AMBER

A. Description

AMBER is a package of molecular simulation programs that stands for Assisted Model Building with Energy Refinement. It represents a set of classical molecula mechanics force fields for the simulation of biomolecules. See AMBER home page http://ambermd.org for additional information.

B. How to obtain AMBER

AMBER is a licensed package. See instructions for obtaining the code.

C. How to build AMBER

Blue Waters does not provide precompiled AMBER binaries. The users are expected to obtain their own copy of the code and install it for the personal use.

C.1 Building CPU and GPU versions under GNU environment

module swap PrgEnv-cray PrgEnv-gnu
module add cray-netcdf
module add fftw
module add bwpy
module add bwpy-mpi
module add cudatoolkit                        # only for Amber16 or newer
module add cudatoolkit/6.5.14-1.0502.9836.8.1 # only for Amber14 GPU
 
export AMBERHOME=$HOME/amber
export CUDA_HOME=$CRAY_CUDATOOLKIT_DIR
 
export CRAYPE_LINK_TYPE=dynamic
export CRAY_ADD_RPATH=yes
 
cd $AMBERHOME
 
# build 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
 
# build parallel GPU version
make clean
./configure -nomtkpp -crayxt5 -noX11 --with-python $PYTHON --with-netcdf $NETCDF_DIR -cuda -mpi gnu
make install
 
# build serial CPU version
make clean
./configure -nomtkpp -crayxt5 -noX11 --with-python $PYTHON --with-netcdf $NETCDF_DIR gnu
make install
 
# build parallel CPU version
make clean
./configure -nomtkpp -crayxt5 -noX11 --with-python $PYTHON --with-netcdf $NETCDF_DIR -mpi gnu
make install
 
Successful compilation will create executables in $AMBERHOME/bin directory, e.g. sander.MPI.
 

D. Sample test

AMBER comes with an extensive suit of tests located in $AMBERHOME/test directory. To make sure that the compiled code works, we will run one of the supplied tests.

cd $AMBERHOME/test/ubiquitine

create run.pbs file having the following content:
 
#!/bin/bash
#PBS -l nodes=2:ppn=32:xe
#PBS -l walltime=00:05:00
#PBS -q debug
cd $PBS_O_WORKDIR
export AMBERHOME=/insert_absolute_path_to_amber14
aprun -n 32 -N 16 -d 2 $AMBERHOME/bin/sander.MPI -O -i mdin -p prmtop -c inpcrd -o job.out
 
Submit the job

qsub run.pbs