[Users] Follow-up: How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion

Mon May 21 15:03:46 CDT 2012

Thanks. I just downgraded to Visit 2.4.2 and now it looked like I got rid of that error.
However, when trying to see a h5 file, I got the 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/student/Cactus/VizTools/ks-mclachlan_metric.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.

Moreover, when I am trying to run Cactus, I am getting this:

./cactus_tov tov.rpar 
dyld: Symbol not found: __ZN3MPI3Win14Set_errhandlerERKNS_10ErrhandlerE
  Referenced from: /Users/student/Cactus/exe/./cactus_tov
  Expected in: /usr/lib/libmpi_cxx.0.dylib

Trace/BPT trap

I checked, and I do have /usr/lib/libmpi_cxx.0.dylib
Any ideas?

thanks,
Maria

________________________________________
From: Scott Hawley [scott.hawley at belmont.edu]
Sent: Monday, May 21, 2012 3:18 PM
To: Babiuc-Hamilton, Maria
Cc: users at einsteintoolkit.org
Subject: Re: Follow-up: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS X Lion

Yes, I remember seeing that error too; although it may have only been with
version 2.5 that I saw that.

So apparently some other libraries also used to be native, and are no
longer, and I had already created the other links.

So in addition to lipmpi*, you'll also want to do

% cd /usr/lib/; sudo ln -s /opt/local/lib/libopen-pal*
/opt/local/lib/libopen-rte* .

Let me know if that helps.

On 5/21/12 2:11 PM, "Babiuc-Hamilton, Maria" <babiuc at marshall.edu> wrote:

>Scott,
>
>I finally got around to check follow your instructions, but I ran into
>this problem:
>
>-----------------------------------------------------------------
>               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 GNU
>-- 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
>-- Checking whether CXX compiler has -isysroot
>-- Checking whether CXX compiler has -isysroot - yes
>-- Checking whether CXX compiler supports OSX deployment target flag
>-- Checking whether CXX compiler supports OSX deployment target flag - yes
>-- 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
>CMake Error at CMakeLists.txt:90 (VISIT_PLUGIN_TARGET_RTOD):
>  Unknown CMake command "VISIT_PLUGIN_TARGET_RTOD".
>
>
>-- Configuring incomplete, errors occurred!
>make: *** No targets specified and no makefile found.  Stop.
>
>
>The only difference was that I did a
> ./configure --enable-cxx
>first in my hdf5-1.8.9 directory.
>
>
>Could you please help me out?
>
>Christian, do you have any suggestions?
>
>thanks,
>Maria
>________________________________________
>From: Babiuc-Hamilton, Maria
>Sent: Tuesday, May 15, 2012 8:42 AM
>To: Scott Hawley
>Subject: Re: [Users] How I got Visit 2.4.2 & CarpetHDF5 to work on Mac OS
>X Lion
>
>Scott,
>
>Fantastic! I'll try it right away! I had problems making Visit work with
>MacOS last year, and had to do my own little hack, but haven't use it for
>a while, because I was afraid that if I upgrade I'll run into problems
>again.
>Have had any success with ygraph?
>
>Cheers,
>Maria
>
>On 5/14/12 5:23 PM, "Scott Hawley" <scott.hawley at belmont.edu> wrote:
>
>>
>>Here's what I did:
>>
>>1. Downloaded the 64-bit binary of Visit 2.4.2 from the Visit web site
>>2. Downloaded the CarpetHDF directory via svn.
>>3. Downloaded hdf5-1.8.9 source via ftp.  I just put it in the CarpetHDF5
>>directory.  Did a make and make installŠ.
>>    "HDF5 Directory" is then .../hdf5-1.8.9/hdf5/ (see below)
>>4. Made sure "Remote Login" is enabled under "Sharing" in "System
>>Preferences".  Visit uses this.
>>    Went ahead and did a "ssh localhost" just to make sure. I was
>>actually
>>prompted to confirm an address because I'm on LSU's network right now.
>>    (Presumably Visit needs a clean login with no pesky questions or
>>password prompts.)
>>5. Created symbolic links in /usr/lib to whichever MPI libraries I
>>planned
>>to use.
>>   Older versions of OS X had native MPI support, and this is hard coded
>>in the binary you get from the visit site.
>>    I use OpenMPI and MacPorts, so I went to /usr/lib and did "sudo ln -s
>>/opt/local/lib/libmpi* ."
>>6. Deleted my ~/.visit directory entirely.  This may not be necessary.
>>7. Went in the CarpetHDF5 and ran ./install and Šbasically just did what
>>was in the readme, that is:
>>  in the xmledit window, clicked on "Cmake" and then updated the flags,
>>as
>>in
>>
>>   CXXFLAGS =
>>-I/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/include
>>-I/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/include
>>   LDFLAGS =
>>-L/Applications/VisIt.app/Contents/Resources/2.4.2/darwin-x86_64/lib
>>-L/Users/shawley/apps/VizTools/CarpetHDF5/hdf5-1.8.9/hdf5/lib
>>  Saved and closed the window, let it do its thing...
>>8. Ran visit from the command line, using the -noconfig option.   The
>>latest version of Visit has a problem with "localhost" on Mac, for some
>>reason.
>>so
>>visit -noconfig
>>
>>..and then visit came up, I opened a .h5 file and was able to do all the
>>usual things with it!
>>
>>Good luck!
>>-Scott
>>
>>
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>
>