Ok, I deactivated mpich and have run simfactory/bin/sim build --optionlist=osx-macports.cfg >build2.log 2>&1 and get similar errors. I have pasted the contents of build2.log to http://pastebin.com/kcua0vKQ. It does not seem that the deactivation of mpich had the desired effect.
Thanks. Comer On Wed, May 20, 2015 at 12:24 PM, Comer Duncan <[email protected]> wrote: > Erik, > > Thanks. I think I had mpich first and then added openmpi. I will > deactivate mpich-default. The question is do I need to > run simfactory/bin/sim build --optionlist=osx-macports.cfg >build.log 2>&1 > with build2.log instead of build.log so I get a new log file? Will it do > just what is necessary relative to openmpi libs or do the whole business > from scratch? > > Comer > > On Wed, May 20, 2015 at 12:13 PM, Erik Schnetter <[email protected]> > wrote: > >> 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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