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

Tue May 22 09:06:36 CDT 2012

Scott,

Yes, I did. The error I am getting now when configuring Cactus is: 
dyld: Symbol not found: _orte_ess
  Referenced from: /usr/local/lib/libmpi.0.dylib
  Expected in: /usr/local/lib/libopen-rte.0.dylib
 in /usr/local/lib/libmpi.0.dylib

Looking on the web, it seems that other Apple users had this problem when trying to link libraries. 
I'm afraid that I made this mess when I linked libopen-rte*? 
Is there a clean and quick fix, or I need to reinstall my whole operating system? :O

Please help!
Maria

________________________________________
From: Scott Hawley [scott.hawley at belmont.edu]
Sent: Monday, May 21, 2012 4:05 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

You compiled the CarpetHDF plugin like I said, and are running visit with
-noconfig?

On 5/21/12 3:03 PM, "Babiuc-Hamilton, Maria" <babiuc at marshall.edu> wrote:

>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
>>>
>>>
>>>_______________________________________________
>>>Users mailing list
>>>Users at einsteintoolkit.org
>>>http://lists.einsteintoolkit.org/mailman/listinfo/users
>>
>>
>
>
>