Compile of plumed 2.1.2 with gcc and mpi rather than mpicc

[Ben Cossins]

Dear Plumed users,

I am trying to produce a openmpi version of plumed 2.1.2 but i don not have access to a functional mpicc wrapper. I have gcc-4.7 and openmpi-1.4.4 and I provide all the mpi headers and libraries through CPPFLAGS.

The configure script detects openmpi except for the MPI_Init test and does not enable __PLUMED_MPI.

Is there a way for me to produce a mpi enabled plumed?

Many thanks

Ben Cossins

[Giovanni Bussi]

Hi,

you should specify a proper mpi compiler with CXX=yourmpicxx.

If the configure script cannot compile a program containing "MPI_Init" that for sure indicates that it is trying to use a compiler not supporting MPI. Perhaps you have to supply the proper value also to LDFLAGS. Can you try to compiler yourself a short test MPI program?

Giovanni

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[Ben Cossins]

Hi,

Thanks for such a rapid reply.

I have used this combination of gcc-4.7 and openmpi to compile quite a bit of MD software using MPI, so I think it can work.

I have also tried placing the "-D__PLUMED_MPI" flag in CPPFLAGS but this did not help.

Is it the case that I need to use mpicxx and cannot just provide gcc/g++ and the required libraries and headers?

Sorry to be so difficult,

Thanks

Ben

[Ben Cossins]

Hi,

Maybe it helps if I post the configure call I am using:-

./configure --prefix=/home/model/MD-SOFTWARE/plumed-2.1.2-install CXX=g++ CC=gcc CPPFLAGS="-I/usr/lib64/mpi/gcc/openmpi/include" LDFLAGS="-L/usr/lib64/mpi/gcc/openmpi/lib64 -D__PLUMED_MPI"

Thanks again

ben

[Giovanni Bussi]

I think it should be fine to use a compiler named "g++" plus libraries and correct include path. My suggestion is to make a double check with a short MPI program (I guess you can find an example with google) and understand which flags are missing.

Giovanni

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[Ben Cossins]

Hi,

So I needed to give the "-lmpi" flag. I guess maybe this is provided automatically when i have compiled other mpi codes like this which may have confused me.

Thanks for you help

Ben

[Ben Cossins]

Dear all,

Sorry but i have another problem compiling with mpi.

I am now configuring with the following:-

./configure --prefix=/home/model/MD-SOFTWARE/plumed-2.1.2-install CXX=g++ CC=gcc CPPFLAGS="-I/usr/lib64/mpi/gcc/openmpi/include" LDFLAGS="-lmpi_cxx -lmpi -L/usr/lib64/mpi/gcc/openmpi/lib64 -Wl,-rpath,/usr/lib64/mpi/gcc/openmpi/lib64"

When I compile it dies at the following point when starting on plumed-runtime:-

g++  ../main/main.o ../wrapper/Plumed.o -o plumed-runtime -ldl
../main/main.o: In function `main':
main.cpp:(.text+0x43): undefined reference to `MPI_Init'
main.cpp:(.text+0xac): undefined reference to `ompi_mpi_comm_world'
main.cpp:(.text+0xb1): undefined reference to `MPI_Comm_dup'
main.cpp:(.text+0xf3): undefined reference to `MPI_Finalize'
../main/main.o: In function `MPI::Intercomm::Clone() const':
main.cpp:(.text._ZNK3MPI9Intercomm5CloneEv[_ZNK3MPI9Intercomm5CloneEv]+0xe): undefined reference to `MPI_Comm_dup'
../main/main.o: In function `MPI::Win::Set_name(char const*)':
main.cpp:(.text._ZN3MPI3Win8Set_nameEPKc[_ZN3MPI3Win8Set_nameEPKc]+0x9): undefined reference to `MPI_Win_set_name'
../main/main.o: In function `MPI::Win::Set_attr(int, void const*)':
main.cpp:(.text._ZN3MPI3Win8Set_attrEiPKv[_ZN3MPI3Win8Set_attrEiPKv]+0x9): undefined reference to `MPI_Win_set_attr'
../main/main.o: In function `MPI::Win::Get_name(char*, int&) const':
main.cpp:(.text._ZNK3MPI3Win8Get_nameEPcRi[_ZNK3MPI3Win8Get_nameEPcRi]+0x9): undefined reference to `MPI_Win_get_name'
../main/main.o: In function `MPI::Win::Delete_attr(int)':
main.cpp:(.text._ZN3MPI3Win11Delete_attrEi[_ZN3MPI3Win11Delete_attrEi]+0x9): undefined reference to `MPI_Win_delete_attr'
../main/main.o: In function `MPI::Win::Call_errhandler(int) const':
main.cpp:(.text._ZNK3MPI3Win15Call_errhandlerEi[_ZNK3MPI3Win15Call_errhandlerEi]+0x9): undefined reference to `MPI_Win_call_errhandler'

I cannot work out what i need to change.

I do seem to have a functional plumed-patch binary which gives.

Any advise would be gratefully received.

Thanks

Ben

[Giovanni Bussi]

Hi, don't worry everything should work correctly.

We compile three executables:

plumed

plumed-runtime

plumed-shared

plumed is the one that you actually use to do driver, sum_hills, etc.

The other two are basically there to check if an md patched with --runtime or --shared would work correctly. The reason why it complained is that the linker is not using the correct flags.

I think this should be fixed setting

./configure STATIC_LIBS="-L/path/to/mpi/lib -lmpi" etc...

Anyway, it should be harmless.

Giovanni

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[Ben Cossins]

Thanks, it is now compiling fine.