you are trying to use an MPI function, but PLUMED has been compiled without MPI support (plumed-2.0-beta and gromacs-4.6.1)

[cand...@gmail.com]

Hello,

I am having trouble compiling gromacs 4.6.1 to work with plumed-2.0-beta and MPI. I wonder if there is a compilation switch somewhere to compile PLUMED 2.0 with MPI other than simply having those libaries available at compile-time?

I can compile successfully and run in serial, but with MPI I always get the following error:

+++ Internal PLUMED error

+++ file Communicator.cpp, line 96

+++ message: you are trying to use an MPI function, but PLUMED has been compiled without MPI support

I compile plumed like this:

module purge

module load intel/13.1.1 openmpi/intel/1.6.4

./configure.sh

make

## Note that lapack is not available on this cluster, so before running make I need to edit configurations/linux.icc and replace:

DYNAMIC_LIBS=-lstdc++ -llapack -lblas

with:

DYNAMIC_LIBS=-lstdc++ -mkl

THen I source sourceme.sh and patch gromacs 4.6.1 source with "plumed patch -p"

Then I compile gromacs in parallel like this:

module purge

module load gcc/4.6.1

module load cmake/2.8.6

module load intel/13.1.1

module load openmpi/intel/1.6.4

export FFTW_LOCATION=/project/p/pomes/cneale/GPC/exe/intel/fftw-3.1.2_centos6computeA/exec

cmake ../source__B/ \

      -DCMAKE_PREFIX_PATH=$FFTW_LOCATION \

      -DCMAKE_INSTALL_PREFIX=$(pwd) \

      -DGMX_X11=OFF \

      -DCMAKE_CXX_COMPILER=mpicxx \

      -DCMAKE_C_COMPILER=mpicc \

      -DGMX_MPI=ON \

      -DGMX_PREFER_STATIC_LIBS=ON

make mdrun

make install-mdrun

And that installation goes fine.

But when I try to run, I get the error noted above. I run like this:

module load intel/13.1.1

module load openmpi/intel/1.6.4

mpirun -np 4 /project/p/pomes/cneale/GPC/exe/intel/gromacs-4.6.1_plumed2.0/exec2/bin/mdrun_mpi -deffnm test -dlb yes -npme -1 -cpt 60 -maxh 0.1 -px test.pull.pos.xvg -pf test.pull.force.xvg -xvg none -plumed plumed.dat 

and I get the error message noted above, namely:

+++ Internal PLUMED error

+++ file Communicator.cpp, line 96

+++ message: you are trying to use an MPI function, but PLUMED has been compiled without MPI support

I also tried to compile gromacs with thread-MPI (=without MPI) and again it worked with -mdrun -nt 1 but not with mpirun -nt 2, for which it gave the same error about PLUMED not being compiled with MPI.

Finally, if I use these patched compilations without the -plumed flag to mdrun, then they work just fine.

Thank you for your assistance.

[Giovanni Bussi]

Hi,

PLUMED (both 1.3 and 2.0) are not compatible with thread-MPI, so you have to use normal MPI for gromacs (as you already guessed).

Then you should also compile PLUMED with MPI. Select the proper configuration file (likely linux.mpi.icc).

Regards,

Giovanni

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[riccard...@gmail.com]

Hi,

I'm having the same problem that you seemed to be able to solve (plumed not being able to run in parallel, though it was compiled with mpi). Did you have to recompile gromacs with normal MPI, or is there any option of mdrun to set? 

Thanks

On Wednesday, May 8, 2013 8:29:09 PM UTC+2, Chris Neale wrote:

Seems so obvious in retrospect. Thanks for the help Giovanni. I got it compiled in parallel.

[Carlo Camilloni]

Hi Riccardo,

you need to 

1) compile plumed with mpi

2) patch gromacs with plumed

3) create a folder where to build gromacs

4) from the folder you can do something like that:

cmake “where gromacs is”  -DGMX_CPU_ACCELERATION=AVX_256  -DCMAKE_INSTALL_PREFIX=“where to install gromacs" -DCMAKE_CXX_COMPILER=/usr/bin/g++ -DCMAKE_C_COMPILER=/usr/bin/gcc -DGMX_MPI=ON -DGMX_FORCE_CXX=ON -i

so the important flag here is :  -DGMX_MPI=ON which will automatically turn ON mpi and turn OFF multithreading.

Best,

Carlo

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[riccard...@gmail.com]

Thanks Carlo!

the option  -DGMX_MPI=ON fixed my problem!

Riccardo