[Users] Visit & CarpetHDF5 mismatch?

Tue Apr 17 12:17:40 CDT 2012

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<mailto: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<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?

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The instructions in the latter's README.txt seem a bit out of date, which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<mailto:'@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<mailto: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

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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>
web: http://www.brunogiacomazzo.org

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