[Users] failed build on local mac osx yosemite

Wed May 20 11:04:40 CDT 2015

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 at 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 at 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 at aei.mpg.de>
>> wrote:
>>
>>>
>>> On 19 May 2015, at 21:03, Comer Duncan <comer.duncan at 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).
>>>
>>> --
>>> Ian Hinder
>>> http://members.aei.mpg.de/ianhin
>>>
>>>
>>
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>>
>
>
> --
> Erik Schnetter <schnetter at cct.lsu.edu>
> http://www.perimeterinstitute.ca/personal/eschnetter/
>
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