[Users] failed build on local mac osx yosemite

Wed May 20 11:13:20 CDT 2015

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 at 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 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/
>>
>
>

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