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MPI version for Mac OS X? (Read 2114 times)

Jeremy YaBB Newbies Offline Feed your monkey! Posts: 3	MPI version for Mac OS X? Oct 9^th, 2008 at 9:15am Hello I am wondering whether there is an MPI version for the Mac. I downloaded the UNIX version to compile but no success. Thanks!
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: MPI version for Mac OS X? Reply #1 - Oct 9^th, 2008 at 3:06pm Dear Jeremy, You need to make sure you have all the Mac OS X developer tools installed. Also, the default distribution of Mac OS X doesn't usually include MPI libraries, but they can be downloaded for free and installed quite easily (just Google mpich on Mac OS X). Cheers, Sergei
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Jeremy

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Re: MPI version for Mac OS X?
Reply #2 - Oct 9^th, 2008 at 8:07pm

Mac OS X Leopard actually provide openmpi

Thanks I did not know I can directly compile mpich. I installed it from MacPorts but it did not work.

I installed MPICH2 and I got this:

Quote:

Code:

  "_MPI_Type_size", referenced from:
	MPI::Datatype::Get_size() constin HYNetInterface.cpp.o
	MPI::Datatype::Get_size() constin baseobj.cpp.o
	MPI::Datatype::Get_size() constin batchlan.cpp.o
	MPI::Datatype::Get_size() constin batchlan2.cpp.o
	MPI::Datatype::Get_size() constin bgm.cpp.o
	MPI::Datatype::Get_size() constin calcnode.cpp.o
	MPI::Datatype::Get_size() constin category.cpp.o
	MPI::Datatype::Get_size() constin hyphyunixutils.cpp.o
	MPI::Datatype::Get_size() constin likefunc.cpp.o
	MPI::Datatype::Get_size() constin main-unix.cxx.o
	MPI::Datatype::Get_size() constin matrix.cpp.o
	MPI::Datatype::Get_size() constin nexus.cpp.o
	MPI::Datatype::Get_size() constin parser.cpp.o
	MPI::Datatype::Get_size() constin parser2.cpp.o
	MPI::Datatype::Get_size() constin scfg.cpp.o
	MPI::Datatype::Get_size() constin site.cpp.o
	MPI::Datatype::Get_size() constin strings.cpp.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
Finished

Then I uninstalled it and installed MPICH2 and I got this:

Code:

Undefined symbols:
  "_PMPI_Keyval_create", referenced from:
	_MPIR_Topology_init in libmpich.a(topo_util.o)
  "_PMPI_Bcast", referenced from:
	_MPIR_Context_alloc in libmpich.a(context_util.o)
  "_PMPI_Sendrecv", referenced from:
	_MPIR_Context_alloc in libmpich.a(context_util.o)
  "_PMPI_Keyval_free", referenced from:
	_MPIR_Topology_finalize in libmpich.a(topo_util.o)
  "_PMPI_Allreduce", referenced from:
	_MPIR_Context_alloc in libmpich.a(context_util.o)
	_MPIR_Context_alloc in libmpich.a(context_util.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
Finished

Is there a specific version of MPICH required? Thanks!!!! Embarrassed

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Jeremy YaBB Newbies Offline Feed your monkey! Posts: 3	Re: MPI version for Mac OS X? Reply #3 - Oct 9^th, 2008 at 10:10pm I got it fixed. I modified build.sh and use mpicc mpi++ already in Leopard. And also specify -I/path/to/10.5/SDK/mpi.h It is now running GARD.bf But HyPhy seems to be much harder to use than I expected... I am totally no programmer.. And 010010 for HKY85? How about other models?
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Re: MPI version for Mac OS X?
Reply #4 - Oct 10^th, 2008 at 3:30am

Dear Jeremy,

Glad you got the program running. Sorry it's not as user friendly as I would like it to be, but we don't get scientific (or career-advancing) credit for writing documentation, so it is usually put on a backburner.

Model specification strings are discussed at some length (along with other handy HyPhy usage tips) in Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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