[Users] Visit & CarpetHDF5 mismatch?

Tue Apr 17 12:27:30 CDT 2012

Scott,
	I'm running Lion (OSX 10.7.3). I used MacPorts only to install the libraries needed by pygraph. For the VisIt CarpetHFDF5 plugin I use the hdf5 libraries installed by Fink in /sw/lib. I also needed to set HDF5_DISABLE_VERSION_CHECK=2. I'm using VisIt 2.3.2.

Cheers,
Bruno

On Apr 17, 2012, at 11:17 AM, Scott Hawley wrote:

> Bruno,
> 
>   You are using MacPorts, right?    What version of OS X do you have?  I'm running Lion.
> 
> "yes, this is the correct repository. I didn't need to update the path in my case. I just followed the standard installation instructions and it worked without problems."
> 
> That hasn't been true for me -- can't get it to work even after surmounting various problems along the way --   and don't think it has for Bernard, but we'd really like to get it working!
> 
> -Scott
> 
> 
> 
> From: Bruno Giacomazzo <bruno.giacomazzo at jila.colorado.edu>
> Date: Wednesday, April 11, 2012 12:36 PM
> To: "Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY]" <bernard.j.kelly at nasa.gov>
> Cc: Einstein Toolkit Users <users at einsteintoolkit.org>
> Subject: Re: [Users] Visit & CarpetHDF5 mismatch?
> 
> Bernard,
> 
> On Apr 11, 2012, at 11:10 AM, Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] wrote:
> 
>> Which reminds me: can frequent Visit/CarpetHDF5 users confirm for me where
>> they get (a) Visit, and (b) CarpetHDF5? For me the answers are:
>> 
>> (a) the "Mac OS X - Intel 64 bit" binary from here:
>> https://wci.llnl.gov/codes/visit/executables.html
> 
> 	I also use the 64 bit binary (version 2.3.2 in my case).
> 
>> (b) the cactuscode VizTools trunk via svn:  svn co
>> https://svn.cactuscode.org/VizTools/CarpetHDF5/trunk/ CarpetHDF5
> 
> 	yes, this is the correct repository. I didn't need to update the path in my case. I just followed the standard installation instructions and it worked without problems.
> 
> Cheers,
> Bruno
> 
>> The instructions in the latter's README.txt seem a bit out of date, which
>> made me suspicious. The lines about "updating the paths to the HDF5
>> library", for instance:
>> 
>> install_name_tool -change '@executable_path/../lib/libhdf5.dylib'
>> '/usr/local/lib/libhdf5.1.dylib'
>> ~/.visit/darwin-i386/plugins/databases/libEvisitCarpetHDF5Database_ser.dyli
>> b
>> 
>> Now my 64-bit installation generates three subdirectories in ~/.visit:
>> "2.4.2", "darwin-i386", and "darwin-x86_64". Of these, only "2.4.2" had
>> any content in the "plugins/databases/" subdirectory, and these dylibs
>> were *similar but not identical* in name to what's mentioned in the README
>> (e.g.,  libECarpetHDF5Database_ser.dylib rather than
>> libEvisitCarpetHDF5Database_ser.dylib).
>> 
>> So ... should I be using a different version of Visit (older, 32-bit,
>> etc.)?
>> 
>> Bernard
>> 
>> On 4/10/12 4:24 PM, "Ian Hinder" <ian.hinder at aei.mpg.de> wrote:
>> 
>>> 
>>> On 10 Apr 2012, at 22:21, 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_c
>>>> ou
>>>> 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?
>>> 
>>> One problem can come from Visit trying to open too many files for the
>>> maximum open file limit of your OS.  Mac OS, for example, has a very
>>> small limit.  Try changing this with ulimit.  But ultimately, you should
>>> try to find the actual error message.  I think there is an option for
>>> Visit to output the errors to a file, but it's so long since I've used
>>> Visit that I don't remember.  Probably someone else can fill that in...
>>> 
>>> -- 
>>> Ian Hinder
>>> http://numrel.aei.mpg.de/people/hinder
>>> 
>> 
>> _______________________________________________
>> Users mailing list
>> Users at einsteintoolkit.org
>> http://lists.einsteintoolkit.org/mailman/listinfo/users
> 
> 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
> web: http://www.brunogiacomazzo.org
> 
> ----------------------------------------------------------------------
> There are only 10 types of people in the world:
> Those who understand binary, and those who don't
> ----------------------------------------------------------------------
> 

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
web: http://www.brunogiacomazzo.org

----------------------------------------------------------------------
There are only 10 types of people in the world:
Those who understand binary, and those who don't
----------------------------------------------------------------------

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