[Users] failed build on local mac osx yosemite
Comer Duncan
comer.duncan at gmail.com
Wed May 20 11:35:18 CDT 2015
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 <comer.duncan at gmail.com>
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 <schnetter at cct.lsu.edu>
> 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 <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
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Users mailing list
>>>>> Users at einsteintoolkit.org
>>>>> http://lists.einsteintoolkit.org/mailman/listinfo/users
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> 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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