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 <comer.duncan@gmail.com> 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 <schnetter@cct.lsu.edu> 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 <comer.duncan@gmail.com> 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 <ian.hinder@aei.mpg.de> wrote:

On 19 May 2015, at 21:03, Comer Duncan <comer.duncan@gmail.com> 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).




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Erik Schnetter <schnetter@cct.lsu.edu>
http://www.perimeterinstitute.ca/personal/eschnetter/