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

Tue May 22 14:57:16 CDT 2012

Maria,
   No there are only a few libopen-rte files you can unlink if you want.

I noticed that these errors are coming from /usr/local/lib, which is not a
location I've used.
I put the links in /usr/lib.

On 5/22/12 9:06 AM, "Babiuc-Hamilton, Maria" <babiuc at marshall.edu> wrote:

>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/includ
>>>>e
>>>>-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
>>>
>>>
>>
>>
>>
>
>
>