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Argonne Leadership Computing Facility

Amber on Polaris

What is Amber?

Amber is a suite of biomolecular simulation programs. Amber is distributed in two parts: AmberTools24 and Amber24. Please visit the Amber website for additional information on capabilities and licensing.

Using Amber at ALCF

ALCF offers assistance with building binaries and compiling instructions for Amber. For questions, contact us at [email protected].

Building Amber

The following build instructions can be applied to both free and licensed versions of Amber.

  1. Download AmberTools24 and Amber24 from Amber website. Note, they are two separate downloads. Copy the tarballs AmberTools24.tar.bz2 and Amber24.tar.bz2 into a home or project directory (e.g. $HOME/Amber).
$ cd Amber
$ tar -xf AmberTools.tar.bz2
$ tar -xf Amber24.tar.bz2
$ cd amber24_src

  1. Download and install the bzip2 library. Insert the -fPIC into the CFLAGS variable in the Makefile and build with installation to a local directory (e.g. make install PREFIX=$HOME/bzip2).

  2. Download and install the FFTW3 library, extract the tarball, an rename it as fftw. Proceed to build with installation to a local directory (e.g. ./configure --prefix=$HOME/fftw ; make ; make install).

  3. Update user environment to include the newly installed bzip2 and fftw and use the GNU programming environment.

$ export PATH="/PATH-TO/bzip2/lib:$PATH"
$ export PATH="/PATH-TO/bzip2:$PATH"
$ export PATH="/PATH-TO/bzip2/include:$PATH"
$ export PATH="/PATH-TO/fftw:$PATH"
$ export PATH="/PATH-TO/fftw/lib:$PATH"
$ export PATH="/PATH-TO/fftw/include:$PATH"

$ module use /soft/modulefiles
$ module load PrgEnv-gnu/8.5.0
$ module load cudatoolkit-standalone/12.4.0
  1. Proceed with building Amber binaries by first modifying run_cmake and setting the following.
  2. -DMPI=TRUE
  3. -DCUDA=TRUE
  4. -DCOMPILER=MANUAL
  5. -DDISABLE_TOOLS=FEW
  6. -DCMAKE_C_COMPILER=gcc-12
  7. -DCMAKE_CXX_COMPILER=g++-12
  8. -DCMAKE_Fortran_COMPILER=gfortran-12
$ cd build
$ ./run_cmake
$ make install -j 8

All Amber binaries will be installed to the amber24 folder.