Install AMBERTOOLS14 with MPI in Ubuntu 14.10 64bit.

Because I saw AMBERTOOLS14 supplied sander for MD simulation. But the default configuration was serial. I am curious if sander.MPI would be available for MPI computing. This means AMBER MD simulation engine sander is free! So I did this test.

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set AMBERHOME and enter the directory.

sudo aptitude install libopenmpi-dev openmpi-bin #install MPI

./configure -mpi -noX11 gnu

make install

source amber.sh

export DO_PARALLEL=’mpirun -np 2′ 

make test

export DO_PARALLEL=’mpirun -np 8′ # my cpu is four cores, eight threadings.

make test

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According to the introduction at http://jswails.wikidot.com/installing-amber14-and-ambertools14, some tests require different numbers of processors. Tests with 2 and 8 threads should get almost every test.

I am glad to see sander.MPI runs parallelly in the test procedure. So guys, enjoy your free AMBER MD simulation.

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