Triton Resource Software Packages

Usage Examples

BEAST

Usage

/opt/beast/bin/beast

BEAST, Bayesian Evolutionary Analysis Sampling Trees, is a cross-platform package for evolutionary inference from molecular sequences. It uses the Markov Chain Monte Carlo (MCMC) inference framework, and is oriented toward both strict and relaxed molecular clock analyses. Uses and features include:

• Evolutionary Hypothesis Testing
• Phylogenetics Construction
• Linux/UNIX, Mac OS X, and Windows support
• Java 1.5+ runtime environment
• XML input format
• NEXUS-to-XML file conversion utility

In addition to its Home Page [External], where the software can be downloaded, BEAST also has a User Docs [External], Tutorials [External], and a Wiki [External].

bbFTP

See a discussion of Triton file transfer options, with emphasis on bbFTP, including syntax and examples, on the File & Data Transfer page.

Bowtie

Usage

/opt/biotools/bowtie/bin/bowtie

Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. It aligns 35-base-pair reads to the human genome at a rate of 25 million reads per hour on a typical workstation. Multiple processors can be used simultaneously to achieve greater alignment speed. Bowtie runs on the command line under Windows, Mac OS X, Linux, and Solaris.

Bowtie works best when aligning short reads to large genomes, though it supports arbitrarily small reference sequences (e.g. amplicons) and reads as long as 1024 bases. Bowtie is designed to be extremely fast for sets of short reads where (a) many of the reads have at least one good, valid alignment, (b) many of the reads are relatively high-quality, and (c) the number of alignments reported per read is small (close to 1).

Burrows-Wheeler Aligner (BWA)

Usage

/opt/biotools/bwa/bin/bwa

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates.

Cilk

Usage

/opt/cilk/bin

Cilk is a language for multithreaded parallel programming, based on ANSI C. It is designed for general-purpose parallel programming, but is especially effective for exploiting dynamic, highly asynchronous parallelism. The philosophy behind Cilk is that a programmer should concentrate on structuring programs to expose parallelism and exploit locality. Its algorithmic runtime system handles load balancing, synchronization, communication protocols, scheduling efficiency, and guarantees efficient and predictable performance.

CP2K

Usage

/opt/cp2k/bin

CP2K is a Fortran 95 program used to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a framework for a variety of methods including density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.

CPMD (Car Parrinello Molecular Dynamics)

Usage

/opt/cpmd/bin

The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.

DDT

Usage

/opt/ddt/bin/ddt

For a brief description of debugging on Triton, please read the DDT FAQ section. For more details on using DDT on Triton, see the DDT page.

GAMESS

Usage

Intel:

/opt/gamess/rungms gamess_input 00 num_procs > output_file

Genome Analysis Toolkit (GATK)

Usage

java -jar /opt/biotools/GenomeAnalysisTK/GenomeAnalysisTK.jar --help

The GATK is both a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy and a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.

IDL

Benefits of IDL

IDL is the ideal timesaving computing environment for data analysis, visualization, and application development. IDL requires less code and programming expertise to produce dynamic visualizations and analyses. And, since IDL is based on the Eclipse framework, it truly is a cross-platform solution.

IDL provides their own Product Help System.

Interactive Python (IPython)

Usage

/opt/scipy/bin/ipython

The IPython architecture for parallel and distributed computing abstracts out parallelism in a very general way, enabling it to support many different styles of parallelism:

• Single program, multiple data (SPMD) parallelism
• Multiple program, multiple data (MPMD) parallelism
• Message passing using MPI
• Task farming
• Data parallel
• Combinations of these approaches
• Custom user defined approaches

IPython enables all these types of parallel applications to be developed, executed, debugged and monitored interactively. Here is a good parallel computing tutorial.

matplotlib

Usage

–Shell Environment–
module switch pgi intel
–or–
module load intel
–Python script–
import matplotlib

matplotlib is a library for making 2D plots of arrays in Python. Although it has its origins in emulating the MATLAB® [*] graphics commands, it is independent of MATLAB, and can be used in a Pythonic, object oriented way. Although matplotlib is written primarily in pure Python, it makes heavy use of NumPy and other extension code to provide good performance even for large arrays.

MATLAB

MATLAB is a high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numeric computation. Using MATLAB, you can solve technical computing problems faster than with traditional programming languages like C, C++, and Fortran.

The Parallel Computing Toolbox software allows you to offload work from one MATLAB session (the client) to other MATLAB sessions, called workers. You can use multiple workers to take advantage of parallel processing, and use a local worker to keep your MATLAB client session free for interactive work. With MATLAB Distributed Computing Server, you can leverage the speed of clustered processing cores like Triton.

For an example of how to use the MATLAB Parallel Computing Toolkit with Triton, see the MATLAB page. For details on how to use the Parallel Computing Toolkit, see following documentation from The MathWorks:

• Getting Started Guide [launches new window]
• User Guide [external]

NetCDF

Usage Example

module [ load | add ] netcdf

This will put netCDF into your path and add the appropriate environment variables. You will then be able to link the netCDF libraries when compiling C/C++ and Fortran codes.

NWChem

Usage

Intel:

/opt/openmpi/intel/mx/bin/mpirun -np num_procs -machinefile $PBS_NODEFILE /opt/nwchem/bin/nwchem input_file > output_file

PyFITS

Usage Example

import pyfits

PyFITS provides an interface to FITS (Flexible Image Transport System) formatted files in the Python scripting language and PyRAF, the Python-based interface to IRAF. It is useful both for interactive data analysis and for writing analysis scripts in Python using FITS files as either input or output. PyFITS is a development project of the Science Software Branch at the Space Telescope Science Institute. FITS is a portable file standard widely used in the astronomy community to store images and tables.

In addition to the PyFITS website, documentation can also be found at the Python Packages site.

Python

Usage Example

/opt/bin/python

Several versions of Python are available on Triton. In addition to the specialized Python packages such as NumPy, SciPy, PyFITS and iPython, there are at least three installed versions of Python available to users. To configure your environment to specify which of the available Python interpreters will be invoked by default, configuration setup procedures have been provided.

Numerical Python

Usage Example

module switch pgi intel

To use numpy, you must switch from the pgi to the intel module.

pytz

Usage

–Shell Environment–
module switch pgi intel
–or–
module load intel
–Python script–
import pytz

Pytz brings the Olson timezone database into Python. This library allows accurate and cross platform timezone calculations using Python 2.4 or higher. It also solves the issue of ambiguous times at the end of daylight savings, which you can read more about in the Python Library Reference.

Star-P

Usage

Please access the PDF documentation suite located on Triton at /opt/starp-2.8.0/server/doc/Manuals. Star-P clients are typically started from a remote workstation.

TAU

Overview

TAU Performance System® is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java and Python. TAU gathers its information by allowing users to generate instruments based on their code components. It includes a visualization tool that provides graphical displays of all monitored elements. The TAU website and TAU Portal are useful support tools for users.

Modules

Also see local documentation on the Environment Modules page of this site.

Usage Examples

module [ load | unload ] module_name

module [ list | avail ]

module switch module_1 module_2

FFTW (Fastest Fourier Transform in the West)

FFTW is a fast C library for computing the Discrete Fourier Transform in multiple dimensions. It includes complex, real, symmetric, and parallel transforms, and can handle arbitrary array sizes efficiently. FFTW is typically faster than other publicly-available FFT implementations, and is competitive with vendor-tuned libraries. To achieve this performance, FFTW uses novel code-generation and runtime self-optimization techniques (and many other tricks).

PGI Version

• PGI C/C++ Compiler
• PGI Fortran Compiler

Software : FFTW PGI Library
Roll     : fftw_pgi
Location : /opt/fftw/3.2.1/pgi
Include  : /opt/fftw/3.2.1/pgi/include
Lib      : /opt/fftw/3.2.1/pgi/lib

PGI Usage

C interface:

pgcc -o fftw-testc fftw-test.c -I/opt/fftw/3.2.1/pgi/include -L/opt/fftw/3.2.1/pgi/lib -lfftw3

FORTRAN interface:

pgf90 -o fftw-testf fftw-test.f -I/opt/fftw/3.2.1/pgi/include -L/opt/fftw/3.2.1/pgi/lib -lfftw3

Intel Version

• INTEL C/C++ Compiler
• INTEL Fortran Compiler

Software : FFTW Intel Library
Roll     : fftw_intel
Location : /opt/fftw/3.2.1/intel
Include  : /opt/fftw/3.2.1/intel/include
Lib      : /opt/fftw/3.2.1/intel/lib

Intel Usage

C interface:

icc -o fftw-testc fftw-test.c -I/opt/fftw/3.2.1/intel/include -L/opt/fftw/3.2.1/intel/lib -lfftw3

FORTRAN interface:

ifort -o fftw-testf fftw-test.f -I/opt/fftw/3.2.1/intel/include -L/opt/fftw/3.2.1/intel/lib -lfftw3

FPMPI (Fast Profiling library for MPI)

Library Location

/opt/mpich2/pgi/mx/lib/libfpmpi.a

FPMPI is a simple MPI profiling library. It is intended as a first step towards understanding the nature of the communication patterns and potential bottlenecks in existing applications.

Intel Compilers

Also see local documentation on the Compiling Jobs and Compiling Parallel Codes pages of this site.

Usage Examples

All compiler executables are located in /opt/intel/Compiler/11.1/072/bin/intel64

C usage:

icpc [c_file or c++_file]

C++ usage:

icc [c_file or c++_file]

Fortran77 usage:

ifort [fortran_file]

Fortran90 usage:

ifort [fortran90_file]

PGI Compilers

Also see local documentation on the Compiling Jobs and Compiling Parallel Codes pages of this site.

Usage Examples

All compiler executables are located in /opt/pgi/linux86-64/10.5/bin

C usage:

pgcc [c_file]

C++ usage:

pgCC [c++_file]

Fortran77 usage:

pgf77 [fortran_file]

Fortran90 usage:

pgf90 [fortran90_file]

R Statistical and Graphics Environment

R is installed on the compute nodes of Triton. It can be run from an interactive session with the command /opt/R/bin/R. You can get an interactive session via qsub -I (or qsub -I -q small if you only need one processor).