Comer I would have only one MPI implementation active. I assume you had mpich active, and then added openmpi when you followed our instructions. You can try to deactivate mpich: "sudo port deactivate mpich-default". Alternatively, you can deactivate openmpi. After this, you would need to configure and build from scratch.
-erik On Wed, May 20, 2015 at 12:04 PM, Comer Duncan <[email protected]> wrote: > Hi Erik, > > Here is what I find: > > ComerMacProRetina:Cactus comerduncan$ /opt/local/bin/mpiCC -showme > /usr/bin/clang -I/opt/local/include/openmpi-mp -Wl,-flat_namespace > -L/opt/local/lib/openmpi-mp -lmpi > ComerMacProRetina:Cactus comerduncan$ port installed | grep mpi > mpi-doc @3.1.3_0 > mpi-doc @3.1.4_0 (active) > mpi_select @0.0_3 (active) > mpich-default @3.1.3_0+gcc49 > mpich-default @3.1.4_0+gcc49 (active) > openmpi @1.7.5_3 (active) > openmpi-default @1.7.5_3+gcc47 (active) > petsc @3.5.3_1+accelerate+hwloc+mpich > petsc @3.5.3_1+accelerate+hwloc+openmpi (active) > > Any recommendations for changes? > > Thanks. > > Comer > > On Wed, May 20, 2015 at 9:26 AM, Erik Schnetter <[email protected]> > wrote: > >> Comer >> >> Maybe you have two different MPI implementations installed. What is the >> output of "/opt/local/bin/mpiCC -showme"? What is the output of "port >> installed | grep mpi"? >> >> -erik >> >> On Wed, May 20, 2015 at 9:20 AM, Comer Duncan <[email protected]> >> wrote: >> >>> Hi Ian, >>> >>> I did make sure that all ports mentioned in the osx-macports.cfg file >>> were done before attempting a build. I've followed your suggestion on >>> rebuilding and have pasted the build log to http://pastebin.com/ka7c3QT5 >>> >>> >>> Thanks for your help. >>> >>> Comer >>> >>> >>> On Tue, May 19, 2015 at 6:27 PM, Ian Hinder <[email protected]> >>> wrote: >>> >>>> >>>> On 19 May 2015, at 21:03, Comer Duncan <[email protected]> wrote: >>>> >>>> I have tried to build the new release on my local macbook. I am running >>>> Yosemite and am using the optionlist for macports. Here is the part of the >>>> make which chokes: >>>> . >>>> . >>>> . >>>> Undefined symbols for architecture x86_64: >>>> "MPI::Win::Free()", referenced from: >>>> vtable for MPI::Win in libthorn_PeriodicCarpet.a(periodic.cc.o) >>>> vtable for MPI::Win in libthorn_Carpet.a(helpers.cc.o) >>>> vtable for MPI::Win in >>>> libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o) >>>> vtable for MPI::Win in libthorn_CarpetIOASCII.a(ioascii.cc.o) >>>> vtable for MPI::Win in libthorn_CarpetIOBasic.a(iobasic.cc.o) >>>> vtable for MPI::Win in libthorn_CarpetIOHDF5.a(Input.cc.o) >>>> vtable for MPI::Win in libthorn_CarpetIOHDF5.a(CarpetIOHDF5.cc.o) >>>> ... >>>> "MPI::Comm::Comm()", referenced from: >>>> MPI::Intercomm::Merge(bool) const in >>>> libthorn_PeriodicCarpet.a(periodic.cc.o) >>>> MPI::Intracomm::Split(int, int) const in >>>> libthorn_PeriodicCarpet.a(periodic.cc.o) >>>> MPI::Intracomm::Create(MPI::Group const&) const in >>>> libthorn_PeriodicCarpet.a(periodic.cc.o) >>>> MPI::Graphcomm::Clone() const in >>>> libthorn_PeriodicCarpet.a(periodic.cc.o) >>>> MPI::Cartcomm::Clone() const in >>>> libthorn_PeriodicCarpet.a(periodic.cc.o) >>>> MPI::Intracomm::Clone() const in >>>> libthorn_PeriodicCarpet.a(periodic.cc.o) >>>> MPI::Intracomm::Create_graph(int, int const*, int const*, bool) >>>> const in libthorn_PeriodicCarpet.a(periodic.cc.o) >>>> ... >>>> "MPI::Datatype::Free()", referenced from: >>>> vtable for MPI::Datatype in >>>> libthorn_PeriodicCarpet.a(periodic.cc.o) >>>> vtable for MPI::Datatype in libthorn_Carpet.a(helpers.cc.o) >>>> vtable for MPI::Datatype in >>>> libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o) >>>> vtable for MPI::Datatype in libthorn_CarpetIOASCII.a(ioascii.cc.o) >>>> vtable for MPI::Datatype in libthorn_CarpetIOBasic.a(iobasic.cc.o) >>>> vtable for MPI::Datatype in libthorn_CarpetIOHDF5.a(Input.cc.o) >>>> vtable for MPI::Datatype in >>>> libthorn_CarpetIOHDF5.a(CarpetIOHDF5.cc.o) >>>> ... >>>> "_ompi_mpi_cxx_op_intercept", referenced from: >>>> MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype >>>> const&), bool) in libthorn_PeriodicCarpet.a(periodic.cc.o) >>>> MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype >>>> const&), bool) in libthorn_Carpet.a(helpers.cc.o) >>>> MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype >>>> const&), bool) in libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o) >>>> MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype >>>> const&), bool) in libthorn_CarpetIOASCII.a(ioascii.cc.o) >>>> MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype >>>> const&), bool) in libthorn_CarpetIOBasic.a(iobasic.cc.o) >>>> MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype >>>> const&), bool) in libthorn_CarpetIOHDF5.a(Input.cc.o) >>>> MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype >>>> const&), bool) in libthorn_CarpetIOHDF5.a(CarpetIOHDF5.cc.o) >>>> ... >>>> ld: symbol(s) not found for architecture x86_64 >>>> collect2: error: ld returned 1 exit status >>>> make[1]: *** [/Users/comerduncan/Cactus/exe/cactus_sim] Error 1 >>>> make: *** [sim] Error 2 >>>> >>>> Here is the build I did: >>>> >>>> simfactory/bin/sim build >>>> --optionlist=/Users/comerduncan/Cactus/simfactory/mdb/optionlists/osx-macports.cfg >>>> >>>> Can you please help me figure out what went wrong? >>>> >>>> >>>> Hi Comer, >>>> >>>> My guess would be that there might be more than one version of MPI >>>> installed, or something in the MPI configuration script didn't work quite >>>> right. Did you install all the ports recommended in the comment in the >>>> os-macports.cfg optionlist? Can you post the output from the full build? >>>> I suggest to remove the configuration >>>> >>>> rm -rf configs/sim >>>> >>>> and then build, keeping all output: >>>> >>>> simfactory/bin/sim build --optionlist=osx-macports.cfg >build.log 2>&1 >>>> >>>> You could then copy and paste build.log into http://pastebin.com and >>>> include the link in your reply (to avoid having a large attachment on the >>>> mailing list). >>>> >>>> -- >>>> Ian Hinder >>>> http://members.aei.mpg.de/ianhin >>>> >>>> >>> >>> _______________________________________________ >>> Users mailing list >>> [email protected] >>> http://lists.einsteintoolkit.org/mailman/listinfo/users >>> >>> >> >> >> -- >> Erik Schnetter <[email protected]> >> http://www.perimeterinstitute.ca/personal/eschnetter/ >> > > -- Erik Schnetter <[email protected]> http://www.perimeterinstitute.ca/personal/eschnetter/
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