Hello,
I reinstalled openmpi on Mac OSX because of a broken dyld link, I was able to configure cactus, but at the end of compilation I get: ndefined symbols for architecture x86_64: "MPI::Win::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Win in libthorn_Carpet.a(helpers.cc.o) vtable for MPI::Win in libthorn_Carpet.a(ScheduleWrapper.cc.o) vtable for MPI::Win in libthorn_CarpetIOHDF5.a(CarpetIOHDF5.cc.o) vtable for MPI::Win in libthorn_CarpetInterp.a(interp.cc.o) vtable for MPI::Win in libthorn_CarpetInterp2.a(interp2.cc.o) vtable for MPI::Win in libthorn_CarpetRegrid.a(regrid.cc.o) vtable for MPI::Win in libthorn_CarpetRegrid2.a(regrid.cc.o) ... ld: symbol(s) not found for architecture x86_64 collect2: ld returned 1 exit status
I think this is an easy fix, but I don't remember what do I have to do?
My MPI related config log is: Setting MPI to 'OpenMPI' Setting OPENMPI_DIR to '/usr/local' Setting MPI_LIBS to 'mpi' ........................................ Configuring with MPI OpenMPI selected Using " /usr/local/include/openmpi/" as OpenMPI include path Using no explicit OpenMPI library path
thanks, Maria
On 22 May 2012, at 21:05, Babiuc-Hamilton, Maria wrote:
Hello,
I reinstalled openmpi on Mac OSX because of a broken dyld link, I was able to configure cactus, but at the end of compilation I get:
Hi Maria,
In Mac OS, there is an OpenMPI installed by default as part of the operating system. You could also install from Fink or MacPorts, or you could install a tarball or DMG manually. Since you have set OPENMPI_DIR to /usr/local, I assume you have done the latter?
ndefined symbols for architecture x86_64: "MPI::Win::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Win in libthorn_Carpet.a(helpers.cc.o) vtable for MPI::Win in libthorn_Carpet.a(ScheduleWrapper.cc.o) vtable for MPI::Win in libthorn_CarpetIOHDF5.a(CarpetIOHDF5.cc.o) vtable for MPI::Win in libthorn_CarpetInterp.a(interp.cc.o) vtable for MPI::Win in libthorn_CarpetInterp2.a(interp2.cc.o) vtable for MPI::Win in libthorn_CarpetRegrid.a(regrid.cc.o) vtable for MPI::Win in libthorn_CarpetRegrid2.a(regrid.cc.o) ... ld: symbol(s) not found for architecture x86_64 collect2: ld returned 1 exit status
I think this is an easy fix, but I don't remember what do I have to do?
Was this a fresh build after reinstalling OpenMPI?
My MPI related config log is: Setting MPI to 'OpenMPI' Setting OPENMPI_DIR to '/usr/local' Setting MPI_LIBS to 'mpi' ........................................ Configuring with MPI OpenMPI selected Using " /usr/local/include/openmpi/" as OpenMPI include path Using no explicit OpenMPI library path
I get (using the system installed version of OpenMPI on Snow Leopard):
Setting MPI to 'OpenMPI' Setting MPI_LIBS to 'mpi' ... Configuring with MPI OpenMPI selected OpenMPI selected but no OPENMPI_DIR set. Checking some places... Using "/usr/include/openmpi" as OpenMPI include path Using no explicit OpenMPI library path
I notice in Barry's Lion optionlist he uses MacPorts for OpenMPI, whereas in Snow Leopard we both use the system version. It might be that the system version doesn't work for us in Lion.
Which version of OS X are you using?
On May 23, 2012 3:20 AM, "Ian Hinder" ian.hinder@aei.mpg.de wrote:
I notice in Barry's Lion optionlist he uses MacPorts for OpenMPI, whereas
in Snow Leopard we both use the system version. It might be that the system version doesn't work for us in Lion.
I think the problem was that OpenMPI isn't included in OSX as of Lion.
Barry
Hi,
I fixed the problem. Yes, the config file for Snow-Leopard uses ithe system's own mpi from /usr/include. On one laptop, this was fine, but on the other one, after I linked the libraries, it got messed up. Panicked, I did some hacking in /usr/local, /usr/bin and /usr/include of which I am not proud, but now it works! I might have not needed to do this, but I wanted to clean any residue of openmpi that was there.
Barry, wow, I'm succesfully using your lion configuration on the Snow Leopard!
Bernard, it is safe to use the lion configuration on the Snow Leopard, after you do the macport installs specified in the header, and this will greatly simply your problem with VisIt.
Thanks, Maria
From: Barry Wardell <barry.wardell@gmail.commailto:barry.wardell@gmail.com> Date: Wednesday, May 23, 2012 10:35 AM To: Ian Hinder <ian.hinder@aei.mpg.demailto:ian.hinder@aei.mpg.de> Cc: "users@einsteintoolkit.orgmailto:users@einsteintoolkit.org" <users@einsteintoolkit.orgmailto:users@einsteintoolkit.org>, Maria Babiuc <babiuc@marshall.edumailto:babiuc@marshall.edu> Subject: Re: [Users] MPI problem on Mac OS X
On May 23, 2012 3:20 AM, "Ian Hinder" <ian.hinder@aei.mpg.demailto:ian.hinder@aei.mpg.de> wrote:
I notice in Barry's Lion optionlist he uses MacPorts for OpenMPI, whereas in Snow Leopard we both use the system version. It might be that the system version doesn't work for us in Lion.
I think the problem was that OpenMPI isn't included in OSX as of Lion.
Barry
users@lists.einsteintoolkit.org
-
Babiuc-Hamilton, Maria -
Barry Wardell -
Ian Hinder