[Users] Visit & CarpetHDF5 mismatch?

Thu Apr 12 14:55:22 CDT 2012

Yes, I went to the cmake tab, changed the definitions, and generated code...
 I even changed the mpi lib to -L/sw/lib/openmpi

The error that then results is....

Running: xmledit2.4.2 CarpetHDF5.xml
Running: xml2cmake2.4.2 CarpetHDF5.xml
-----------------------------------------------------------------
               Parsed document of type Plugin
-----------------------------------------------------------------

Plugin: CarpetHDF5 ("Carpet AMR/curvilinear HDF5 output generated by the
Cactus Computational Toolkit", type=database) -- version 2.1
    Attribute:  ()

-- The C compiler identification is GNU
-- The CXX compiler identification is Clang
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - yes
-- Checking whether C compiler supports OSX deployment target flag
-- Checking whether C compiler supports OSX deployment target flag - yes
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
-- Generating done
-- Build files have been written to:
/Users/shawley/apps/VizTools/CarpetHDF5
Scanning dependencies of target ECarpetHDF5Database_par
[  6%] Building CXX object
CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5EnginePluginInfo.C.o
[ 12%] Building CXX object
CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5PluginInfo.C.o
[ 18%] Building CXX object
CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5CommonPluginInfo.C.o
[ 25%] Building CXX object
CMakeFiles/ECarpetHDF5Database_par.dir/avtCarpetHDF5FileFormat.C.o
[ 31%] Building CXX object
CMakeFiles/ECarpetHDF5Database_par.dir/H5Index.C.o
make[2]: *** No rule to make target `/usr/lib/libmpi_cxx.dylib', needed by
`/Users/shawley/.visit/2.4.2/darwin-x86_64/plugins/databases/libECarpetHDF5
Database_par.dylib'.  Stop.
make[1]: *** [CMakeFiles/ECarpetHDF5Database_par.dir/all] Error 2

Not sure why it's looking for /usr/lib/libmpi_cxx.dylib when I told it to
look elsewhere.

On 4/12/12 2:45 PM, "Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND
BALTIMORE COUNTY]" <bernard.j.kelly at nasa.gov> wrote:

>Scott:
>
>That tab is actually the second tab in the window that opens up. It's
>labelled "CMake" rather than "Makefile".
>
>BTW, do you have "cmake" (rather than "make" or "gmake") installed on your
>system?
>
>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&iphon
>e
>bookid=13052
>--------------------------------------------------------------------------
>-
>--
>
>
>
>
>
>
>
>On 4/12/12 3:42 PM, "Scott Hawley" <scott.hawley at belmont.edu> wrote:
>
>>Is THAT where those are?   I didn't see any instructions about that.  I
>>even tried downloading the xmledit plugin for vim...
>>(http://www.vim.org/scripts/script.php?script_id=301)
>>
>>This line should be changed:
>>"To install the package, simply execute the install script contained in
>>the 
>>CarpetHDF5 package."
>>
>>to read
>>
>>"To install the package, first set your path to include the Visin bin/
>>directory (e.g. /Applications/VisIt.app/Contents/Resources/bin/ or
>>/usr/local/visit/bin/ ).  Then run the install script contained in the
>>CarpetHDF5 package."
>>
>>
>>
>>
>>Also... the instruction say
>>"In the "Makefile"-tab modify the library and include path for the
>>HDF5-library
>>to match the installation on your system."
>>
>>....there is no "Makefile" tab.
>>
>>
>>
>>-Scott
>>
>>
>>
>>On 4/12/12 2:32 PM, "Christian Reisswig" <reisswig at tapir.caltech.edu>
>>wrote:
>>
>>>Hi Scott,
>>>
>>>the important errors are:
>>>> ./install: line 8: xmledit: command not found
>>>> ./install: line 9: xml2cmake: command not found
>>>
>>>It appears that you need to set your PATH variable to your visit/bin
>>>directory.
>>>
>>>I hope that helps.
>>>Christian
>>>
>>>> How did you get the plugin to compile?  When I run the script I getŠ
>>>> 
>>>> 
>>>> ~/apps/VizTools/CarpetHDF5] % ./install
>>>> make: *** No rule to make target `clean'.  Stop.
>>>> rm: Makefile: No such file or directory
>>>> rm: CMakeLists.txt: No such file or directory
>>>> rm: CMakeCache.txt: No such file or directory
>>>> rm: CMakeFiles: No such file or directory
>>>> rm: cmake_install.cmake: No such file or directory
>>>> ./install: line 8: xmledit: command not found
>>>> ./install: line 9: xml2cmake: command not found
>>>> CMake Error: The source directory
>>>> "/Users/shawley/apps/VizTools/CarpetHDF5" does not appear to contain
>>>> CMakeLists.txt.
>>>> Specify --help for usage, or press the help button on the CMake GUI.
>>>> make: *** No targets specified and no makefile found.  Stop.
>>>> 
>>>> On 4/10/12 3:24 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::hahnd
>>>>>>o
>>>>>>l
>>>>>>_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...
>>>> 
>>>> _______________________________________________
>>>> Users mailing list
>>>> Users at einsteintoolkit.org
>>>> http://lists.einsteintoolkit.org/mailman/listinfo/users
>>>
>>
>>
>
>