[Users] Visit & CarpetHDF5 mismatch?

Tue Apr 10 23:47:36 CDT 2012

Hi Christian, Bruno, Roland.

h5ls seemed to indicate that the file wasn't corrupted )though perhaps I don't know what HDF5 corruption looks like):

----------------------------------------------------------------------------
> h5ls hahndol\:\:hahndol_coulomb.h5

HAHNDOL::Im_Coulomb\ it=0\ tl=0\ rl=0 Dataset {34, 61, 61}
HAHNDOL::Re_Coulomb\ it=0\ tl=0\ rl=0 Dataset {34, 61, 61}
Parameters\ and\ Global\ Attributes Group
----------------------------------------------------------------------------

Originally my Visit and plugins were compiled with slightly different versions of HDF5 (1.8.6 vs 1.8.7). I tried the HDF5_IGNORE_VERSION_CHECK variable, but it made no difference.

I've now moved to the 1.8.7 for both, but it doesn't help (apart from removing warnings about HDF5_IGNORE_VERSION_CHECK). The terminal output from Visit is:

---------------------------------------------------
Running: gui2.4.2
Running: viewer2.4.2 -host 127.0.0.1 -port 5600 -geometry 875x778+405+0 -borders 20,0,0,1 -shift 0,0 -preshift 0,0 -defer
Running: mdserver2.4.2 -host 127.0.0.1 -port 5601
mdserver(17278) malloc: *** error for object 0x7fff70bc2500: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Running: mdserver2.4.2 -host 127.0.0.1 -port 5601
mdserver(17341) malloc: *** error for object 0x7fff70bc2500: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Running: mdserver2.4.2 -host 127.0.0.1 -port 5601
mdserver(17362) malloc: *** error for object 0x7fff70bc2500: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Running: mdserver2.4.2 -host 127.0.0.1 -port 5600
mdserver(17383) malloc: *** error for object 0x7fff70bc2500: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Running: mdserver2.4.2 -host 127.0.0.1 -port 5600
---------------------------------------------------

I'm not sure it's not my Visit installation itself. I got the pre-compiled Mac package. I'm trying a from-source installation instead, but am briefly hung up getting the pre-requisite VTK on my machine.

Thanks,

Bernard

-----------------------------------------------------------------------------
Bernard Kelly -- CRESST Research Associate, NASA/GSFC

Phone: +1 (301) 286-7243
E-Mail: bernard.j.kelly at nasa.gov
Web: http://science.gsfc.nasa.gov/sed/index.cfm?fuseAction=people.jumpBio&iphonebookid=13052
-----------------------------------------------------------------------------

From: Bruno Giacomazzo <bruno.giacomazzo at jila.colorado.edu<mailto:bruno.giacomazzo at jila.colorado.edu>>
Date: Tue, 10 Apr 2012 15:27:39 -0500
To: Bernard Kelly <bernard.j.kelly at nasa.gov<mailto:bernard.j.kelly at nasa.gov>>
Cc: Einstein Toolkit Users <users at einsteintoolkit.org<mailto:users at einsteintoolkit.org>>
Subject: Re: [Users] Visit & CarpetHDF5 mismatch?

Beany,
I use VisIt without problems with the Maxwell version of the Einstein Toolkit. Was your plugin compiled with the same HDF5 library version used to compile VisIt? Did you use h5ls to check the file is not corrupted?

Cheers,
Bruno

On Apr 10, 2012, at 2:21 PM, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:

Hi all. I'd like to visualise some 3D data produced by an initial-data run
of the EinsteinToolkit (Maxwell).

I'm outputting using CarpetIOHDF5; I have an output file
"hahndol::hahndol_coulomb.h5", and decided to use Visit, as recommended by
cactuscode, etc.

I grabbed the CarpetHDF5 plugin code from svn, and installed as per
instructions (pointing at the ETK-installed HDF5 in my
Cactus/configs/<config-name>/scratch/external directory).

Starting Visit (2.4.2) , and trying to load a .h5 file yields the
following error:

---------------------------------------------------------------------------
----
The metadata server running on host localhost has exited abnormally. VisIt
is trying to restart it.
Shortly thereafter, the following occured...
VisIt was unable to open
"/Users/bjkelly1/Projects/CODES/Cactus/exe/BL_IJS_test/hahndol::hahndol_cou
lomb.h5".  Each attempt to open it caused VisIt's metadata server to
crash.  This can occur when the file is corrupted, or when the underlying
file format has changed and VisIt's readers have not been updated yet, or
when the reader VisIt is using for your file format is not robust.  Please
check whether the file is corrupted and, if not, contact a VisIt developer.
---------------------------------------------------------------------------
----

I have no idea whether the file is corrupted, but wanted to know: is the
CarpetHDF5 plugin up-to-date with the output of Maxwell's CarpetIOHDF5?

Any basic ideas where I might have gone wrong?

Thanks,

Bernard

---------------------------------------------------------------------------
--
Bernard Kelly -- CRESST Research Associate, NASA/GSFC

Phone: +1 (301) 286-7243
E-Mail: bernard.j.kelly at nasa.gov<mailto:bernard.j.kelly at nasa.gov>
Web:
http://science.gsfc.nasa.gov/sed/index.cfm?fuseAction=people.jumpBio&iphone
bookid=13052
---------------------------------------------------------------------------
--

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Dr. Bruno Giacomazzo
JILA - University of Colorado
440 UCB
Boulder, CO 80309
USA

Tel.  : +1 303-492-0389
Fax  : +1 303-492-5235
email : bruno.giacomazzo at jila.colorado.edu<mailto:bruno.giacomazzo at jila.colorado.edu>
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