Installation of AMBER

Step 1: Setting Environment Variable

what package/library you need for compile AMBER is GNU compiler, FFTW, MPI or OpenMPI, and CUDA (only for using GPU)

export AMBERHOME=$HOME/amber

export CUDA_HOME=$CRAY_CUDATOOLKIT_DIR

export CRAYPE_LINK_TYPE=dynamic

export CRAY_ADD_RPATH=yes

Then you are supposed ready to compile AMBER. Below are different commands which would compile AMBER as your desired runtime version.

Step 2: Compile AMBER

# Compile AMBER as serial CPU version

make clean

./configure -nomtkpp -crayxt5 -noX11 --with-python $PYTHON --with-netcdf $NETCDF_DIR gnu

make install

# Compile AMBER as parallel CPU version

make clean

./configure -nomtkpp -crayxt5 -noX11 --with-python $PYTHON --with-netcdf $NETCDF_DIR -mpi gnu

make install

# Compile AMBER as serial GPU version

make clean

find . -name "*.a" -exec rm {} \; find . -name "*.so" -exec rm {} \; find . -name "*.so.*" -exec rm {} \; find . -name netcdf.mod -exec rm {} \; export PYTHON=`which python`

./configure -nomtkpp -crayxt5 -noX11 --with-python $PYTHON --with-netcdf $NETCDF_DIR -cuda gnu

make install

# Compile AMBER as parallel GPU version

make clean

./configure -nomtkpp -crayxt5 -noX11 --with-python $PYTHON --with-netcdf $NETCDF_DIR -cuda -mpi gnu

make install

The AMBER executable file is at $AMBERHOME/bin directory.

Step 3: Test AMBER

cd $AMBERHOME/test/ubiquitine

$AMBERHOME/bin/sander.MPI -O -i mdin -p prmtop -c inpcrd -o job.out

Rangsiman Ketkaew