Benchmarking: AMBER 12

Requirements

1. Cuda 5.0
2. Intel Compilers

Software

Amber12 (amber12.tgz) is available on 10.0.0.220 @ software/hpc/nvidia_gpu
Copy it over to the install location and untar it

tar zxf amber12.tgz
cd amber12

Build Environment

module load intel/compilers/13.0.1

export AMBERHOME=`pwd`

export CXX=icpc
export FC=ifort
export F90=ifort
export CC=icc

Build

Serial Version

./configure -noX11 intel
make install
.
.
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Installation of pmemd.amoeba complete
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Installation of Amber12 (serial) is complete

Single GPU Version

export CUDA_HOME=/shared/apps/cuda/cuda-5.0
./configure -noX11 -cuda intel
make install

Multi GPU Version

module load mvapich2/1.8.1-intel-compilers
./configure -noX11 -cuda -mpi intel
make install