The install script is trying to find the file /usr/lib/libmpi_cxx.dylib, but the file is not there. It's actually in /opt/local/lib.
How does one change this setting?
I've gone through the various tabs in the menu (resulting from running the install script) and I cannot find a place to change this setting. Doing a "grep -r mpi *" in the CarpetHDF5 directory turns up nothing.
I went ahead and did a "sudo ln -s /opt/local/lib/libmpi* /usr/lib". That solved the FIRST problem. Now it's looking for `/usr/lib/libopen-rte.dylib'….
make[2]: *** No rule to make target `/usr/lib/libopen-rte.dylib', needed by `/Users/shawley/.visit/2.4.2/darwin-x86_64/plugins/databases/libECarpetHDF5Database_par.dylib'. Stop. make[1]: *** [CMakeFiles/ECarpetHDF5Database_par.dir/all] Error 2 make: *** [all] Error 2
We need to be able to change the directory it looks in.
Setting LIB_PATHS and/or LD_LIBRARY_PATH has no effect.
Thanks, Scott P.S.- Going back and putting in symbolic links for all the complaining libraries results in a full build! However, when you try to run it in Visit (2.4.2) and load a .h5 file, what you get is….
VisIt was unable to open "/Users/shawley/runs/cactus/bruiser/texmex_test/gxx.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 develop
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/libECarpetHDF5Database_par.dylib'. Stop. make[1]: *** [CMakeFiles/ECarpetHDF5Database_par.dir/all] Error 2 make: *** [all] Error 2 [provision:~/apps/VizTools/CarpetHDF5] shawley% ./install
…And the instructions under "Hint for MacOS-X users" in README.TXT instruct you to ftp to ftp://ftp.hdfgroup.org/HDF5/current/src/
If you do that, you get Permission denied.
% ftp ftp://ftp.hdfgroup.org/HDF5/current/src/ Connected to ftp.hdfgroup.org. 220---------- Welcome to Pure-FTPd [privsep] [TLS] ---------- 220-You are user number 1 of 64 allowed. 220-Local time is now 12:13. Server port: 21. 220-IPv6 connections are also welcome on this server. 220 You will be disconnected after 15 minutes of inactivity. 230 Anonymous user logged in Remote system type is UNIX. Using binary mode to transfer files. 200 TYPE is now 8-bit binary 550 Can't change directory to HDF5: Permission denied 221-Goodbye. You uploaded 0 and downloaded 0 kbytes. 221 Logout.
Ok….
[provision:/tmp] shawley% ftp ftp.hdfgroup.org Connected to ftp.hdfgroup.org. 220---------- Welcome to Pure-FTPd [privsep] [TLS] ---------- 220-You are user number 1 of 64 allowed. 220-Local time is now 12:14. Server port: 21. 220-IPv6 connections are also welcome on this server. 220 You will be disconnected after 15 minutes of inactivity. Name (ftp.hdfgroup.org:shawley): anonymous 230 Anonymous user logged in Remote system type is UNIX. Using binary mode to transfer files. ftp> cd HDF5 550 Can't change directory to HDF5: Permission denied ftp>
From: Scott Hawley <scott.hawley@belmont.edumailto:scott.hawley@belmont.edu> Date: Sat, 14 Apr 2012 09:10:34 -0700 To: "users@einsteintoolkit.orgmailto:users@einsteintoolkit.org" <users@einsteintoolkit.orgmailto:users@einsteintoolkit.org> Subject: [Users] CarpetHDF5 plugin referencing library in wrong spot. How to change?
The install script is trying to find the file /usr/lib/libmpi_cxx.dylib, but the file is not there. It's actually in /opt/local/lib.
How does one change this setting?
I've gone through the various tabs in the menu (resulting from running the install script) and I cannot find a place to change this setting. Doing a "grep -r mpi *" in the CarpetHDF5 directory turns up nothing.
I went ahead and did a "sudo ln -s /opt/local/lib/libmpi* /usr/lib". That solved the FIRST problem. Now it's looking for `/usr/lib/libopen-rte.dylib'….
make[2]: *** No rule to make target `/usr/lib/libopen-rte.dylib', needed by `/Users/shawley/.visit/2.4.2/darwin-x86_64/plugins/databases/libECarpetHDF5Database_par.dylib'. Stop. make[1]: *** [CMakeFiles/ECarpetHDF5Database_par.dir/all] Error 2 make: *** [all] Error 2
We need to be able to change the directory it looks in.
Setting LIB_PATHS and/or LD_LIBRARY_PATH has no effect.
Thanks, Scott P.S.- Going back and putting in symbolic links for all the complaining libraries results in a full build! However, when you try to run it in Visit (2.4.2) and load a .h5 file, what you get is….
VisIt was unable to open "/Users/shawley/runs/cactus/bruiser/texmex_test/gxx.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 develop
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/libECarpetHDF5Database_par.dylib'. Stop. make[1]: *** [CMakeFiles/ECarpetHDF5Database_par.dir/all] Error 2 make: *** [all] Error 2 [provision:~/apps/VizTools/CarpetHDF5] shawley% ./install
On Sat, Apr 14, 2012 at 09:16:38AM -0700, Scott Hawley wrote:
…And the instructions under "Hint for MacOS-X users" in README.TXT instruct you to ftp to ftp://ftp.hdfgroup.org/HDF5/current/src/
If you do that, you get Permission denied.
You might find what you are looking for (I don't know what that is) here:
http://www.hdfgroup.org/HDF5/release/obtain5.html#obtain
Frank
Yea, I got the latest source from the HDF5 website. Just pointing out a place in the instructions that could be updatesŠ
On 4/17/12 8:55 AM, "Frank Loeffler" knarf@cct.lsu.edu wrote:
On Sat, Apr 14, 2012 at 09:16:38AM -0700, Scott Hawley wrote:
ŠAnd the instructions under "Hint for MacOS-X users" in README.TXT instruct you to ftp to ftp://ftp.hdfgroup.org/HDF5/current/src/
If you do that, you get Permission denied.
You might find what you are looking for (I don't know what that is) here:
http://www.hdfgroup.org/HDF5/release/obtain5.html#obtain
Frank
users@lists.einsteintoolkit.org
-
Frank Loeffler -
Scott Hawley