[Users] VisIt could not read from the file

[Christian Reisswig]

Hi Maria,

> 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 CarpetHDF5 plugin for VisIt only works for Carpet.
PUGH organizes the dataset structure and attributes in the HDF5 file 
differently. You need to use Carpet for HDF5 output.

 
> 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?

the CarpetHDF5 plugin will internally combine dataset chunks
that belong to a larger decomposed array or 3D gridfunction.


cheers,
Christian

> 
> 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
> > 
> > _______________________________________________
> > Users mailing list
> > Users at einsteintoolkit.org
> > http://lists.einsteintoolkit.org/mailman/listinfo/users
> 
> --
> Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/
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