.. hightlight:: rst

NAMD Roll

NAMD - Scalable Molecular Dynamics This roll is based on triton's chemistry roll with modifications to enable cuda.

Contents

• NAMD Roll
  • Introduction
  • Downloads
  • Building the roll
  • Installing
  • What is installed

Introduction

This roll installs NAMD tools. There are 2 flavors compiled for each compiler (gnu, intel):

cuda mpi
non-cuda mpi

Downloads

NAMD is a licensed software. Follow a download link info:

NAMD - http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1257
fftw - http://www.fftw.org/download.html
tcl  - http://sourceforge.net/projects/tcl/files/Tcl/8.6.3/tcl8.6.3-src.tar.gz

Building the roll

Dependencies

• The mpi roll must be installed on the build/install host. depends on mpi libraries.
• The intel roll must be installed on the build/install host. In the absence of intel compiler the roll should be buld with ROLLCOMPILER='gnu'.
• The cuda roll must be installed on build/install host . In the absence of cuda, the roll should be build with ROLLCUDA="nocuda"
• The roll sources assumes that modulefiles provided by intel, cuda and mpi rolls are available.

The roll uses openmpi compiled with intel and gnu compilers for eth fabric. ROLLCOMPILER, ROLLNETWORK and ROLLMPI variables are set in Makefile. The build process currently supports one or more of the values for the variables:

ROLLCOMPILER: gnu, intel (default gnu)
ROLLMPI     : openmpi (default openmpi)
ROLLNETWORK : eth (default)
ROLLCUDA    : nocuda (default)

To make a roll and create executable for cuda/non-cuda for intel and gnu compielrs run:

# make ROLLCOMPILER="gnu intel" ROLLMPI=openmpi ROLLNETWORK=eth ROLLCUDA="cuda nocuda" 2>&1 | tee build.log

A successful build will create the file namd-*.disk1.iso.

Installing

To install, execute these instructions on a Rocks frontend:

# rocks add roll *.iso
# rocks enable roll namd
# (cd /export/rocks/install; rocks create distro)
# rocks run roll namd | bash

The installation of cuda-enabled RPMS will be done only on the nodes that have cuda installed and the node attribute cuda is set. The attribute is set during installtion of cuda roll with:

# rocks set host attr compute-X-Y cuda true

What is installed

The roll installs namd and environment module files in:

/opt/namd<VERSION>/gnu - compiled with GNU
/opt/namd<VERSION>/intel - compiled with Intel compilers
/opt/namd2.10/examples - example SGE submit scripts
/opt/namd2.10/tiny - example input for NAMD run
/opt/modulefiles/applications/namd<VERSION> - environment modules
/root/rolltests/namd.t  - roll installation test

Testing

A test script namd.t can be run to verify proper installation of the roll binaries and module files. To run the test scripts execute the following command(s):

# /root/rolltests/amber.t