POV-Ray on Biowulf
POV-Ray (Persistence of Vision RAYtracer) is a high-quality tool for creating three-dimensional graphics. Raytraced images are publication-quality and 'photo-realistic', but are computationally expensive so that large images can take many hours to create. POV-Ray images can also require more memory than many desktop machines can handle. To address these concerns, a parallelized version of POV-Ray has been installed on the Biowulf system.
POV-Ray output is limited to only .png, .tga, or .ppm image formats. There are number of programs which can convert images from one format to another available on Helix Systems (e.g., convert, gimp, imagemagick, xnview).
There are multiple versions of POV-Ray available. An easy way of selecting the version is to use modules. To see the versions available, type
module avail povray
To select a version, type
module load povray/[ver]
where [ver] is the version of choice. This will set your $PATH variable.
POV-Ray options and parameters are available by typing 'man povray' at the Biowulf prompt.
1ASY.pov (1.4 MB)
1AG9.pov (8.6 MB)
Running POV-Ray on Biowulf
The current version of POV-Ray is multithreaded, and can run on any of the nodes in the biowulf cluster. Ideally, all cores on the node should be utilized for the fastest job completion.
Create a qsub script file (runpovray) after downloading the example input files:#!/bin/bash #PBS -N PovRay cd $PBS_O_WORKDIR module load povray povray +H1125 +W858 -I1AG9.pov -O1AG9.pov.tga +P +X +A +FT +C +wt8 povray +H2170 +W1826 -I1ASY.pov -O1ASY.pov.tga +P +A +FT +wt8
Submit the job to the batch queue by typing:[biowulf]$ qsub -l nodes=1:c16 runpovray
The +wtN option sets the number of threads to use. Because the script was submitted to a 8-core node (16 hyperthreads), N is set to 8.
Many programs can produce POV-Ray input files of molecular structures; here are some examples:
Use RasMol to display your molecule, then export a Povray file.
VMD can display molecules and export Povray input files.
Swiss-PDBViewer can produce Povray input files.