SDSC "chemistry" roll

Overview

This roll bundles a collection of chemistry packages: APBS, CP2K, GROMACS, LAMMPS,and NAMD.

For more information about the various packages included in the chemistry roll please visit their official web pages:

• APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation.
• CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems.
• GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
• LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
• NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Requirements

To build/install this roll you must have root access to a Rocks development machine (e.g., a frontend or development appliance).

If your Rocks development machine does not have Internet access you must download the appropriate chemistry source file(s) using a machine that does have Internet access and copy them into the src/<package> directories on your Rocks development machine.

Dependencies

The sdsc-roll must be installed on the build machine, since the build process depends on make include files provided by that roll.

The roll sources assume that modulefiles provided by SDSC compiler, python, and cmake rolls are available, but it will build without them as long as the environment variables they provide are otherwise defined.

The build process requires the MKL, fftw, and cuda libraries and assumes that the modulefiles provided by the corresponding SDSC rolls are available. It will build without the modulefiles as long as the environment variables they provide are otherwise defined.

Building

To build the chemistry-roll, execute this on a Rocks development machine (e.g., a frontend or development appliance):

% make 2>&1 | tee build.log

A successful build will create the file chemistry-*.disk1.iso. If you built the roll on a Rocks frontend, proceed to the installation step. If you built the roll on a Rocks development appliance, you need to copy the roll to your Rocks frontend before continuing with installation.

This roll source supports building with different compilers and for different MPI flavors. The ROLLCOMPILER and ROLLMPI make variables can be used to specify the names of compiler and MPI modulefiles to use for building the software, e.g.,

make ROLLCOMPILER=intel ROLLMPI=mvapich2_ib 2>&1 | tee build.log

The build process recognizes "gnu", "intel" or "pgi" as the value for the ROLLCOMPILER variable; any MPI modulefile name may be used as the value of the ROLLMPI variable. The default values are "gnu" and "rocks-openmpi".

The ROLLOPTS variable has options for "avx" and "avx2" architectures and a "cuda" option for gpu support. gpu support is available for cp2k, gromacs, lammps and namd.

For example, if a build for the "avx2" architecture is chosen along with the default cuda version:

make ROLLCOMPILER=intel ROLLMPI=mvapich2_ib ROLLOPTS='avx2 cuda' 2>&1 | tee build.log

If another version of cuda is needed, the cuda version is specified as follows:

make ROLLCOMPILER=intel ROLLMPI=mvapich2_ib ROLLOPTS='avx2 cuda=cuda/8.0' 2>&1 | tee build.log

The lammps cuda build requires specification of the cuda capability (CC) of the gpu hardware that the roll will be deployed on. You can specify this by including "cudacapabilities=value[,value...]" in the ROLLOPTS variable, e.g.,

make ROLLCOMPILER=intel ROLLMPI=mvapich2_ib ROLLOPTS='cuda cudacapabilties=37,60' 2>&1 | tee build.log

In this case 2 gpu enabled lammps executables, along with a lammps cpu executable, will be compiled. A "lammps.cuda" script is available that at run time selects the correct gpu executable.

In order to find the cuda capability of a node, run the "deviceQuery" executable provided in the src/lammps directory on a gpu node. In order to extract the cuda capability, run:

deviceQuery 2>&1 | grep 'CUDA Capability' |uniq |awk  '{print $6}'|sed 's/\.//

NOTE: Because of limitations of the system gfortran, the cp2k package in the chemistry-roll cannot be built successfully with ROLLMPI=rocks-openmpi under a Rocksv6 install. For "vanilla" chemistry-roll builds, it is recommended to build and install the SDSC mpi-roll first, then build the chemistry-roll with ROLLMPI=openmpi_eth.

Installation

To install, execute these instructions on a Rocks frontend:

% rocks add roll *.iso
% rocks enable roll chemistry
% cd /export/rocks/install
% rocks create distro

Subsequent installs of compute and login nodes will then include the contents of the chemistry-roll. To avoid cluttering the cluster frontend with unused software, the chemistry-roll is configured to install only on compute and login nodes. To force installation on your frontend, run this command after adding the chemistry-roll to your distro

% rocks run roll chemistry host=NAME | bash

where NAME is the DNS name of a compute or login node in your cluster.

In addition to the software itself, the roll installs package environment module files in:

/opt/modulefiles/applications/{apbs,cp2k,gromacs,lammps,namd}

Testing

The chemistry-roll includes a test script which can be run to verify proper installation of the roll documentation, binaries and module files. To run the test scripts execute the following command(s):

% /root/rolltests/chemistry.t