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Subject: Re: [OMPI users] open-mpi on Mac OS 10.9 (Mavericks)
From: Meredith, Karl (karl.meredith_at_[hidden])
Date: 2013-11-27 13:55:23


So, I decided to try out your configuration flags to see if that’d work. All Apple tools, no macports.

With openmpi-1.7.3 I did the following:

make clean
./configure --prefix=/opt/trunk/apple-only --enable-shared --disable-static --enable-debug --disable-io-romio --enable-contrib-no-build=vt,libtrace --enable-mpirun-prefix-by-default
make
make install

export PATH=/opt/trunk/apple-only/bin/:$PATH
export LD_LIBRARY_PATH=/opt/trunk/apple-only/lib/:$LD_LIBRARY_PATH
export DYLD_LIBRARY_PATH=/opt/trunk/apple-only/lib/:$DYLD_LIBRARY_PATH

bash-4.2$ echo $PATH
/opt/trunk/apple-only/bin/:/usr/bin:/bin:/usr/sbin:/sbin
bash-4.2$ echo $LD_LIBRARY_PATH
/opt/trunk/apple-only/lib/:
bash-4.2$ echo $DYLD_LIBRARY_PATH
/opt/trunk/apple-only/lib/:

cd /Users/meredithk/tools/openmpi-1.7.3-src/examples
bash-4.2$ make clean
rm -f hello_c hello_cxx hello_mpifh hello_usempi hello_usempif08 Hello.class ring_c ring_cxx ring_mpifh ring_usempi ring_usempif08 Ring.class connectivity_c *~ *.o
bash-4.2$ make
mpicc -g hello_c.c -o hello_c
mpicc -g ring_c.c -o ring_c
mpicc -g connectivity_c.c -o connectivity_c
mpic++ -g hello_cxx.cc -o hello_cxx
mpic++ -g ring_cxx.cc -o ring_cxx

bash-4.2$ mpirun -np 2 ./hello_c
(No output, program stalls.)

Is your version of clang the same as mine? Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)

Are you using openmpi-1.7.3?

Karl

On Nov 27, 2013, at 1:26 PM, George Bosilca <bosilca_at_[hidden]> wrote:

> Puzzling! I removed my entire Mac Ports installation in order to fall back to the default set of tools provided by Apple via the command tool package. I recompile a fresh copy of Open MPI with the following configure:
>
> ./configure —prefix=/opt/trunk/apple-only —enable-shared —disable-static --enable-debug --disable-io-romio --enable-contrib-no-build=vt,libtrace --enable-mpirun-prefix-by-default
>
> And every test I throw at it passed without any issue. Totally puzzling …
>
> George.
>
>
> On Nov 27, 2013, at 18:04 , Meredith, Karl <karl.meredith_at_[hidden]> wrote:
>
>> None of the C or C++ examples run. For example, the hello_c.c example in the examples directory included with openmpi. It compiles, but hangs on MPI_Init().
>>
>> Are your compiler versions different from the ones I’m showing? Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
>>
>> Karl
>>
>>
>> On Nov 27, 2013, at 11:51 AM, Nathan Hjelm <hjelmn_at_[hidden]> wrote:
>>
>>> Been running on Mavericks all summer with no issues. I do not use the C++ interface
>>> though (C++ bindings were removed from the MPI standard in 3.0.) Can you try a C
>>> example and see if that works?
>>>
>>> -Nathan Hjelm
>>> Application Readiness, HPC-5, LANL
>>>
>>> On Wed, Nov 27, 2013 at 11:43:05AM -0500, Meredith, Karl wrot
>>>> Okay, in order to try and track down this problem I have done a fresh install of OpenMPI-1.7.3 on Mac OS 10.9 (Mavericks). I am using the Apple compilers, and not using anything from macports. The code compiles fine, but when running the examples for openmpi-1.7.3, the code hangs in MPI::Init() and never returns. No error message. No warning. It just hangs. If I compile in debug mode and do a stack trace, it shows that it is stalled inside of MPI::Init() every time. Has anyone been able to successfully get openmpi working on 10.9? If so, what, if anything, are you doing differently?
>>>>
>>>> This is how I installed openmpi:
>>>> ./configure --prefix=$HOME/tools/openmpi-1.7.3
>>>> make
>>>> make install
>>>>
>>>> Here are my settings, environment variables, compilers, etc:
>>>>
>>>> bash-4.2$ which g++
>>>> /usr/bin/g++
>>>>
>>>> bash-4.2$ which gcc
>>>> /usr/bin/gcc
>>>>
>>>> bash-4.2$ which clang
>>>> /usr/bin/clang
>>>>
>>>> bash-4.2$ g++ --version
>>>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
>>>> Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
>>>> Target: x86_64-apple-darwin13.0.0
>>>> Thread model: posix
>>>>
>>>> bash-4.2$ gcc --version
>>>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
>>>> Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
>>>> Target: x86_64-apple-darwin13.0.0
>>>> Thread model: posix
>>>>
>>>> bash-4.2$ which mpicc
>>>> /Users/meredithk/tools/openmpi-1.7.3-noenv/bin/mpicc
>>>>
>>>> bash-4.2$ which mpic++
>>>> /Users/meredithk/tools/openmpi-1.7.3-noenv/bin/mpic++
>>>>
>>>> bash-4.2$ which mpirun
>>>> /Users/meredithk/tools/openmpi-1.7.3-noenv/bin/mpirun
>>>>
>>>> bash-4.2$ mpicc -show
>>>> gcc -I/Users/meredithk/tools/openmpi-1.7.3-noenv/include -L/Users/meredithk/tools/openmpi-1.7.3-noenv/lib -lmpi
>>>>
>>>> bash-4.2$ mpic++ -show
>>>> g++ -I/Users/meredithk/tools/openmpi-1.7.3-noenv/include -L/Users/meredithk/tools/openmpi-1.7.3-noenv/lib -lmpi_cxx -lmpi
>>>>
>>>> bash-4.2$ pwd
>>>> /Users/meredithk/tools/openmpi-1.7.3-src
>>>>
>>>> bash-4.2$ otool -L hello_cxx
>>>> hello_cxx:
>>>> /Users/meredithk/tools/openmpi-1.7.3-noenv/lib/libmpi_cxx.1.dylib (compatibility version 3.0.0, current version 3.3.0)
>>>> /Users/meredithk/tools/openmpi-1.7.3-noenv/lib/libmpi.1.dylib (compatibility version 4.0.0, current version 4.0.0)
>>>> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)
>>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
>>>>
>>>> bash-4.2$ mpirun -n 5 hostname
>>>> meredithk-mac.corp.fmglobal.com<http://meredithk-mac.corp.fmglobal.com>
>>>> meredithk-mac.corp.fmglobal.com<http://meredithk-mac.corp.fmglobal.com>
>>>> meredithk-mac.corp.fmglobal.com<http://meredithk-mac.corp.fmglobal.com>
>>>> meredithk-mac.corp.fmglobal.com<http://meredithk-mac.corp.fmglobal.com>
>>>> meredithk-mac.corp.fmglobal.com<http://meredithk-mac.corp.fmglobal.com>
>>>>
>>>> bash-4.2$ echo $PATH
>>>> /Users/meredithk/tools/openmpi-1.7.3-noenv/bin:/usr/bin:/bin:/usr/sbin:/sbin
>>>>
>>>> bash-4.2$ echo $LD_LIBRARY_PATH
>>>> /Users/meredithk/tools/openmpi-1.7.3-noenv/lib:
>>>>
>>>> bash-4.2$ echo $DYLD_LIBRARY_PATH
>>>> /Users/meredithk/tools/openmpi-1.7.3-noenv/lib:
>>>>
>>>> bash-4.2$ ls /Users/meredithk/tools/openmpi-1.7.3-noenv/lib/
>>>> libmca_common_sm.4.dylib libmpi_cxx.1.dylib libopen-pal.6.dylib libopen-trace-format.1.dylib libotfaux.dylib libvt-mpi-unify.0.dylib libvt-mpi.dylib libvt.0.dylib
>>>> libmca_common_sm.dylib libmpi_cxx.dylib libopen-pal.dylib libopen-trace-format.a libotfaux.la libvt-mpi-unify.a libvt-mpi.la libvt.a
>>>> libmca_common_sm.la libmpi_cxx.la libopen-pal.la libopen-trace-format.dylib libvt-hyb.0.dylib libvt-mpi-unify.dylib libvt-mt.0.dylib libvt.dylib
>>>> libmpi.1.dylib libompitrace.0.dylib libopen-rte.6.dylib libopen-trace-format.la libvt-hyb.a libvt-mpi-unify.la libvt-mt.a libvt.la
>>>> libmpi.dylib libompitrace.dylib libopen-rte.dylib libotfaux.0.dylib libvt-hyb.dylib libvt-mpi.0.dylib libvt-mt.dylib openmpi
>>>> libmpi.la libompitrace.la libopen-rte.la libotfaux.a libvt-hyb.la libvt-mpi.a libvt-mt.la pkgconfig
>>>>
>>>> bash-4.2$ otool -L /Users/meredithk/tools/openmpi-1.7.3-noenv/lib/libmpi_cxx.dylib
>>>> /Users/meredithk/tools/openmpi-1.7.3-noenv/lib/libmpi_cxx.dylib:
>>>> /Users/meredithk/tools/openmpi-1.7.3-noenv/lib/libmpi_cxx.1.dylib (compatibility version 3.0.0, current version 3.3.0)
>>>> /Users/meredithk/tools/openmpi-1.7.3-noenv/lib/libmpi.1.dylib (compatibility version 4.0.0, current version 4.0.0)
>>>> /Users/meredithk/tools/openmpi-1.7.3-noenv/lib/libopen-rte.6.dylib (compatibility version 7.0.0, current version 7.0.0)
>>>> /Users/meredithk/tools/openmpi-1.7.3-noenv/lib/libopen-pal.6.dylib (compatibility version 7.0.0, current version 7.0.0)
>>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
>>>> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)
>>>>
>>>> On Nov 27, 2013, at 9:41 AM, Meredith, Karl <karl.meredith_at_[hidden]<mailto:karl.meredith_at_[hidden]>> wrote:
>>>>
>>>> I’m pretty sure it is using the correct g++
>>>>
>>>> $ )which g++
>>>> /opt/local/bin/g++
>>>>
>>>>
>>>> $ )echo $PATH
>>>> /Users/meredithk/tools/openmpi/bin:/opt/local/bin:/opt/local/sbin:/Users/meredithk/tools/bin:/Users/meredithk/OpenFOAM/fireFoam-2.2.x/scripts:/Users/meredithk/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/gperftools-svn/bin:/Applications/paraview.app/Contents/bin:/Users/meredithk/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/paraview-3.12.0/bin:/Users/meredithk/OpenFOAM/meredithk-2.2.x/platforms/darwinIntel64Gcc46DPOpt/bin:/Users/meredithk/OpenFOAM/site/2.2.x/platforms/darwinIntel64Gcc46DPOpt/bin:/Users/meredithk/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/bin:/Users/meredithk/OpenFOAM/OpenFOAM-2.2.x/bin:/Users/meredithk/OpenFOAM/OpenFOAM-2.2.x/wmake:/Developer/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin
>>>>
>>>>
>>>> $ )g++ --version
>>>> g++ (MacPorts gcc46 4.6.4_3) 4.6.4
>>>>
>>>>
>>>> Karl
>>>>
>>>>
>>>>
>>>> On Nov 27, 2013, at 3:23 AM, Iliev, Hristo <Iliev_at_[hidden]<mailto:Iliev_at_[hidden]><mailto:Iliev_at_[hidden]>> wrote:
>>>>
>>>> Karl,
>>>>
>>>> The Xcode command-line tools provide a g++ command that is effectively
>>>> clang++. Since mpic++ invokes g++ without the full path to it, it might pick
>>>> the wrong g++. Make sure that /opt/local/bin is the first item in your
>>>> $PATH.
>>>>
>>>> Hristo
>>>>
>>>> --
>>>> Hristo Iliev, PhD - High Performance Computing Team / JARA-HPC
>>>> RWTH Aachen University, Center for Computing and Communication
>>>> Rechen- und Kommunikationszentrum der RWTH Aachen
>>>> Seffenter Weg 23, D-52074 Aachen (Germany)
>>>>
>>>> -----Original Message-----
>>>> From: users [mailto:users-bounces_at_[hidden]] On Behalf Of Meredith,
>>>> Karl
>>>> Sent: Tuesday, November 26, 2013 9:33 PM
>>>> To: Open MPI Users
>>>> Subject: Re: [OMPI users] open-mpi on Mac OS 10.9 (Mavericks)
>>>>
>>>> Here are the results of those two commands:
>>>>
>>>> $ )mpic++ -show
>>>> g++ -I/Users/meredithk/tools/openmpi/include -
>>>> L/Users/meredithk/tools/openmpi/lib -lmpi_cxx -lmpi -lm
>>>>
>>>> $ )otool -L /Users/meredithk/tools/openmpi/lib/libmpi_cxx.dylib
>>>> /Users/meredithk/tools/openmpi/lib/libmpi_cxx.dylib:
>>>> /Users/meredithk/tools/openmpi/lib/libmpi_cxx.1.dylib
>>>> (compatibility version 2.0.0, current version 2.2.0)
>>>> /Users/meredithk/tools/openmpi/lib/libmpi.1.dylib (compatibility
>>>> version 2.0.0, current version 2.8.0)
>>>> /opt/local/lib/libgcc/libstdc++.6.dylib (compatibility version
>>>> 7.0.0,
>>>> current version 7.18.0)
>>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
>>>> version
>>>> 1197.1.1)
>>>> /opt/local/lib/libgcc/libgcc_s.1.dylib (compatibility version 1.0.0,
>>>> current version 1.0.0)
>>>>
>>>> It looks like libstdc++ is being used and g++ is being used.
>>>>
>>>> Karl
>>>>
>>>>
>>>> On Nov 25, 2013, at 6:56 PM, Pierre Jolivet <jolivet_at_[hidden]<mailto:jolivet_at_[hidden]><mailto:jolivet_at_[hidden]>>
>>>> wrote:
>>>>
>>>> Karl,
>>>> What does "mpic++ -show" returns ? It is possible that you are
>>>> compiling/linking with "c++", which will defaults to clang++, while you
>>>> compiled OpenMPI with g++.
>>>> Since libstdc++ and libc++ have incompatible ABI, that might be why you
>>>> are getting a wrong behavior.
>>>> Also, it could be worthwhile to have a look at "otool -L
>>>> /Users/meredithk/tools/openmpi/lib/libmpi_cxx.dylib"
>>>> Pierre
>>>>
>>>> On Nov 25, 2013, at 7:38 AM, Meredith, Karl
>>>> <karl.meredith_at_[hidden]<mailto:karl.meredith_at_[hidden]><mailto:karl.meredith_at_[hidden]>> wrote:
>>>>
>>>> I do have DYLD_LIBRARY_PATH set as well, and I get the same problem:
>>>>
>>>> DYLD_LIBRARY_PATH=/Users/meredithk/tools/openmpi/lib
>>>>
>>>> Here's the directory listing of /Users/meredithk/tools/openmpi/lib
>>>>
>>>> $ )ls -1
>>>> libmca_common_sm.3.dylib*
>>>> libmca_common_sm.dylib@
>>>> libmca_common_sm.la*
>>>> libmpi.1.dylib*
>>>> libmpi.dylib@
>>>> libmpi.la*
>>>> libmpi_cxx.1.dylib*
>>>> libmpi_cxx.dylib@
>>>> libmpi_cxx.la*
>>>> libmpi_f77.1.dylib*
>>>> libmpi_f77.dylib@
>>>> libmpi_f77.la*
>>>> libmpi_f90.a
>>>> libmpi_f90.la*
>>>> libompitrace.0.dylib*
>>>> libompitrace.dylib@
>>>> libompitrace.la*
>>>> libopen-pal.4.dylib*
>>>> libopen-pal.dylib@
>>>> libopen-pal.la*
>>>> libopen-rte.4.dylib*
>>>> libopen-rte.dylib@
>>>> libopen-rte.la*
>>>> libopen-trace-format.1.dylib*
>>>> libopen-trace-format.a
>>>> libopen-trace-format.dylib@
>>>> libopen-trace-format.la*
>>>> libotfaux.0.dylib*
>>>> libotfaux.a
>>>> libotfaux.dylib@
>>>> libotfaux.la*
>>>> libvt-hyb.0.dylib*
>>>> libvt-hyb.a
>>>> libvt-hyb.dylib@
>>>> libvt-hyb.la*
>>>> libvt-mpi-unify.0.dylib*
>>>> libvt-mpi-unify.a
>>>> libvt-mpi-unify.dylib@
>>>> libvt-mpi-unify.la*
>>>> libvt-mpi.0.dylib*
>>>> libvt-mpi.a
>>>> libvt-mpi.dylib@
>>>> libvt-mpi.la*
>>>> libvt-mt.0.dylib*
>>>> libvt-mt.a
>>>> libvt-mt.dylib@
>>>> libvt-mt.la*
>>>> libvt-pomp.a
>>>> libvt-pomp.la*
>>>> libvt.0.dylib*
>>>> libvt.a
>>>> libvt.dylib@
>>>> libvt.la*
>>>> mpi.mod*
>>>> openmpi/
>>>> pkgconfig/
>>>>
>>>>
>>>> I don't notice anything out of ordinary.
>>>>
>>>> Karl
>>>>
>>>>
>>>> On Nov 25, 2013, at 8:31 AM, Reuti <reuti_at_[hidden]<mailto:reuti_at_[hidden]><mailto:reuti_at_[hidden]>> wrote:
>>>>
>>>> Am 25.11.2013 um 14:25 schrieb Meredith, Karl:
>>>>
>>>> I do have these two environment variables set:
>>>>
>>>> LD_LIBRARY_PATH=/Users/meredithk/tools/openmpi/lib
>>>>
>>>> On a Mac it should DYLD_LIBRARY_PATH - and there are *.dylib files in
>>>> your /Users/meredithk/tools/openmpi/lib?
>>>>
>>>> -- Reuti
>>>>
>>>>
>>>> PATH=/Users/meredithk/tools/openmpi/bin
>>>>
>>>> Running mpirun seems to work fine with a simple command, like
>>>> hostname:
>>>>
>>>> $ )mpirun -n 2 hostname
>>>> meredithk-mac.corp.fmglobal.com<http://meredithk-mac.corp.fmglobal.com/><http://meredithk-mac.corp.fmglobal.com>>
>>>> meredithk-mac.corp.fmglobal.com<
http://meredithk-mac.corp.fmglobal.com/>
>>>>
>>>> I am trying to run the simple hello_cxx example from the openmpi
>>>> distribution, compiled as such:
>>>> mpic++ -g hello_cxx.cc -o hello_cxx
>>>>
>>>> It compiles fine, without warning or error. However, when I go to
>>>> run
>>>> the example, it stalls on the MPI::Init() command:
>>>> mpirun -np 1 hello_cxx
>>>> It never errors out or crashes. It simply hangs.
>>>>
>>>> I am using the same mpic++ and mpirun version:
>>>> $ )which mpirun
>>>> /Users/meredithk/tools/openmpi/bin/mpirun
>>>>
>>>> $ )which mpic++
>>>> /Users/meredithk/tools/openmpi/bin/mpic++
>>>>
>>>> Not quite sure what else to check.
>>>>
>>>> Karl
>>>>
>>>>
>>>> On Nov 23, 2013, at 5:29 PM, Ralph Castain <rhc_at_[hidden]<mailto:rhc_at_[hidden]><mailto:rhc_at_[hidden]>>
>>>> wrote:
>>>>
>>>> Strange - I run on Mavericks now without problem. Can you run
>>>> "mpirun -n 1 hostname"?
>>>>
>>>> You also might want to check your PATH and LD_LIBRARY_PATH to
>>>> ensure you have the prefix where you installed OMPI 1.6.5 at the front.
>>>> Mac
>>>> distributes a very old version of OMPI with its software and you don't
>>>> want
>>>> to pick it up by mistake.
>>>>
>>>>
>>>> On Nov 22, 2013, at 1:45 PM, Meredith, Karl
>>>> <karl.meredith_at_[hidden]<mailto:karl.meredith_at_[hidden]><mailto:karl.meredith_at_[hidden]>> wrote:
>>>>
>>>> I recently upgraded my 2013 Macbook Pro (Retina display) from 10.8
>>>> to 10.9. I downloaded and installed openmpi-1.6.5 and compiled it with
>>>> gcc
>>>> 4.8 (gcc installed from macports).
>>>> openmpi compiled and installed without error.
>>>>
>>>> However, when I try to run any of the example test cases, the code
>>>> gets stuck inside the first MPI::Init() call and never returns.
>>>>
>>>> Any thoughts on what might be going wrong?
>>>>
>>>> The same install on OS 10.8 works fine and the example test cases
>>>> run without error.
>>>>
>>>> Karl
>>>>
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