SDSC "vmd" roll

Overview

This roll bundles the Visual Molecular Dynamics package. For more information about the package, please visit the official web page.

NOTE: Starting with version 1.9.4 vmd uses Python 3.x in order to use the latest numpy which requires the use of Python 3.x.

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 vmd 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 MPI rolls are available, but it will build without them as long as the environment variables they provide are otherwise defined.

The build process requires cmake and the NETCDF and HDF5 libraries and assumes that the modulefiles provided by the SDSC cmake-roll, netcdf-roll and hdf-roll are available. It will build without the modulefiles as long as the environment variables they provide are otherwise defined.

Building

To build the vmd-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 vmd-*.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. with installation.

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

make ROLLCOMPILER=intel ROLLMPI=mvapich2_ib ROLLPY=opt-python 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, and any python modulefile name for the ROLLPY variable. The default values are "gnu", "rocks-openmpi", and "python".

Installation

To install, execute these instructions on a Rocks frontend:

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

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

% rocks run roll vmd 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 vmd environment module files in:

/opt/modulefiles/applications/vmd

Testing

The vmd-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/vmd.t