ABAQUS

ABAQUSsuite of engineering analysis software packages is used to simulate the physical response of structures and solid bodies to load, temperature, contact,impact, and other environmental conditions.

Version History

• 2013/12/14 ABAQUS 6.9-1 • 2013/11/29 ABAQUS 6.12-1 How to Use

ABAQUS is a commercial licensed software. Please contact HPC admin to learn the details.

F.11.4. LAMMPS

LAMMPSstands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grain systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the mesoscale or continuum levels.

Version History

• 2014/11/27 LAMMPS 30Oct14 • 2014/01/07 LAMMPS 5Nov10 • 2013/12/03 LAMMPS 1DEC13 How to Use

To use LAMMPS, add one of the following modules in the job script.

module load lammps/30Oct14 module load lammps/1Dec13 module load lammps/5Nov10

Job Script Example

An example job script is shown as below and can be found in /hpc/tmp/examples/lammps/1Dec13/crack #!/bin/bash #PBS -l nodes=1:ppn=16 #PBS -l cput=30:00:00 #PBS -j eo #PBS -e test.err #PBS -N lmk.job #======================================================#

# USER CONFIG

#======================================================# # Input file name

INPUT_FILE=in.crack

# Output file name

OUTPUT_FILE=test.log # Module name MODULE_NAME=lammps/1Dec13 # Program name PROGRAM_NAME=lmp #======================================================# # MODULE is loaded #======================================================# NP=‘wc -l < $PBS_NODEFILE‘ source /etc/profile.d/modules.sh module load $MODULE_NAME

cat $PBS_NODEFILE

#======================================================# # PROGRAM is executed with the output or log file

# direct to the working directory

#======================================================#

cd $PBS_O_WORKDIR

mpirun -np $NP $PROGRAM_NAME < $INPUT_FILE >& $OUTPUT_FILE

#======================================================# # ALL DONE

#======================================================#

For more details on using LAMMPS, please read it’sonline tutorials.

F.11.5. Materials Studio

Materials Studiois a comprehensive materials modeling and simulation application designed for scientists in chemicals and materials R&D as well as pharmaceuticals development. At present, we have 3 modules installed on the cluster: amorphouscell, discover and compass.

Version History

• 2013/12/10 Materials Studio 7.0 How to Use

Materials Studio is a commercial licensed software. Please contactHPC adminto get the access to it.

F.12. Biology

F.12.1. ATSAS

ATSASis a program suite for small-angle scattering data analysis from biological macromolecules. Version History

How to Use

To use ATSAS, add one of the following modules in the job script.

module load atsas/2.5.1-1

For more details on using ATSAS, please read itsonline manual.

F.12.2. MrBayes

MrBayesis a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes’s theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. Since version 3.2, MrBayes prints all parameter values of all chains (cold and heated) to a checkpoint file every Checkfreq generations, by default every 100,000 generations. The checkpoint file has the suffix .ckp. If you run an analysis and it is stopped prematurely, you can restart it from the last checkpoint by using mcmc append=yes.MrBayes will start the new analysis from the checkpoint; it will even read in all the old trees and include them in the convergence diagnostics. At the end of the new run, you will have parameter and tree files that are indistinguishable from those you would have obtained from an uninterrupted analysis. Our data set is so small, however, that we are likely to get an adequate sample from the posterior before the first checkpoint is reached.

Version History

• 2013/10/24 Mrbayes 3.2.2 How to Use

To use Mrbayes, add one of the following modules in the job script.

module load mrbayes/3.2.2

Job Script Example

An example job script is shown as below and can be found in /hpc/tmp/examples/mrbayes/3.2.2 #!/bin/sh #PBS -N mrbayes #PBS -l cput=01:00:00 #PBS -l mem=1GB #PBS -j eo #PBS -e test.err #PBS -m abe #PBS -l nodes=1:ppn=8 #======================================================# # USER CONFIG #======================================================# # Input file name

INPUT_FILE=hymfossil.nex

# Output file name

OUTPUT_FILE=hymfossil.log # Module name MODULE_NAME=mrbayes/3.2.2 # Program name PROGRAM_NAME=mb #======================================================# # MODULE is loaded #======================================================# NP=‘wc -l < $PBS_NODEFILE‘ source /etc/profile.d/modules.sh module load $MODULE_NAME

cat $PBS_NODEFILE

#======================================================# # PROGRAM is executed with the output or log file

# direct to the working directory

#======================================================#

cd $PBS_O_WORKDIR

mpirun -np $NP $PROGRAM_NAME $INPUT_FILE >& $OUTPUT_FILE

#======================================================# # ALL DONE

#======================================================#

For more details on using Mrbayes, please read it’sonline manual.

F.12.3. PartitionFinder

PartitionFinder is free open source software to select best-fit partitioning schemes and models of molecular evolution for phylogenetic analyses. Most of the lab’s coding output currently goes into PartitionFinder.

Version History

• 2014/05/20 PartitionFinder 1.1.1 How to Use

To use PartitionFinder, add the following modules in the job script.

module load partitionfinder/1.1.1

Job Script Example

An example job script is shown as below and can be found under

/hpc/tmp/examples/partitionfinder/1.1.1/nucleotide. #!/bin/sh #PBS -N job #PBS -l nodes=1:ppn=4 #PBS -l cput=10:00:00 #PBS -j eo #PBS -e job.std.out #PBS -m abe #======================================================# # USER CONFIG #======================================================#

INPUT_DIR="/hpc/tmp/examples/partitionfinder/1.1.1/nucleotide" OUTPUT_FILE="logfile"

MODULE_NAME="partitionfinder/1.1.1" PROGRAM_NAME="PartitionFinder.py"

#Option: see program manual for additional flags. #FLAGS="--raxml" #======================================================# # MODULE is loaded #======================================================# NP=‘wc -l < $PBS_NODEFILE‘ source /etc/profile.d/modules.sh module load $MODULE_NAME

cat $PBS_NODEFILE

#======================================================# # PROGRAM is executed with the output or log file

# direct to the working directory

#======================================================#

cd $PBS_O_WORKDIR

# Run a system wide sequential application

$PROGRAM_NAME -p $NP $FLAGS $INPUT_DIR >& $OUTPUT_FILE

#======================================================# # ALL DONE

#======================================================#

Another example of running PartitionFinderProtein.py can be found under /hpc/tmp/examples/partitionfinder/1.1.1/aminoacid

To run your own job, please specify the input directory (absolute path) and output files in the line of ‘INPUT DIR’ and ‘OUTPUT FILE’. Only two programs available for the ‘PROGRAM NAME’ line, i.e.

• PartitionFinder.py

• PartitionFinderProtein.py

You could also add additional flags like ‘--raxml’ in the ‘FLAGS’ line and remove the heading ‘#’. Please check the program manual for other flags you can use.

For more details on using PartitionFinder, please read theonline documents.

F.12.4. QIIME

QIIME(canonically pronounced ”chime”) stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). QIIME takes users from their raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has been applied to studies based on billions of sequences from thousands of samples.

Version History

• 2014/05/05 QIIME 1.8.0 • 2013/11/13 QIIME 1.7.0

How to Use

To use Mrbayes, add one of the following modules in the job script.

module load qiime/1.7.0

or

module load qiime/1.8.0