[Users] VisIt could not read from the file

[Babiuc-Hamilton, Maria]

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 at cct.lsu.edu]
Sent: Thursday, February 03, 2011 10:40 AM
To: Babiuc-Hamilton, Maria
Cc: users at 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 at 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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--
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/