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Error when compiling HYPHYMPI (Read 1868 times)
Javier Forment
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Error when compiling HYPHYMPI
Sep 15th, 2010 at 2:04am
 
Hi,

When compiling HYPHYMPI with 'bash build.sh MPI' from the HYPHY folder (created when running 'bash buildFromSVN.sh' without errors), I've got the following error:

obj_MPI/baseobj.cpp.o: In function `GlobalShutdown()':
baseobj.cpp:(.text+0x833): undefined reference to `ompi_mpi_comm_world'
baseobj.cpp:(.text+0x9c8): undefined reference to `SEEK_END'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Set_name(char const*)':
baseobj.cpp:(.text._ZN3MPI8Datatype8Set_nameEPKc[MPI:Cheesyatatype::Set_name(char const*)]+0x5): undefined reference to `MPI_Type_set_name'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Set_attr(int, void const*)':
baseobj.cpp:(.text._ZN3MPI8Datatype8Set_attrEiPKv[MPI:Cheesyatatype::Set_attr(int, void const*)]+0x5): undefined reference to `MPI_Type_set_attr'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Get_name(char*, int&) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype8Get_nameEPcRi[MPI:Cheesyatatype::Get_name(char*, int&) const]+0x5): undefined reference to `MPI_Type_get_name'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Get_attr(int, void*) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype8Get_attrEiPv[MPI:Cheesyatatype::Get_attr(int, void*) const]+0xe): undefined reference to `MPI_Type_get_attr'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype:Cheesyelete_attr(int)':
baseobj.cpp:(.text._ZN3MPI8Datatype11Delete_attrEi[MPI:Cheesyatatype:Cheesyelete_attr(int)]+0x5): undefined reference to `MPI_Type_delete_attr'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Get_true_extent(long&, long&) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype15Get_true_extentERlS1_[MPI:Cheesyatatype::Get_t
rue_extent(long&, long&) const]+0x5): undefined reference to `MPI_Type_get_true_extent'
obj_MPI/baseobj.cpp.o: In function `MPI:Cheesyatatype::Get_extent(long&, long&) const':
baseobj.cpp:(.text._ZNK3MPI8Datatype10Get_extentERlS1_[MPI:Cheesyatatype::Get_extent(long&, long&) const]+0x5): undefined reference to `MPI_Type_get_extent'
obj_MPI/baseobj.cpp.o: In function `MPI::Grequest::Complete()':
baseobj.cpp:(.text._ZN3MPI8Grequest8CompleteEv[MPI::Grequest::Complete()]+0x5): undefined reference to `MPI_Grequest_complete'
obj_MPI/baseobj.cpp.o: In function `MPI::Request::Get_status() const':
baseobj.cpp:(.text._ZNK3MPI7Request10Get_statusEv[MPI::Request::Get_status() const]+0x10): undefined reference to `MPI_Request_get_status'
obj_MPI/baseobj.cpp.o: In function `MPI::Request::Get_status(MPI::Status&) const':
baseobj.cpp:(.text._ZNK3MPI7Request10Get_statusERNS_6StatusE[MPI::Request::Get_status(MPI::Status&) const]+0x1d): undefined reference to `MPI_Request_get_status'
obj_MPI/baseobj.cpp.o: In function `MPI::Comm:Cheesyisconnect()':
baseobj.cpp:(.text._ZN3MPI4Comm10DisconnectEv[MPI::Comm:Cheesyisconnect()]+0x5): undefined reference to `MPI_Comm_disconnect'
obj_MPI/baseobj.cpp.o: In function `MPI:Shockedp::Init(void (*)(void const*, void*, int, MPI:Cheesyatatype const&), bool)':
baseobj.cpp:(.text._ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb[MPI:Shockedp::Init(void

(*)(void const*, void*, int, MPI:Cheesyatatype const&), bool)]+0x19): undefined reference to `ompi_mpi_cxx_op_intercept'
baseobj.cpp:(.text._ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb[MPI:Shockedp::Init(void

(*)(void const*, void*, int, MPI:Cheesyatatype const&), bool)]+0x3e): undefined reference to `ompi_op_set_cxx_callback'
(... error follows with many lines)

Any help?

Cheers and thanks in advance,

Javier.
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Sergei
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Re: Error when compiling HYPHYMPI
Reply #1 - Sep 15th, 2010 at 7:15am
 
HI Javier,

Looks like the linker is not including the MPI libraries. Can you post the entire output of the build script?

Sergei
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