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/ >
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