Compilation puzzle ?

[Shozeb Haider]

Hello all,

I am trying to patch plumed 2.0.1 with gromacs-4.6.7.

Plumed compiles on its own fine and so goes gromacs in the MPI mode.

Now when I patch plumed using plumed patch -p and recompile gromacs with -DGMX_MPI=on I get the following error message. 

Linking CXX executable mdrun_mpi

/usr/local/plumed-2.1.0/src/analysis/Analysis.o: In function `MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)':

Analysis.cpp:(.text._ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb[MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)]+0x21): undefined reference to `ompi_mpi_cxx_op_intercept'

/usr/local/plumed-2.1.0/src/analysis/Analysis.o: In function `MPI::Graphcomm::Clone() const':

Analysis.cpp:(.text._ZNK3MPI9Graphcomm5CloneEv[MPI::Graphcomm::Clone() const]+0x23): undefined reference to `MPI::Comm::Comm()'

/usr/local/plumed-2.1.0/src/analysis/Analysis.o: In function `MPI::Intracomm::Clone() const':

Analysis.cpp:(.text._ZNK3MPI9Intracomm5CloneEv[MPI::Intracomm::Clone() const]+0x27): undefined reference to `MPI::Comm::Comm()'

/usr/local/plumed-2.1.0/src/analysis/Analysis.o: In function `MPI::Intracomm::Create_cart(int, int const*, bool const*, bool) const':

Analysis.cpp:(.text._ZNK3MPI9Intracomm11Create_cartEiPKiPKbb[MPI::Intracomm::Create_cart(int, int const*, bool const*, bool) const]+0x8e): undefined reference to `MPI::Comm::Comm()'

/usr/local/plumed-2.1.0/src/analysis/Analysis.o: In function `MPI::Intracomm::Create_graph(int, int const*, int const*, bool) const':

Analysis.cpp:(.text._ZNK3MPI9Intracomm12Create_graphEiPKiS2_b[MPI::Intracomm::Create_graph(int, int const*, int const*, bool) const]+0x26): undefined reference to `MPI::Comm::Comm()'

/usr/local/plumed-2.1.0/src/analysis/Analysis.o: In function `MPI::Cartcomm::Sub(bool const*) const':

Analysis.cpp:(.text._ZNK3MPI8Cartcomm3SubEPKb[MPI::Cartcomm::Sub(bool const*) const]+0x74): undefined reference to `MPI::Comm::Comm()'

/usr/local/plumed-2.1.0/src/analysis/Analysis.o:Analysis.cpp:(.text._ZNK3MPI8Cartcomm5CloneEv[MPI::Cartcomm::Clone() const]+0x23): more undefined references to `MPI::Comm::Comm()' follow

/usr/local/plumed-2.1.0/src/analysis/Analysis.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'

/usr/local/plumed-2.1.0/src/analysis/Analysis.o:(.data.rel.ro._ZTVN3MPI3WinE[vtable for MPI::Win]+0x48): undefined reference to `MPI::Win::Free()'

collect2: ld returned 1 exit status

make[2]: *** [src/kernel/mdrun_mpi] Error 1

make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2

make: *** [all] Error 2

Any advise would be much appreciated.

Best wishes

Shozeb

[Giovanni Bussi]

Hi Shozeb,

have a look at this thread:

https://groups.google.com/d/msgid/plumed-users/CAB1aw3zbdV_qyxZaLM9NH%2BBcUtu7%2BRYE2fEjZ0QX051%3D0SDWsQ%40mail.gmail.com?utm_medium=email&utm_source=footer

There are a few suggestions that might be useful.

Giovanni

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