Maria babiuc@marshall.edu wrote:
Hello,
I have problems trying to visualize in visit the h5 files created with the new HDF and zlib thorns. The errors are:
$ visit -debug-5 Running: gui2.2.0 -debug-5 Running: viewer2.2.0 -host 127.0.0.1 -port 5600 -debug-5 -geometry 1558x1150+362+25 -borders 24,5,5,5 -shift 5,25 -preshift 0,-1 -defer Running: mdserver2.2.0 -host 127.0.0.1 -port 5601 -debug-5 HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0: #000: H5L.c line 1184 in H5Literate(): link iteration failed major: Symbol table minor: Iteration failed #001: H5G.c line 1532 in H5G_iterate(): error iterating over links major: Symbol table minor: Iteration failed #002: H5Gobj.c line 599 in H5G_obj_iterate(): can't iterate over symbol table major: Symbol table minor: Iteration failed #003: H5Gstab.c line 506 in H5G_stab_iterate(): unable to protect symbol table heap major: Symbol table minor: Protected metadata error #004: H5HL.c line 360 in H5HL_protect(): unable to load heap major: Heap minor: Unable to load metadata into cache #005: H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed. major: Object cache minor: Unable to protect metadata #006: H5C.c line 6160 in H5C_protect(): can't load entry major: Object cache minor: Unable to load metadata into cache #007: H5C.c line 10990 in H5C_load_entry(): unable to load entry major: Object cache minor: Unable to load metadata into cache #008: H5HLcache.c line 259 in H5HL_load(): bad heap free list major: Heap minor: Unable to load metadata into cache
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