ABAQUS is a finite element analysis program owned and supported by SIMULIA, the Dassault Systèmes brand for Realistic Simulation.

Availability and Restrictions

The available programs are ABAQUS/CAE, ABAQUS/Standard and ABAQUS/Explicit. The versions currently available at OSC are:

You can use  module spider abaqus  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access for Academic Users

OSC's ABAQUS license can only be used for educational, institutional, instructional, and/or research purposes. Only users who are faculty, research staff or students at the following institutions are permitted to utilized OSC's license:

• The Ohio State University
• University of Toledo
• University of Cincinnati
• Miami University of Ohio
• Wright State University
• University of Akron

Users from additional degree granting academic institutions may request to be added to this list per a cost by contacting OSC Help.

The use of ABAQUS for academic purposes requires validation. In order to obtain validation, please contact OSC Help for further instruction. 

Access for Commerical Users

Contact OSC Help for getting access to ABAQUS if you are a commercial user.

Usage

Token Usage

ABAQUS software usage is monitored though a token-based license manager. This means very time you run a ABAQUS job, tokens are checked out from our pool for your tasks usage. To ensure your job is only started when its required ABAQUS tokens are available it is important to include a software flag within your job script's PBS directives.  A minimum of 5 tokens are required per a job, so a 1 node, 1 processor ABAQUS job would need the following PBS software flag: #PBS -l software=abaqus+5 . Jobs requiring more cores will need to request more tokens as calculated with the formula: M = int(5 x N^0.422) , where N is the total number of cores.  For common requests, you can refer to the following table:

Usage on Oakley

qsub -I -l nodes=1:ppn=12 -l walltime=1:00:00

#PBS -N knee
#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=1
#PBS -l software=abaqus+5
#PBS -j oe
#
# The following lines set up the ABAQUS environment
#
module load abaqus
#
# Move to the directory where the job was submitted
#
cd $PBS_O_WORKDIR
cp *.inp $TMPDIR
cd $TMPDIR
#
# Run ABAQUS
#
abaqus job=knee_bolster interactive
#
# Now, copy data (or move) back once the simulation has completed
#
cp * $PBS_O_WORKDIR

#PBS -l walltime=1:00:00
#PBS -l nodes=2:ppn=12
#PBS -N my_abaqus_job
#PBS -l software=abaqus+19
#PBS -j oe
#
# The following lines set up the ABAQUS environment
#
module load abaqus
#
# Move to the directory where the job was submitted
#
cd $PBS_O_WORKDIR
cp *.inp $TMPDIR/
cd $TMPDIR
#
# Run ABAQUS, note that in this case we have provided the names of the input files explicitly
#
abaqus job=test input=<my_input_file_name1>.inp cpus=24 interactive
#
# Now, move data back once the simulation has completed
#
mv * $PBS_O_WORKDIR

Usage on Ruby

qsub -I -l nodes=1:ppn=20 -l walltime=1:00:00

#PBS -N knee
#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=20
#PBS -l software=abaqus+17
#PBS -j oe
#
# The following lines set up the ABAQUS environment
#
module load abaqus
#
# Move to the directory where the job was submitted
#
cd $PBS_O_WORKDIR
cp *.inp $TMPDIR
cd $TMPDIR
#
# Run ABAQUS
#
abaqus job=knee_bolster cpus=20 interactive
#
# Now, copy data (or move) back once the simulation has completed
#
cp * $PBS_O_WORKDIR

#PBS -l walltime=1:00:00
#PBS -l nodes=2:ppn=20
#PBS -N my_abaqus_job
#PBS -l software=abaqus+23
#PBS -j oe
#
# The following lines set up the ABAQUS environment
#
module load abaqus
#
# Move to the directory where the job was submitted
#
cd $PBS_O_WORKDIR
cp *.inp $TMPDIR/
cd $TMPDIR
#
# Run ABAQUS, note that in this case we have provided the names of the input files explicitly
#
abaqus job=test input=<my_input_file_name1>.inp cpus=40 interactive
#
# Now, move data back once the simulation has completed
#
mv * $PBS_O_WORKDIR

Usage on Owens

qsub -I -l nodes=1:ppn=28 -l walltime=1:00:00

#PBS -N knee
#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=1
#PBS -l software=abaqus+5
#PBS -j oe
#
# The following lines set up the ABAQUS environment
#
module load abaqus
#
# Move to the directory where the job was submitted
#
cd $PBS_O_WORKDIR
cp *.inp $TMPDIR
cd $TMPDIR
#
# Run ABAQUS
#
abaqus job=knee_bolster interactive
#
# Now, copy data (or move) back once the simulation has completed
#
cp * $PBS_O_WORKDIR

#PBS -l walltime=1:00:00
#PBS -l nodes=2:ppn=28:pfsdir
#PBS -N my_abaqus_job
#PBS -l software=abaqus+27
#PBS -j oe
#
# The following lines set up the ABAQUS environment
#
module load abaqus
#
# Move to the directory where the job was submitted
#
cd $PBS_O_WORKDIR
#
# Cope input files to /fs/scratch and run Abaqus there
#
cp *.inp $PFSDIR
cd $PFSDIR
#
# Run ABAQUS, note that in this case we have provided the names of the input files explicitly
#
abaqus job=test input=<my_input_file_name1>.inp cpus=56 interactive
#
# Now, move data back once the simulation has completed
#
mv * $PBS_O_WORKDIR

Further Reading

See Also

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties.

Availability and Restrictions

The following versions of ABINIT are available on OSC clusters:

You can use  module spider abinit  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

ABINIT is available to all OSC users without restriction.

Usage on Oakley

Further Reading

• The ABINIT Official Webpage

The Assisted Model Building with Energy Refinement (AMBER) package contains many molecular simulation programs targeted at biomolecular systems. A wide variety of modelling techniques are available. It generally scales well on modest numbers of processors, and the GPU enabled CUDA programs are very efficient.

Availability and Restrictions

AMBER is available on Oakley, Ruby, and Owens Clusters. The following versions are currently available at OSC (S means serial executables, P means parallel, C means CUDA, i.e., GPU enabled, and M means MIC, i.e., Xeon Phi enabled):

You can use module spider amber to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access for Academic Users

OSC's Amber is available to not-for-profit OSC users; simply contact OSC Help to request the appropriate form for access.

Access for Commerical Users

For-profit OSC users must obtain their own Amber license. 

Usage on Oakley

tleap

mpiexec pmemd.MPI

pmemd.cuda

qsub -I -l nodes=1:ppn=12 -l walltime=1:00:00

~srb/workshops/compchem/amber/

# AMBER Example Batch Script for the Basic Tutorial in the Amber manual
#PBS -N 6pti
#PBS -l nodes=1:ppn=1
#PBS -l walltime=0:20:00
module load amber
# Use TMPDIR for best performance.
cd $TMPDIR
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cp -p $PBS_O_WORKDIR/6pti.prmtop .
cp -p $PBS_O_WORKDIR/6pti.prmcrd .
# Running minimization for BPTI
cat << eof > min.in
# 200 steps of minimization, generalized Born solvent model
&cntrl
maxcyc=200, imin=1, cut=12.0, igb=1, ntb=0, ntpr=10,
/
eof
sander -i min.in -o 6pti.min1.out -p 6pti.prmtop -c 6pti.prmcrd -r 6pti.min1.xyz
cp -p min.in 6pti.min1.out 6pti.min1.xyz $PBS_O_WORKDIR

Usage on Ruby

tleap

mpiexec pmemd.MPI

pmemd.cuda

qsub -I -l nodes=1:ppn=20 -l walltime=1:00:00

~srb/workshops/compchem/amber/

# AMBER Example Batch Script for the Basic Tutorial in the Amber manual
#PBS -N 6pti
#PBS -l nodes=1:ppn=20
#PBS -l walltime=0:20:00
module load amber
# Use TMPDIR for best performance.
cd $TMPDIR
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cp -p $PBS_O_WORKDIR/6pti.prmtop .
cp -p $PBS_O_WORKDIR/6pti.prmcrd .
# Running minimization for BPTI
cat << eof > min.in
# 200 steps of minimization, generalized Born solvent model
&cntrl
maxcyc=200, imin=1, cut=12.0, igb=1, ntb=0, ntpr=10,
/
eof
sander -i min.in -o 6pti.min1.out -p 6pti.prmtop -c 6pti.prmcrd -r 6pti.min1.xyz
cp -p min.in 6pti.min1.out 6pti.min1.xyz $PBS_O_WORKDIR

Usage on Owens

tleap

mpiexec pmemd.MPI

qsub -I -l nodes=1:ppn=28 -l walltime=1:00:00

~srb/workshops/compchem/amber/

# AMBER Example Batch Script for the Basic Tutorial in the Amber manual
#PBS -N 6pti
#PBS -l nodes=1:ppn=28
#PBS -l walltime=0:20:00
module load amber
# Use TMPDIR for best performance.
cd $TMPDIR
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cp -p $PBS_O_WORKDIR/6pti.prmtop .
cp -p $PBS_O_WORKDIR/6pti.prmcrd .
# Running minimization for BPTI
cat << eof > min.in
# 200 steps of minimization, generalized Born solvent model
&cntrl
maxcyc=200, imin=1, cut=12.0, igb=1, ntb=0, ntpr=10,
/
eof
sander -i min.in -o 6pti.min1.out -p 6pti.prmtop -c 6pti.prmcrd -r 6pti.min1.xyz
cp -p min.in 6pti.min1.out 6pti.min1.xyz $PBS_O_WORKDIR

Further Reading

• Amber Tutorials
• Amber Home Page

ANSYS offers a comprehensive software suite that spans the entire range of physics, providing access to virtually any field of engineering simulation that a design process requires. Supports are provided by ANSYS, Inc. 

Availability and Restrictions

OSC has academic license of structural-fluid dynamics academic products, which offer structural mechanics, explicit dynamics, fluid dynamics and thermal simulation capabilities. These bundles also include ANSYS Workbench, relevant CAD import tools, solid modeling and meshing, and High Performance Computing (HPC) capability. See "Academic Research -> ANSYS Academic Research Mechanical and CFD" in this table for all available products at OSC.

Access for Academic Users

OSC has an "Academic Research " license for ANSYS. This allows for academic use of the software by Ohio faculty and students, with some restrictions. To view current ANSYS node restrictions, please see ANSYS's Terms of Use.

Use of ANSYS products at OSC for academic purposes requires validation. Please contact OSC Help for further instruction.

Access for Commerical Users

Contact OSC Help for getting access to ANSYS if you are a commerical user.

Usage

For more information on how to use each ANSYS product at OSC systems, refer to its documentation page provided at the end of this page.

Note

Due to the way our Fluent and ANSYS modules are configured, simultaneously loading multiple of either module will cause a cryptic error. The most common case of this happening is when multiple of a users jobs are started at the same time and all load the module at once. In order for this error to manifest, the modules have to be loaded at precisely the same time; a rare occurrence, but a probable occurrence over the long term.

If you encounter this error you are not at fault. Please resubmit the failed job(s).

If you frequently submit large amounts of Fluent or ANSYS jobs, we recommend you stagger your job submit times to lower the chances of two jobs starting at the same time, and hence loading the module at the same time. Another solution is to establish job dependencies between jobs, so jobs will only start one after another. To do this, you would add the PBS directive:

#PBS -W after:jobid

To jobs you want to only start after another job has started. You would replace jobid with the job ID of the job to wait for. If you have additional questions, please contact OSC Help.

Further Reading

• ANSYS homepage

See Also

Allinea software analyzes how HPC software runs. It consists of two applications, Allinea Performance Reports and Allinea MAP: 

• Allinea Performance Reports: simple tool to generate a single-page HTML or plain text report that presents overall performance characteristics of HPC applications.
• Allinea MAP: HPC application profiler with easy-to-use GUI environment.

Availability & Restrictions

Versions

The following versions of Allinea are available on OSC clusters:

Access

Allinea Performance Reports and Allinea MAP are available to all OSC users.

Usage

Allinea Performance Reports

Allinea Performance Reports analyzes and documents information on CPU, MPI, I/O, and Memory performance characteristics of HPC software, even third party code, to aid understanding about the overall performance. Although it should not be used all the time, Allinea Performance Reports is recommended to OSC users as a viable option to analyze how an HPC application runs. View an example report to navigate the format of a typical report. For more example reports, visit Characterization of HPC Codes and Problems on Allinea's website.

For usage instructions and more information, read Allinea Performance Reports.

Allinea MAP

Allinea MAP produces a more detailed profile of HPC software. Unlike Allinea Performance Reports, you must have the source code to run Allinea MAP because its analysis details the software line-by-line. For more features and benefits, visit Profiler Features and Benefits on Allinea's website. 

For usage instructions and more information, read Allinea MAP.

Troubleshooting

Using Allinea software with MVAPICH2

This note from Allinea's Getting Started Guide applies to both perf-report and MAP:

Some MPIs, most notably MVAPICH, are not yet supported by Allinea's Express Launch mode
(in which you can just put “perf-report” in front of an existing mpirun/mpiexec line). These can
still be measured using the Compatibility Launch mode.

Instead of this Express Launch command:

perf-report mpiexec <mpi args> <program> <program args> # BAD

Use the compatibility launch version instead:

perf-report -n <num procs> --mpiargs="<mpi args>" <program> <program args>

Further Reading

• Allinea Performance Reports homepage
• Allinea MAP homepage

See Also

HyperWorks is a high-performance, comprehensive toolbox of CAE software for engineering design and simulation.

Availability & Restrictions

HyperWorks is available to all academic clients.

The following version of Altair Hyperworks can be found for the following environments:

Please contact OSC Help to request the appropriate form for access.

Usage

Using HyperWorks through OSC installation

To use HyperWorks on the OSC clusters, first ensure that X11 forwarding is enabled as the HyperWorks workbench is a graphical application. Then, load the hyperworks module:

module load hyperworks

The HyperWorks GUI can be launched then with the following command:

hw

State-wide access for HyperWorks

For information on downloading and installing a local copy through the state-wide license, follow the steps below. 

NOTE: To run Altair HyperWorks, your computer must have access to the internet. The software contacts the license server at OSC to check out a license when it starts and periodically during execution. The amount of data transferred is small, so network connections over modems are acceptable.

Usage of HyperWorks on a local machine using the statewide license will vary from installation to installation.

1. Go to http://www.altairhyperworks.com/ 

2. Click on "Login" in the upper right hand corner of the page. 

3. If you have already registered with the Altair web site, enter the e-mail address that you registered with and your password and skip to step #5.

4. If you have not registered yet, click the link that says "Click here to register now". You will be prompted for some contact information and an e-mail address which will be your unique identifier.

   • IMPORTANT: The e-mail address you give must be from your academic institution. Under the statewide license agreement, registration from Ohio universities is allowed on the Altair web site. Trying to log in with a yahoo or hotmail e-mail account will not work. If you enter your university e-mail and the system will not register you, please contact OSChelp at oschelp@osc.edu.

5. Once you have logged in, click on "SUPPORT" and then "SOFTWARE DOWNLOADS"

6. In addition to downloading the software, download the "Installation Guide and Release Notes" for instructions on how to install the software.

   • IMPORTANT: If you have any questions or problems, please contact OSChelp at oschelp@osc.edu, rather than HyperWorks support. The software agreements outlines that problems should first be sent to OSC. If the OSC support line cannot answer or resolve the question, they have the ability to raise the problem to Altair support.

7. Please contact OSC Help for further instruction and license server information. In order to be added to the allowed list for the state-wide software access, we will need your IP address/range of machine that will be running this software. 

8. You need to set an environment variable (ALTAIR_LICENSE_PATH) on your local machine to point at our license server (7790@license6.osc.edu). See this link for instructions if necessary.

Further Reading

For more information about HyperWorks, see the following:

• Altair HyperWorks Documentation Page (Requires registration with Altair)
• Altair HyperWorks Academic Blog

See Also

• ABAQUS
• Altair HyperWorks statewide license

The BLAST programs are widely used tools for searching DNA and protein databases for sequence similarity to identify homologs to a query sequence. While often referred to as just "BLAST", this can really be thought of as a set of programs: blastp, blastn, blastx, tblastn, and tblastx.

Availability & Restrictions

BLAST is available without restriction to all OSC users.

The following versions of BLAST are available on OSC systems:

If you need to use blastx, you will need to load one of the C++ implimenations modules of blast (any version with a "+").

Set-up

To load BLAST, type the following into the command line:

module load blast

Then create a resource file .ncbirc, and put it under your home directory.

Using BLAST

The five flavors of BLAST mentioned above perform the following tasks:

blastp: compares an amino acid query sequence against a protein sequence database

blastn: compares a nucleotide query sequence against a nucleotide sequence database

blastx: compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database

tblastn: compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands).

tblastx: compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. (Due to the nature of tblastx, gapped alignments are not available with this option)

We provide local access to nt and refseq_protein databases. You can access the database using BLASTDB environment variable. If you need other databases, please send a request email to OSC Help .

Batch Usage

A sample batch script is below:

#PBS -l nodes=1:ppn=1
#PBS -l walltime=10:00
#PBS -N Blast
#PBS -S /bin/bash
#PBS -j oe
module load blast
set -x
cd $PBS_O_WORKDIR
mkdir $PBS_JOBID
cp 100.fasta $TMPDIR
cd $TMPDIR
/usr/bin/time blastn -db nt -query 100.fasta -out test.out
cp test.out $PBS_O_WORKDIR/$PBS_JOBID

Further Reading

• The BLAST Homepage
• Bioperl
• BLAT

BLAT is a sequence analysis tool which performs rapid mRNA/DNA and cross-species protein alignments. BLAT is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.

BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome (but not the genome itself) in memory. Since the index takes up a bit less than a gigabyte of RAM, BLAT can deliver high performance on a reasonably priced Linux box. The index is used to find areas of probable homology, which are then loaded into memory for a detailed alignment. Protein BLAT works in a similar manner, except with 4-mers rather than 11-mers. The protein index takes a little more than 2 gigabytes.

Availability & Restrictions

BLAT is available without restriction to all OSC users.

The following versions of BLAT are available at OSC:

Usage

Set-up

To initalize the Oakley system prior to using BLAT, run the following commands:

module load blat

Using BLAT

The main programs in the blat suite are:

gfServer – a server that maintains an index of the genome in memory and uses the index to quickly find regions with high levels of sequence similarity to a query sequence.

gfClient – a program that queries gfServer over the network, and then does a detailed alignment of the query sequence with regions found by gfServer.

blat –combines client and server into a single program, first building the index, then using the index, and then exiting. 

webBlat – a web based version of gfClient that presents the alignments in an interactive fashion. (not included on OSC server)

Building an index of the genome typically takes 10 or 15 minutes.  Typically for interactive applications one uses gfServer to build a whole genome index.  At that point gfClient or webBlat can align a single query within few seconds.  If one is aligning a lot of sequences in a batch mode then blat can be more efficient, particularly if run on a cluster of computers.  Each blat run is typically done against a single chromosome, but with a large number of query sequences.

Other programs in the blat suite are:

pslSort – combines and sorts the output of multiple blat runs.  (The blat default output format is .psl).

pslReps – selects the best alignments for a particular query sequence, using a ‘near best in genome’ approach.

pslPretty – converts alignments from the psl format, which is tab-delimited format and does not include the bases themselves, to a more readable alignment format.

faToTwoBit – convert Fasta format sequence files to a dense randomly-accessable  .2bit format that gfClient can use.

twoBitToFa – convert from the .2bit format back to fasta

faToNib – convert from Fasta to a somewhat less dense randomly accessible format that predates .2bit.  Note each .nib file can only contain a single sequence.

nibFrag – convert portions of a nib file back to fasta.

The command line options of each of the programs is described below. Similar summaries of usage are printed when a command is run with no arguments.

Batch Usage

A sample batch script is as below:

#PBS -N blat
#PBS -j oe
#PBS -l nodes=1:ppn=1
#PBS -S /bin/bash

module load blat 

cd $PBS_O_WORKDIR
cp $BLAT_TEST_DIR/gfServer-tests/input/creaGeno.2bit .
cp $BLAT_TEST_DIR/gfServer-tests/input/crea.mrna .

blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 creaGeno.2bit crea.mrna output.psl 

Further Reading

• The BLAT homepage

See Also

• Bioperl
• BLAST

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.

Availability and Restrictions

The following versions of BWA are available on OSC clusters:

You can use  module spider bwa to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

BWA is available to all OSC users without restriction.

Usage on Oakley

Usage on Owens

Further Reading

• The BWA Official Webpage

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

Availability and Restrictions

The following versions of BamTools are available on OSC clusters:

You can use  module spider bamtools to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

BamTools is available to all OSC users without restriction.

Usage on Oakley

Usage on Owens

Further Reading

• The BamTools Official Webpage

Bioperl offers a set of perl modules which can be used for sequence manipulation. Knowledge of PERL programming is required.

Availability & Restrictions

Bioperl is available without restriction to all OSC users.

The following versions of Bioperl are available:

Usage

Using Bioperl

This is an example of how to use bioperl and access the sequence package on the Oakley Cluster.

use lib '/usr/local/bioperl/1.6.1/lib/perl5/'
use Bio::Seq;

Further Reading

• The Bioperl home page

See Also

• BLAST
• BLAT

Boost is a set of C++ libraries that provide helpful data structures and numerous support functions in a wide range of aspects of programming, such as, image processing, gpu programming, concurrent programming, along with many algorithms.  Boost is portable and performs well on a wide variety of platforms.

Availability & Restrictions

Boost is available without restriction to all OSC Users

The following version of Boost are available on OSC systems:

Usage on Oakley

module load boost

cp /usr/local/src/boost/boost-1.56.0/test.osc/example2.cpp .
cp /usr/local/src/boost/boost-1.56.0/test.osc/jayne.txt .
module load boost
g++ $BOOST_CFLAGS example2.cpp -o boostTest $BOOST_LIBS -lboost_regex
./boostTest < jayne.txt

Usage on Ruby

module load boost

cp /usr/local/src/boost/boost-1_56_0/test.osc/example2.cpp ~
cp /usr/local/src/boost/boost-1_56_0/test.osc/jayne.txt ~

module load boost
g++ $BOOST_CFLAGS example2.cpp -o boostTest $BOOST_LIBS -lboost_regex
./boostTest < jayne.txt

Usage on Owens

cp /usr/local/src/boost/boost-1_56_0/test.osc/example2.cpp ~
cp /usr/local/src/boost/boost-1_56_0/test.osc/jayne.txt ~

g++ example2.cpp -o boostTest -lboost_regex
./boostTest < jayne.txt

Bowtie1 is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

Availability and Restrictions

The following versions of Bowtie1 are available on OSC clusters:

You can use  module spider bowtie1   to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

Bowtie1 is available to all OSC users without restriction.

Usage on Oakley

Usage on Owens

Further Reading

• The Bowtie1 Official Webpage

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

Availability and Restrictions

The following versions of Bowtie2 are available on OSC clusters:

You can use  module spider bowtie2  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

Bowtie2 is available to all OSC users without restriction.

Usage on Oakley

Usage on Owens

Further Reading

• The Bowtie2 Official Webpage

CDO (Climate Data Operators) is a collection of command line operator to manipulate and analyse climate and NWP model data. It is open source and released under the terms of the GNU General Public License v2 (GPL).

Availability and Restrictions

Versions

CDO is available on Oakley Cluster. The versions currently available at OSC are:

You can use module spider cdo  to view available modules on Oakley. Feel free to contact OSC Help if you need other versions for your work.

Access 

CDO is available for use by all OSC users.

Usage

Usage on Oakley

qsub -I -l nodes=1:ppn=12 -l walltime=1:00:00

cdo info infile

Further Reading

Official documentation can be obtained from https://code.zmaw.de/projects/cdo/wiki/Cdo#Documentation

COMSOL Multiphysics (formerly FEMLAB) is a finite element analysis and solver software package for various physics and engineering applications, especially coupled phenomena, or multiphysics. owned and supported by COMSOL, Inc.

Availability and Restrictions

COMSOL is available on the Oakley and Ruby clusters. The versions currently available at OSC are

You can use module spider comsol  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access for Academic Users

To use COMSOL you will have to be added to the license server first.  Please contact OSC Help to be added.

Access for Commerical Users

Contact OSC Help for getting access to COMSOL if you are a commercial user. 

Usage on Oakley

qsub -I -l nodes=1:ppn=12 -l walltime=1:00:00 -l software=comsolscript

#PBS -N COMSOL
#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=1
#PBS -j oe
#PBS -l software=comsolscript
#
# The following lines set up the COMSOL environment
#
module load comsol
#
# Move to the directory where the job was submitted
#
cd $PBS_O_WORKDIR
cp *.m $TMPDIR
cd $TMPDIR
#
# Run COMSOL
#
comsol batch mycomsol
#
# Now, copy data (or move) back once the simulation has completed
#
cp * $PBS_O_WORKDIR

#PBS -l walltime=01:00:00
#PBS -l nodes=2:ppn=12
#PBS -N COMSOL
#PBS -j oe
#PBS -r n
#PBS -l software=comsolscript
cd ${PBS_O_WORKDIR}
module load comsol
echo "--- Copy Input Files to TMPDIR and Change Disk to TMPDIR"
cp input_cluster.mph $TMPDIR
cd $TMPDIR
np=12
echo "--- Running on ${np} processes (cores) on the following nodes:"
cat $PBS_NODEFILE | uniq > hostfile
echo "--- COMSOL run"
comsol -nn 2 -np ${np} batch -f hostfile -mpirsh rsh -inputfile input_cluster.mph -outputfile output_cluster.mph
echo "--- Copy files back"
cp output_cluster.mph output_cluster.mph.status ${PBS_O_WORKDIR}
echo "---Job finished at: 'date'"
echo "---------------------------------------------"

Usage on Ruby

qsub -I -l nodes=1:ppn=20 -l walltime=1:00:00 -l software=comsolscript

#PBS -N COMSOL
#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=1
#PBS -j oe
#PBS -l software=comsolscript
#
# The following lines set up the COMSOL environment
#
module load comsol
#
# Move to the directory where the job was submitted
#
cd $PBS_O_WORKDIR
cp *.m $TMPDIR
cd $TMPDIR
#
# Run COMSOL
#
comsol batch mycomsol
#
# Now, copy data (or move) back once the simulation has completed
#
cp * $PBS_O_WORKDIR

#PBS -l walltime=01:00:00
#PBS -l nodes=2:ppn=20
#PBS -N COMSOL
#PBS -j oe
#PBS -r n
#PBS -l software=comsolscript
cd ${PBS_O_WORKDIR}
module load comsol
echo "--- Copy Input Files to TMPDIR and Change Disk to TMPDIR"
cp input_cluster.mph $TMPDIR
cd $TMPDIR
np=20
echo "--- Running on ${np} processes (cores) on the following nodes:"
cat $PBS_NODEFILE | uniq > hostfile
echo "--- COMSOL run"
comsol -nn 2 -np ${np} batch -f hostfile -mpirsh rsh -inputfile input_cluster.mph -outputfile output_cluster.mph
echo "--- Copy files back"
cp output_cluster.mph output_cluster.mph.status ${PBS_O_WORKDIR}
echo "---Job finished at: 'date'"
echo "---------------------------------------------"

Usage on Owens

qsub -I -l nodes=1:ppn=28 -l walltime=1:00:00 -l software=comsolscript

#PBS -N COMSOL
#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=1
#PBS -j oe
#PBS -l software=comsolscript
#
# The following lines set up the COMSOL environment
#
module load comsol
#
# Move to the directory where the job was submitted
#
cd $PBS_O_WORKDIR
cp *.m $TMPDIR
cd $TMPDIR
#
# Run COMSOL
#
comsol batch mycomsol
#
# Now, copy data (or move) back once the simulation has completed
#
cp * $PBS_O_WORKDIR

#PBS -l walltime=01:00:00
#PBS -l nodes=2:ppn=28
#PBS -N COMSOL
#PBS -j oe
#PBS -r n
#PBS -l software=comsolscript
cd ${PBS_O_WORKDIR}
module load comsol
echo "--- Copy Input Files to TMPDIR and Change Disk to TMPDIR"
cp input_cluster.mph $TMPDIR
cd $TMPDIR
np=28
echo "--- Running on ${np} processes (cores) on the following nodes:"
cat $PBS_NODEFILE | uniq > hostfile
echo "--- COMSOL run"
comsol -nn 2 -np ${np} batch -f hostfile -mpirsh rsh -inputfile input_cluster.mph -outputfile output_cluster.mph
echo "--- Copy files back"
cp output_cluster.mph output_cluster.mph.status ${PBS_O_WORKDIR}
echo "---Job finished at: 'date'"
echo "---------------------------------------------"

Further Reading

• The Official COMSOL Website

CUDA™ (Compute Unified Device Architecture) is a parallel computing platform and programming model developed by Nvidia that enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU).

Availability and Restrictions

CUDA is available on the clusters supporting GPUs. The versions currently available at OSC are

You can use module spider cuda to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

CUDA is available for use by all OSC users.

Usage

Usage on Oakley

qsub -I -l nodes=1:ppn=1:gpus=1 -l walltime=00:20:00

#PBS -l walltime=01:00:00
#PBS -l nodes=1:ppn=1:gpus=1
#PBS -N compute
#PBS -j oe
module load cuda
cd $HOME/cuda
cp mycudaApp $TMPDIR
cd $TMPDIR
./mycudaApp

Usage on Ruby

-l nodes=1:ppn=20:gpus=1:default
-l nodes=1:ppn=20:gpus=1:exclusive
-l nodes=1:ppn=20:gpus=1:exclusive_process

qsub -I -l nodes=1:ppn=20:gpus=1 -l walltime=00:20:00 

#PBS -l walltime=01:00:00
#PBS -l nodes=1:ppn=20:gpus=1
#PBS -N compute
#PBS -j oe
module load cuda
cd $HOME/cuda
cp mycudaApp $TMPDIR
cd $TMPDIR
./mycudaApp

Further Reading

Online documentation is available at http://developer.nvidia.com/nvidia-gpu-computing-documentation

See Also

• http://developer.nvidia.com/cuda-books

Caffe is "a fast open framework for deep learning".

From their README:

Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors. Yangqing Jia created the project during his PhD at UC Berkeley. Caffe is released under the BSD 2-Clause license.

Caffe also includes interfaces for both Python and Matlab, which have been built but have not been tested.

Availability and Restrictions

Versions

The following versions of Caffe are available on OSC clusters:

The current versions of Caffe on Ruby require the use of python/2.7.8, cuda/7.5.18, boost/1.56.0, opencv/3.1.0 on Ruby for GPU calculations.

The current version of Caffe on Owens requires cuda/8.0.44 for GPU calculations.

Feel free to contact OSC Help if you need other versions for your work.

Access 

Caffe is available to all OSC users without restriction.

Usage

Usage on Ruby or Owens

module load caffe

#PBS -N Caffe
#PBS -l nodes=1:ppn=20:gpus=1:default
#PBS -l walltime=30:00
#PBS -j oe
#PBS -S /bin/bash 
cd $PBS_O_WORKDIR
. /etc/profile.d/lmod.sh
# Load the modules for Caffe
ml caffe
# Migrate to job temp directory and copy folders over
cd $TMPDIR
cp -r $CAFFE_HOME/{examples,build,data} .
# Download, create, train
./data/mnist/get_mnist.sh
./examples/mnist/create_mnist.sh
./examples/mnist/train_lenet.sh
# Serialize log files
echo; echo 'LOG 1'
cat convert_mnist_data.bin.$(hostname)*
echo; echo 'LOG 2'
cat caffe.INFO
echo; echo 'LOG 3'
cat convert_mnist_data.bin.INFO
echo; echo 'LOG 4'
cat caffe.$(hostname).*
cp examples/mnist/lenet_iter_10000.* $PBS_O_WORKDIR

qsub job.txt

#!/bin/bash
#PBS -N Caffe
#PBS -l nodes=1:ppn=28:gpu
#PBS -l walltime=30:00
#PBS -j oe
#PBS -S /bin/bash 
cd $PBS_O_WORKDIR
. /etc/profile.d/lmod.sh
# Load the modules for Caffe
ml caffe
# Migrate to job temp directory and copy folders over
cd $TMPDIR
cp -r $CAFFE_HOME/{examples,data} .
# Download, create, train
./data/mnist/get_mnist.sh
./examples/mnist/create_mnist.sh
./examples/mnist/train_lenet.sh
# Serialize log files
echo; echo 'LOG 1'
cat convert_mnist_data.bin.$(hostname)*
echo; echo 'LOG 2'
cat caffe.INFO
echo; echo 'LOG 3'
cat convert_mnist_data.bin.INFO
echo; echo 'LOG 4'
cat caffe.$(hostname).*
cp examples/mnist/lenet_iter_10000.* $PBS_O_WORKDIR

qsub job.txt

Further Reading

http://caffe.berkeleyvision.org/

Cairo is a 2D graphics library with support for multiple output devices. It is designed to produce consistent output on all output media while taking advantage of display hardware acceleration when available.

Availability and Restrictions

Versions

The following versions of Cairo are available on OSC clusters:

You can use  module spider cairo  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

Cairo is available to all OSC users without restriction.

Usage on Oakley

icc -o myprog myprog.c $CAIRO_LIBS $CAIRO_CFLAGS

Usage on Owens

icc -o myprog myprog.c -lcairo

Further Reading

• The Cario Official Webpage

Introduction

The Cambridge Structural Database (CSD) contains complete structure information on hundreds of thousands of small molecule crystals. The Cambridge Crystallographic Data Centre (CCDC) is a suite of programs for CSD search and analysis. It includes the graphical user interface (GUI) programs ConQuest or searching and retrieving information from the CSD and Mercury for structural visualization and analysis. The Cambridge Crystallographic Data Centre Home Page has additional information.

Version

CSD 2017 is available only for academic OSU users.

There are also a limited number of licenses for the web version WebCSD.

Before you can use CSD we need to add you to our system. Please contact OSC Help for availability.

Availability

CSD is available on Oakley login nodes.  For the GUI applications, one should use an OnDemand VDI (Virtual Desktop Interface) or have X11 forwarding enabled (see Setting up X Windows). Note that X11 forwarding can be distractingly slow for interactive applications.

Usage

CSD is only available to The Ohio State University academic users. In order to access this software license, please contact OSC Help for further instruction.

To run conquest:

module load csd
cq

Documentation

General documentation is available at the CCDC Documentation page and in the local machine directories.

Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.

Availability & Restrictions

Clustal W is available without restriction to all OSC users.

The following versions of Clustal W are available on OSC systems:

Usage

Set-up

On the Oakley system load the clustalw module:

module load clustalw

Using Clustal W

Once the clustalw module has been loaded, the commands are available for your use. On the Oakley system, the command is

clustalw2

The options can be listed interactively by typing clustalw -help or clustalw -check on the command-line.

                DATA (sequences)
-INFILE=file.ext                             :input sequences.
-PROFILE1=file.ext  and  -PROFILE2=file.ext  :profiles (old alignment).

                VERBS (do things)
-OPTIONS            :list the command line parameters
-HELP  or -CHECK    :outline the command line params.
-ALIGN              :do full multiple alignment 
-TREE               :calculate NJ tree.
-BOOTSTRAP(=n)      :bootstrap a NJ tree (n= number of bootstraps; def. = 1000).
-CONVERT            :output the input sequences in a different file format.

                PARAMETERS (set things)
***General settings:****
-INTERACTIVE :read command line, then enter normal interactive menus
-QUICKTREE   :use FAST algorithm for the alignment guide tree
-TYPE=       :PROTEIN or DNA sequences
-NEGATIVE    :protein alignment with negative values in matrix
-OUTFILE=    :sequence alignment file name
-OUTPUT=     :GCG, GDE, PHYLIP, PIR or NEXUS
-OUTORDER=   :INPUT or ALIGNED
-CASE        :LOWER or UPPER (for GDE output only)
-SEQNOS=     :OFF or ON (for Clustal output only)
-SEQNO_RANGE=:OFF or ON (NEW: for all output formats) 
-RANGE=m,n   :sequence range to write starting m to m+n. 

***Fast Pairwise Alignments:***
-KTUPLE=n    :word size
-TOPDIAGS=n  :number of best diags.
-WINDOW=n    :window around best diags.
-PAIRGAP=n   :gap penalty
-SCORE       :PERCENT or ABSOLUTE

***Slow Pairwise Alignments:***
-PWMATRIX=    :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename
-PWDNAMATRIX= :DNA weight matrix=IUB, CLUSTALW or filename
-PWGAPOPEN=f  :gap opening penalty        
-PWGAPEXT=f   :gap opening penalty

***Multiple Alignments:***
-NEWTREE=      :file for new guide tree
-USETREE=      :file for old guide tree
-MATRIX=       :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename
-DNAMATRIX=    :DNA weight matrix=IUB, CLUSTALW or filename
-GAPOPEN=f     :gap opening penalty        
-GAPEXT=f      :gap extension penalty
-ENDGAPS       :no end gap separation pen. 
-GAPDIST=n     :gap separation pen. range
-NOPGAP        :residue-specific gaps off  
-NOHGAP        :hydrophilic gaps off
-HGAPRESIDUES= :list hydrophilic res.    
-MAXDIV=n      :% ident. for delay
-TYPE=         :PROTEIN or DNA
-TRANSWEIGHT=f :transitions weighting

***Profile Alignments:***
-PROFILE      :Merge two alignments by profile alignment
-NEWTREE1=    :file for new guide tree for profile1
-NEWTREE2=    :file for new guide tree for profile2
-USETREE1=    :file for old guide tree for profile1
-USETREE2=    :file for old guide tree for profile2

***Sequence to Profile Alignments:***
-SEQUENCES   :Sequentially add profile2 sequences to profile1 alignment
-NEWTREE=    :file for new guide tree
-USETREE=    :file for old guide tree

***Structure Alignments:***
-NOSECSTR1     :do not use secondary structure-gap penalty mask for profile 1 
-NOSECSTR2     :do not use secondary structure-gap penalty mask for profile 2
-SECSTROUT=STRUCTURE or MASK or BOTH or NONE   :output in alignment file
-HELIXGAP=n    :gap penalty for helix core residues 
-STRANDGAP=n   :gap penalty for strand core residues
-LOOPGAP=n     :gap penalty for loop regions
-TERMINALGAP=n :gap penalty for structure termini
-HELIXENDIN=n  :number of residues inside helix to be treated as terminal
-HELIXENDOUT=n :number of residues outside helix to be treated as terminal
-STRANDENDIN=n :number of residues inside strand to be treated as terminal
-STRANDENDOUT=n:number of residues outside strand to be treated as terminal 

***Trees:***
-OUTPUTTREE=nj OR phylip OR dist OR nexus
-SEED=n        :seed number for bootstraps.
-KIMURA        :use Kimura's correction.   
-TOSSGAPS      :ignore positions with gaps.
-BOOTLABELS=node OR branch :position of bootstrap values in tree display

Batch Usage

Sample batch script for the Oakley system:

#PBS -N clustalw
#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=1
#PBS -j oe

cd $PBS_O_WORKDIR
module load clustalw
clustalw2 -INFILE=myfile.seqs -GAPOPEN=2 -GAPEXT=4

Further Reading

• The Clustal W homepage

See Also

• Bioperl
• BLAST
• BLAT

Darshan is a lightweight "scalable HPC I/O characterization tool".  It is intended to profile I/O by emitting log files to a consistent log location for systems administrators, and also provides scripts to create summary PDFs to characterize I/O in MPI-based programs.

Availability and Restrictions

Versions

The following versions of Darshan are available on OSC clusters:

Access 

Darshan is available to all OSC users without restriction.

Usage on Owens

module load darshan

gnu/4.8.5  mvapich2/2.2
gnu/4.8.5  mvapich2/2.2rc1
gnu/4.8.5  openmpi/1.10
intel/16.0.3  intelmpi/5.1.3
intel/16.0.3  mvapich2/2.2
intel/16.0.3  mvapich2/2.2rc1
intel/16.0.3  openmpi/1.10

# basic call to darshan 
mpiexec.darshan [args] ./my_mpi_program
# to show evidence that Darshan is working and to see internal timing
mpiexec.darshan.timing [args] ./my_mpi_program

#!/bin/bash
#PBS -l nodes=1:ppn=28:pfsdir
#PBS -j oe
# one may need to perform 'shopt -s expand_aliases' inside the shell before calling this script to expand darshan aliases
shopt -s expand_aliases
ml r --quiet
module load darshan
ml
function run_darshan() {
COMPILER=mpicc
MPIPROCS=$1
PROGNAME=$2
BLOKSIZE=$3
LOCATION=$4
cp ${DARSHAN_EXAMPLE}/${PROGNAME}.c $LOCATION
cd $LOCATION
$COMPILER -DDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -o $PROGNAME ${PROGNAME}.c
mpiexec_darshan() { eval mpiexec.darshan "$@"; }
mpiexec_darshan -n $MPIPROCS ./$PROGNAME -f test -l $BLOKSIZE
du -sh test # show the human-readable file size
rm test # we are not keeping the large file around
}
# run the parallel version of mpi-io to write to a file but use the local tmp directory
run_darshan $PBS_NP mkrandpfile 256 $TMPDIR
# run the parallel version of mpi-io to write to a file but use the parallel file system scratch location
run_darshan $PBS_NP mkrandpfile 256 $PFSDIR
# for each darshan log generate a PDF report
JOBID=$([[ $tmp =~ ([0-9]*)\..* ]]; echo "${BASH_REMATCH[1]}")
for log in $(ls $DARSHAN_LOG/$(date "+%Y/%-m/%-d")/${USER:0:8}_*_id${JOBID}*.darshan); do
darshan-job-summary.pl $log
done
cp *.pdf $PBS_O_WORKDIR

qsub mpiio_with_darshan.qsub

Further Reading

http://www.mcs.anl.gov/research/projects/darshan/

EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

Within EMBOSS you will find around hundreds of programs (applications) covering areas such as:

• Sequence alignment,
• Rapid database searching with sequence patterns,
• Protein motif identification, including domain analysis,
• Nucleotide sequence pattern analysis---for example to identify CpG islands or repeats,
• Codon usage analysis for small genomes,
• Rapid identification of sequence patterns in large scale sequence sets,
• Presentation tools for publication

Availability & Restrictions

The EMBOSS software package is available without restriction for all academic OSC users.

The following versions of EMBOSS are available on OSC systems:

Usage on Oakley

module load emboss

Further Reading

• The EMBOSS homepage

See Also

• BLAST
• BLAT

Elmer is an open source multiphysical simulation software developed by CSC - IT (Finland).

From their Github README:

Elmer is a finite element software for numerical solution of partial
differential equations. Elmer is capable of handling any number of equations
and is therefore ideally suited for the simulation of multiphysical problems.
It includes models, for example, of structural mechanics, fluid dynamics, heat
transfer and electromagnetics. Users can also write their own equations that
can be dynamically linked with the main program.
Elmer consists of several parts. The most important ones are ElmerSolver, the
finite element solver, ElmerGUI, the graphical user interface, and ElmerGrid,
the mesh creation and manipulation tool. Also a visualization tool, ElmerPost,
is included in the package but it is no longer developed.  
Elmer software is licensed under GPL except for the ElmerSolver library which
is licensed under LGPL license. 
Elmer is mainly developed at CSC - IT Center for Science, Finland. However,
there have been numerous contributions from other organizations and developers
as well, and the project is open for new contributions.

Availability and Restrictions

Versions

The following versions of Elmer are available on OSC clusters:

The current versions of Elmer are compiled with GNU 4.8.4 (requirement > 4.8) and BLAS libraries from MKL/11.2.3.

Feel free to contact OSC Help if you need other versions for your work.

Access 

Elmer is available to all OSC users without restriction.

Usage

Usage on Oakley or Ruby

module load gnu/4.8.4
module load mkl/11.2.3
module load elmer

#PBS -N Elmer
#PBS -l nodes=1:ppn=1 
#PBS -l walltime=30:00
#PBS -j oe 
#PBS -S /bin/bash 
# Load the modules for Elmer
module load gnu/4.8.4
module load mkl/11.2.3
module load elmer
# Move to the problem directory
cd $PBS_O_WORKDIR
# Copy files to $TMPDIR and move there to execute the program
cp -r * $TMPDIR
cd $TMPDIR
# Convert the mesh - see Elmer webpage for more examples of 'ElmerGrid'
ElmerGrid 14 2 beam.msh -autoclean
# Run the solver 
ElmerSolver beam.sif
# Finally, copy files back to your home directory 
cp -r * $PBS_O_WORKDIR

qsub job.txt

Further Reading

https://www.csc.fi/web/elmer/

https://github.com/ElmerCSC/elmerfem

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

Availability and Restrictions

The following versions of FASTX-Toolkit are available on OSC clusters:

You can use  module spider fastx to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

FASTX-Toolkit is available to all OSC users without restriction.

Usage on Oakley

Usage on Owens

Further Reading

• The FASTX-Toolkit Official Webpage

FFTW is a C subroutine library for computing the Discrete Fourier Transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. It is portable and performs well on a wide variety of platforms.

Availability and Restrictions

FFTW is available on Oakley, Ruby, and Owens Clusters. The versions currently available at OSC are:

• X(G): gnu versions only,
• X(I): intel version only
• X(GI): available with both gnu and intel
• X: available with gnu, intel, and pgi

You can use module spider fftw2  or module spider fftw3   to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

FFTW is available without restriction to all OSC Users

Usage on Oakley

module load fftw3
icc $FFTW3_CFLAGS my-fftw.c -o my-fftw $FFTW3_LIBS 
ifort $FFTW3_FFLAGS more-fftw.f -o more-fftw $FFTW3_LIBS

Usage on Ruby

module load fftw3
icc $FFTW3_CFLAGS my-fftw.c -o my-fftw $FFTW3_LIBS 
ifort $FFTW3_FFLAGS more-fftw.f -o more-fftw $FFTW3_LIBS

Usage on Owens

module load fftw3
icc $FFTW3_CFLAGS my-fftw.c -o my-fftw $FFTW3_LIBS 
ifort $FFTW3_FFLAGS more-fftw.f -o more-fftw $FFTW3_LIBS

Further Reading

• The FFTW homepage

See Also

• The Intel MKL

FreeSurfer is a software package used to anaylze nueroimaging data.

Availability & Restrictions

Versions

The following versions of FreeSurfer are available on OSC clusters:

Access

FreeSurfer is available to all academic OSC users with proper validation. In order to obtain validation, please contact OSC Help for further instruction. 

Usage

Usage on Owens

source $FREESURFER_HOME/SetUpFreeSurfer.sh

source $FREESURFER_HOME/SetUpFreeSurfer.csh

export SUBJECTS_DIR=<path to subject data>

setenv SUBJECTS_DIR=<path to subject data>

Further Reading 

• FreeSurfer website

FreeType is a freely available software library to render fonts. It is written in C, designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images) of most vector and bitmap font formats.

Availability and Restrictions

Versions

The following versions of FreeType are available on OSC clusters:

You can use  module spider freetype  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

FreeType is available to all OSC users without restriction.

Usage

Usage on Oakley

Further Reading

• The FreeType Official Webpage

Introduction

The General Atomic and Molecular Electronic Structure System (GAMESS) is a flexible ab initio electronic structure program. Its latest version can perform general valence bond, multiconfiguration self-consistent field, Möller-Plesset, coupled-cluster, and configuration interaction calculations. Geometry optimizations, vibrational frequencies, thermodynamic properties, and solution modeling are available. It performs well on open shell and excited state systems and can model relativistic effects. The GAMESS Home Page has additional information.

Availability

GAMESS is available on the Oakley and Owens Clusters.

Version

* - Default Version

Usage

Users are not required to complete a license agreement.

Location

The root of the GAMESS directory tree is /usr/local/gamess/

Execution

GAMESS usage is controlled via modules. Load one of the GAMESS modulefiles at the command line, in your shell initialization script, or in your batch scripts, for example:

module load gamess  

Examples

• Test input files are in the tests subdirectory
• Computational Chemistry Workshop materials are in ~srb/workshops/compchem/gamess

Further Reading

General documentation is available from the GAMESS Home page and in the local machine directories.

GATK is a software package for analysis of high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.

Availability and Restrictions

The following versions of GATK are available on OSC clusters:

You can use  module spider gatk to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access for Academic Users

GATK is available to academic OSC users with proper validation. In order to obtain validation, please contact OSC Help for further instruction. 

Usage on Oakley

Usage on Owens

Further Reading

• The GATK Official Webpage

GLPK (GNU Linear Programming Kit) is a set of open source LP (linear programming) and MIP (mixed integer problem) routines written in ANSI C, which can be called from within C programs. 

Availability & Restrictions

GLPK is available to all OSC users without restriction. 

The following versions are available on OSC systems:

Usage

Setup

To set up your environment for using GLPK on Oakley, run the following command:

module load glpk

Compiling and Linking

To compile your C code using GLPK API routines, use the environment variable $GLPK_CFLAGS provided by the module:

gcc $GLPK_CFLAGS -c my_prog.c

To link your code, use the variable $GLPK_LIBS:

gcc my_prog.o $GLPK_LIBS -o my_prog

glpsol

Additionally, the GLPK module contains a stand-alone LP/MIP solver, which can be used to process files written in the GNU MathProg modeling language.  The solver can be invoked using the following command syntax:

glpsol [options] [filename]

For a complete list of options, use the following command:

glpsol --help

Further Reading

GLPK Homepage

GMAP: a genomic mapping and alignment program for mRNA and EST sequences.

Availability and Restrictions

The following versions of GMAP are available on OSC clusters:

You can use  module spider gmap   to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

GMAP is available to all OSC users without restriction.

Usage on Oakley

Usage on Owens

Further Reading

• The GMAP Official Webpage

Fortran, C and C++ compilers produced by the GNU Project. 

Availability and Restrictions

GNU Compiler is available on Oakley, Ruby, and Owens Clusters. The versions currently available at OSC are:

You can use module spider gnu  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

To find out what version of gcc you are using, type gcc --version.

Access

The GNU compilers are available to all OSC users without restriction.

Usage

Usage on Oakley

qsub -I -l nodes=1:ppn=12 -l walltime=1:00:00

#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=12
#PBS -N jobname
#PBS -j oe
cd $PBS_O_WORKDIR
module load gnu
cp hello.c $TMPDIR
cd $TMPDIR
gcc -O3 hello.c -o hello
./hello > hello_results
cp hello_results $PBS_O_WORKDIR

qsub job.txt

#PBS -l walltime=1:00:00
#PBS -l nodes=2:ppn=12
#PBS -N jobname
#PBS -j oe
cd $PBS_O_WORKDIR
module load gnu
mpicc -O3 hello.c -o hello
pbsdcp hello $TMPDIR
cd $TMPDIR
mpiexec hello > hello_results
pbsdcp -g hello_results $PBS_O_WORKDIR

Usage on Ruby

qsub -I -l nodes=1:ppn=20 -l walltime=1:00:00

#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=20
#PBS -N jobname
#PBS -j oe
cd $PBS_O_WORKDIR
module load gnu
cp hello.c $TMPDIR
cd $TMPDIR
gcc -O3 hello.c -o hello
./hello > hello_results
cp hello_results $PBS_O_WORKDIR

qsub job.txt

#PBS -l walltime=1:00:00
#PBS -l nodes=2:ppn=20
#PBS -N jobname
#PBS -j oe
cd $PBS_O_WORKDIR
module load gnu
mpicc -O3 hello.c -o hello
cp hello $TMPDIR
cd $TMPDIR
mpiexec ./hello > hello_results
cp hello_results $PBS_O_WORKDIR

Usage on Owens

qsub -I -l nodes=1:ppn=28 -l walltime=1:00:00

#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=28
#PBS -N jobname
#PBS -j oe
cd $PBS_O_WORKDIR
module load gnu
cp hello.c $TMPDIR
cd $TMPDIR
gcc -O3 hello.c -o hello
./hello > hello_results
cp hello_results $PBS_O_WORKDIR

qsub job.txt

#PBS -l walltime=1:00:00
#PBS -l nodes=2:ppn=28
#PBS -N jobname
#PBS -j oe
cd $PBS_O_WORKDIR
module load gnu
mpicc -O3 hello.c -o hello
cp hello $TMPDIR
cd $TMPDIR
mpiexec ./hello > hello_results
cp hello_results $PBS_O_WORKDIR

Further Reading

• GCC, the GNU Compiler Collection

See Also

• Intel Compilers
• PGI Compilers
• Compilation Guide

GPU-BLAST is an accelerated version of the popular NCBI-BLAST (www.ncbi.nlm.nih.gov) that uses general-purpose graphics processing unit (GPU). In comparison to the sequential NCBI-BLAST, GPU-BLAST is nearly four times faster, while producing identical results.

Availability & Restrictions

GPU-BLAST is available without restriction to all OSC users.

The following versions of GPU-BLAST are available on OSC systems:

Note that GPU-BLAST is not available on the Owens system. GPU-BLAST requires the CUDA nvcc compiler, but the GPU-BLAST software is only compatible with CUDA versions up to 7.5. CUDA 8, installed on the Owens cluster, is incompatible with GPU-BLAST.

Usage

Usage on Oakley

module load cuda/4.1.28
module load gpu-blast

#PBS -l nodes=1:ppn=1:gpus=1
#PBS -l walltime=10:00
#PBS -N GPU-Blast
#PBS -S /bin/bash
#PBS -j oe
module load gpu-blast
module load cuda/4.1.28
set -x
cd $PBS_O_WORKDIR
mkdir $PBS_JOBID
cp 100.fasta $TMPDIR
cd $TMPDIR
/usr/bin/time blastn -db nt -query 100.fasta -out test.out
cp * $PBS_O_WORKDIR/$PBS_JOBID

Usage on Ruby

module load cuda/7.5.18
module load gpu-blast

#PBS -l nodes=1:ppn=1:gpus=1
#PBS -l walltime=10:00
#PBS -N GPU-Blast
#PBS -S /bin/bash
#PBS -j oe
module load gpu-blast
module load cuda/7.5.18
set -x
cd $PBS_O_WORKDIR
mkdir $PBS_JOBID
cp 100.fasta $TMPDIR
cd $TMPDIR
/usr/bin/time blastn -db nt -query 100.fasta -out test.out
cp * $PBS_O_WORKDIR/$PBS_JOBID

Further Reading

• The GPU-BLAST homepage

See Also

• BLAST
• BLAT

GROMACS is a versatile package of molecular dynamics simulation programs. It is primarily designed for biochemical molecules, but it has also been used on non-biological systems.  GROMACS generally scales well on OSC platforms. Starting with version 4.6 GROMACS includes GPU acceleration.

Availability and Restrictions

GROMACS is available on Oakley and Owens Clusters. The versions currently available at OSC are the following (S means serial single node executables, P means parallel multinode, and C means CUDA, i.e., GPU enabled):

You can use module spider gromacs  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

GROMACS is available to all OSC users without restriction.

Usage on Oakley

pdb2gmx

gmx pdb2gmx

mpiexec mdrun_mpi_d

mpiexec gmx_mpi_d mdrun

qsub -I -l nodes=1:ppn=12 -l walltime=1:00:00

~srb/workshops/compchem/gromacs/

# GROMACS Tutorial for Solvation Study of Spider Toxin Peptide
# see fwspider_tutor.pdf
#PBS -N fwsinvacuo.oakley
#PBS -l nodes=2:ppn=12
module unload intel
module load intel/12.1.4.319
module load mvapich2/1.7
module load gromacs/4.6.3
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cd $PBS_O_WORKDIR
pbsdcp -p 1OMB.pdb em.mdp $TMPDIR
# Use TMPDIR for best performance.
cd $TMPDIR
pdb2gmx -ignh -ff gromos43a1 -f 1OMB.pdb -o fws.gro -p fws.top -water none
editconf -f fws.gro -d 0.7
editconf -f out.gro -o fws_ctr.gro -center 2.0715 1.6745 1.914
grompp -f em.mdp -c fws_ctr.gro -p fws.top -o fws_em.tpr
mpiexec mdrun_mpi -s fws_em.tpr -o fws_em.trr -c fws_ctr.gro -g em.log -e em.edr
cat em.log
cp -p * $PBS_O_WORKDIR/

Usage on Owens

gmx pdb2gmx

mpiexec gmx_mpi_d mdrun

qsub -I -l nodes=1:ppn=28 -l walltime=1:00:00

~srb/workshops/compchem/gromacs/

# GROMACS Tutorial for Solvation Study of Spider Toxin Peptide
# see fwspider_tutor.pdf
#PBS -N fwsinvacuo.owens
#PBS -l nodes=2:ppn=28
module load gromacs
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cd $PBS_O_WORKDIR
pbsdcp -p 1OMB.pdb em.mdp $TMPDIR
# Use TMPDIR for best performance.
cd $TMPDIR
pdb2gmx -ignh -ff gromos43a1 -f 1OMB.pdb -o fws.gro -p fws.top -water none
editconf -f fws.gro -d 0.7
editconf -f out.gro -o fws_ctr.gro -center 2.0715 1.6745 1.914
grompp -f em.mdp -c fws_ctr.gro -p fws.top -o fws_em.tpr
mpiexec gmx_mpi mdrun -s fws_em.tpr -o fws_em.trr -c fws_ctr.gro -g em.log -e em.edr
cat em.log
cp -p * $PBS_O_WORKDIR/

Further Reading

• The GROMACS homepage

Gaussian is the most popular general purpose electronic structure program. Its latest version, g09, can perform density functional theory, Hartree-Fock, Möller-Plesset, coupled-cluster, and configuration interaction calculations among others. Geometry optimizations, vibrational frequencies, magnetic properties, and solution modeling are available. It performs well as black-box software on closed-shell ground state systems. 

Availability and Restrictions

Gaussian is available on Ruby, Oakley, and Owen Clusters. The versions currently available at OSC are:

You can use module spider gaussian  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access for Academic Users

Use of Gaussian for academic purposes requires validation. In order to obtain validation, please contact OSC Help for further instruction.

Access for Commerical Users

Contact OSC Help for getting access to Gaussian if you are a commerical user.

Usage

Usage on Oakley

g09 < input.com

g09 input.com

qsub -I -l nodes=1:ppn=12 -l walltime=1:00:00

/users/appl/srb/workshops/compchem/gaussian/

#PBS -N GaussianJob
#PBS -l nodes=1:ppn=1
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cd $PBS_O_WORKDIR
cp input.com $TMPDIR
# Use TMPDIR for best performance.
cd $TMPDIR
module load gaussian
g16 < input.com
cp -p input.log *.chk $PBS_O_WORKDIR

Usage on Ruby

g09 < input.com

g09 input.com

qsub -I -l nodes=1:ppn=20 -l walltime=1:00:00

/users/appl/srb/workshops/compchem/gaussian/

#PBS -N GaussianJob
#PBS -l nodes=1:ppn=20
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cd $PBS_O_WORKDIR
cp input.com $TMPDIR
# Use TMPDIR for best performance.
cd $TMPDIR
module load gaussian
g09 < input.com
cp -p input.log *.chk $PBS_O_WORKDIR

Running Gaussian jobs with GPU

#PBS -S /bin/tcsh
#PBS -N methane 
#PBS -o methane.log
#PBS -l nodes=1:ppn=20:gpus=1:default
set echo
cd $TMPDIR
set INPUT=methane.com
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cp $PBS_O_WORKDIR/$INPUT .
module load gaussian/g16a03
g16 < ./$INPUT
ls -al
cp *.chk $PBS_O_WORKDIR
cp *.log $PBS_O_WORKDIR

%nproc=20
%mem=8gb
%CPU=0-19
%GPUCPU=0=0
%chk=methane.chk
#b3lyp/6-31G(d) opt
methane B3LYP/6-31G(d) opt freq
0,1
C        0.000000        0.000000        0.000000
H        0.000000        0.000000        1.089000
H        1.026719        0.000000       -0.363000
H       -0.513360       -0.889165       -0.363000
H       -0.513360        0.889165       -0.363000

Usage on Owens

g09 < input.com

g09 input.com

qsub -I -l nodes=1:ppn=28 -l walltime=1:00:00

/users/appl/srb/workshops/compchem/gaussian/

#PBS -N GaussianJob
#PBS -l nodes=1:ppn=28
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cd $PBS_O_WORKDIR
cp input.com $TMPDIR
# Use TMPDIR for best performance.
cd $TMPDIR
module load gaussian
g09 < input.com
cp -p input.log *.chk $PBS_O_WORKDIR

Further Reading

• The Gaussian homepage
• The Gaussian users group on Armstrong

Introduction

Gnuplot is a portable command-line driven data and function plotting utility.  It was originally intended to allow scientists and students to visualize mathematical functions and data.  

Gnuplot supports many types of plots in two or three dimensions.  It can draw using points, lines, boxes, contours, vector fields surfaces and various associated text.  It also supports various specialized plot types.  

Gnuplot supports many different types of output:  interactive screen display (with mouse and hotkey functionality), pen plotters (like hpgl), printers (including postscript and many color devices), and file formats as vectorial pseudo-devices like LaTeX, metafont, pdf, svg, or bitmap png.  

Version

Usage on Oakley

module load gnuplot

gnuplot

Usage on Owens

Further Reading

For more information, visit the Gnuplot Homepage.  

HDF5 is a general purpose library and file format for storing scientific data. HDF5 can store two primary objects: datasets and groups. A dataset is essentially a multidimensional array of data elements, and a group is a structure for organizing objects in an HDF5 file. Using these two basic objects, one can create and store almost any kind of scientific data structure, such as images, arrays of vectors, and structured and unstructured grids.

Availability and Restrictions

HDF5 is available on Oakley, Ruby, and Owens Clusters. The versions currently available at OSC are:

• X(P): pgi only
• X(PI): available with pgi and intel
• X(GI): available with gnu and intel
• X: available with pgi, gnu, and intel

You can use module spider hdf5  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

HDF5 is available without restriction to all OSC users.

Usage on Oakley

icc -c $HDF5_C_INCLUDE myprog.c
icc -o myprog myprog.o $HDF5_C_LIBS
ifort -c $HDF5_F90_INCLUDE myprog.f90
ifort -o myprog myprog.o $HDF5_F90_LIBS

#PBS -N AppNameJob
#PBS -l nodes=1:ppn=12
module load hdf5
cd $PBS_O_WORKDIR
cp foo.dat $TMPDIR
cd $TMPDIR
appname
cp foo_out.h5 $PBS_O_WORKDIR

Usage on Ruby

icc -c $HDF5_C_INCLUDE myprog.c
icc -o myprog myprog.o $HDF5_C_LIBS
ifort -c $HDF5_F90_INCLUDE myprog.f90
ifort -o myprog myprog.o $HDF5_F90_LIBS

#PBS -N AppNameJob
#PBS -l nodes=1:ppn=20
module load hdf5
cd $PBS_O_WORKDIR
cp foo.dat $TMPDIR
cd $TMPDIR
appname
cp foo_out.h5 $PBS_O_WORKDIR

Usage on Owens

icc -c $HDF5_C_INCLUDE myprog.c
icc -o myprog myprog.o $HDF5_C_LIBS
ifort -c $HDF5_F90_INCLUDE myprog.f90
ifort -o myprog myprog.o $HDF5_F90_LIBS

#PBS -N AppNameJob
#PBS -l nodes=1:ppn=28
module load hdf5
cd $PBS_O_WORKDIR
cp foo.dat $TMPDIR
cd $TMPDIR
appname
cp foo_out.h5 $PBS_O_WORKDIR

Further Reading

• The HDF5 home page
• HDF5 tutorials

• NetCDF

Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER uses profile HMMs, and can be useful in situations like:

• if you are working with an evolutionarily diverse protein family, a BLAST search with any individual sequence may not find the rest of the sequences in the family.
• the top hits in a BLAST search are hypothetical sequences from genome projects.
• your protein consists of several domains which are of different types.

HMMER (pronounced 'hammer', as in a more precise mining tool than BLAST) was developed by Sean Eddy at Washington University in St. Louis.

HMMER is a very cpu-intensive program and is parallelized using threads, so that each instance of hmmsearch or the other search programs can use all the cpus available on a node. HMMER on OSC clusters are intended for those who need to run HMMER searches on large numbers of query sequences.

Availability & Restrictions

HMMER is available to all OSC users without restriction.

The following versions of HMMER are available on OSC systems:

Usage

Set-up

To use HMMER on Oakley, first run the following command:

module load hmmer

Using HMMER

Once the hmmer module is loaded, the following commands will be available for your use:

Single sequence queries: new to HMMER3
phmmer Search a sequence against a sequence database. (BLASTP-like)
jackhmmer Iteratively search a sequence against a sequence database. (PSIBLAST-like)

Replacements for HMMER2’s functionality
hmmbuild Build a profile HMM from an input multiple alignment.
hmmsearch Search a profile HMM against a sequence database.
hmmscan Search a sequence against a profile HMM database.
hmmalign Make a multiple alignment of many sequences to a common profile HMM.

Other utilities
hmmconvert Convert profile formats to/from HMMER3 format.
hmmemit Generate (sample) sequences from a profile HMM.
hmmfetch Get a profile HMM by name or accession from an HMM database.
hmmpress Format an HMM database into a binary format for hmmscan.
hmmstat Show summary statistics for each profile in an HMM database.

If you need to know options for a command, type the command name followed by "-h", for example:

hmmalign -h 

Batch Usage

A sample batch job is below:

#PBS -N hmmer
#PBS -j oe
#PBS -l nodes=1:ppn=1
#PBS -S /bin/bash

cd $PBS_O_WORKDIR
hmmalign globins4.align globins45
hmmbuild globins4.hmm globins4.align
hmmsearch globins4.hmm /fdb/fastadb/nr.aa.fas > globins.out

Further Reading

• The HMMER home page
• The HMMER user group on Armstrong

See Also

• ClustalW

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.

Availability and Restrictions

The following versions of HOMER are available on OSC clusters:

You can use  module spider homer  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

HOMER is available to all OSC users without restriction.

Usage on Oakley

Usage on Owens

Further Reading

• The HOMER Official Webpage

A hadoop cluster can be launched within the HPC environment, but managed by the PBS job scheduler using  Myhadoop framework developed by San Diego Supercomputer Center. (Please see http://www.sdsc.edu/~allans/MyHadoop.pdf)

Availability & Restrictions

Hadoop is available to all OSC users without restriction.

The following versions of Hadoop are available on OSC systems: 

NOTE: * means it is the default version.

Set-up

In order to configure your environment for the usage of Hadoop, run the following command:

module load hadoop

In order to access a particular version of Hadoop, run the following command

module load hadoop/3.0.0-alpha1

Using Hadoop

In order to run Hadoop in batch, reference the example batch script below. This script requests 6 node on the Owens cluster for 1 hour of walltime. 

#PBS -N hadoop-example

#PBS -l nodes=6:ppn=12

#PBS -l walltime=01:00:00

setenv WORK $PBS_O_WORKDIR

module load hadoop/3.0.0-alpha1

module load myhadoop/v0.40

setenv HADOOP_CONF_DIR $TMPDIR/mycluster-conf-$PBS_JOBID

cd $TMPDIR

myhadoop-configure.sh -c $HADOOP_CONF_DIR -s $TMPDIR

$HADOOP_HOME/sbin/start-dfs.sh

hadoop dfsadmin -report

hadoop  dfs -mkdir data

hadoop  dfs -put $HADOOP_HOME/README.txt  data/

hadoop  dfs -ls data

hadoop jar $HADOOP_HOME/share/hadoop/mapreduce/hadoop-mapreduce-examples-3.0.0-alpha1.jar wordcount data/README.txt wordcount-out

hadoop  dfs -ls wordcount-out

hadoop  dfs  -copyToLocal -f  wordcount-out  $WORK

$HADOOP_HOME/sbin/stop-dfs.sh

myhadoop-cleanup.sh

Example Jobs

Please check /usr/local/src/hadoop/3.0.0-alpha1/test.osc folder for more examples of hadoop jobs

Further Reading

• Hadoop home page

See Also

• Spark

The Intel compilers for both C/C++ and FORTRAN.

Availability and Restrictions

The versions currently available at OSC are:

You can use module avail intel  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

The Intel Compilers are available to all OSC users without restriction.

Usage

Usage on Oakley

module load cxx11

module load cxx14

qsub -I -l nodes=1:ppn=12 -l walltime=1:00:00

#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=12
#PBS -N jobname
#PBS -j oe
cd $PBS_O_WORKDIR
module load intel
cp hello.c $TMPDIR
cd $TMPDIR
icc -O2 hello.c -o hello
./hello > hello_results
cp hello_results $PBS_O_WORKDIR

qsub job.txt

#PBS -l walltime=1:00:00
#PBS -l nodes=2:ppn=12
#PBS -N jobname
#PBS -j oe
cd $PBS_O_WORKDIR
module load intel
mpicc -O2 hello.c -o hello
pbsdcp hello $TMPDIR
cd $TMPDIR
mpiexec hello > hello_results
pbsdcp -g hello_results $PBS_O_WORKDIR

Usage on Ruby

module load cxx11

module load cxx14

qsub -I -l nodes=1:ppn=20 -l walltime=1:00:00

#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=20
#PBS -N jobname
#PBS -j oe
cd $PBS_O_WORKDIR
module load intel
cp hello.c $TMPDIR
cd $TMPDIR
icc -O2 hello.c -o hello
./hello > hello_results
cp hello_results $PBS_O_WORKDIR

qsub job.txt

#PBS -l walltime=1:00:00
#PBS -l nodes=2:ppn=20
#PBS -N jobname
#PBS -j oe
cd $PBS_O_WORKDIR
module load intel
mpicc -O2 hello.c -o hello
cp hello $TMPDIR
cd $TMPDIR
mpiexec ./hello > hello_results
cp hello_results $PBS_O_WORKDIR​

Usage on Owens

module load cxx11

qsub -I -l nodes=1:ppn=28 -l walltime=1:00:00

#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=28
#PBS -N jobname
#PBS -j oe
cd $PBS_O_WORKDIR
module load intel
cp hello.c $TMPDIR
cd $TMPDIR
icc -O2 hello.c -o hello
./hello > hello_results
cp hello_results $PBS_O_WORKDIR

qsub job.txt

#PBS -l walltime=1:00:00
#PBS -l nodes=2:ppn=28
#PBS -N jobname
#PBS -j oe
cd $PBS_O_WORKDIR
module load intel
mpicc -O2 hello.c -o hello
cp hello $TMPDIR
cd $TMPDIR
mpiexec ./hello > hello_results
cp hello_results $PBS_O_WORKDIR​

Further Reading

• The Intel Compiler Home Page

See Also

• Intel Math Kernel Library
• AMD Core Math Library
• Compilation Guide

https://www.osc.edu/supercomputing/software/intel-compilers Intel's implementation of the Message Passing Interface (MPI) library.

Availability and Restrictions

Intel MPI may be used as an alternative to - but not in conjunction with - the MVAPICH2 MPI libraries. The versions currently available at OSC are:

You can use module spider intelmpi  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

Intel MPI is available to all OSC users without restriction.

Usage

Usage on Oakley

#PBS -N MyIntelMPIJob
#PBS -l nodes=4:ppn=12
#PBS -l walltime=5:00:00
module swap mvapich2 intelmpi
cd $PBS_O_WORKDIR
mpiexec my-impi-application

Usage on Ruby

#PBS -N MyIntelMPIJob
#PBS -l nodes=4:ppn=20
#PBS -l walltime=5:00:00
module swap mvapich2 intelmpi
cd $PBS_O_WORKDIR
mpiexec my-impi-application

Usage on Owens

#PBS -N MyIntelMPIJob
#PBS -l nodes=4:ppn=28
#PBS -l walltime=5:00:00
module swap mvapich2 intelmpi
cd $PBS_O_WORKDIR
mpiexec my-impi-application

Further Reading

• Intel MPI page at Intel.com
• Vendor documentation

See Also

• MVAPICH2
• OpenMPI
• Intel Compilers
• Intel Math Kernel Library

Introduction

JasPer is an extensible open source utility designed for the manipulation, conversion, compression and decompression of digital images.  Currently supported image formats include bmp, jp2, jpc, jpg, pgx, mif and ras.    

Availability

Version 1.900.1 is available on the Oakley cluster.  

Usage

In order to use the JasPer library, you must load the JasPer module into your environment.  To load the JasPer module, type the following command:

module load jasper

Useful commands

In addition to the JasPer libraries, a few default applications are also provided when the JasPer module is loaded.     

To convert an image from one format to another, use the jasper command.   

jasper [options]

For a comprehensive list of options available for this command, type

jasper --help

To compare particular qualities of two images, use the imgcmp command.

imgcmp -f [file 1] -F [file 2] -m [metric]

For a full list of acceptable metric arguments, type

imgcmp --help

To view a sequence of one or more images, use the jiv command.  

jiv image

Alternatively, if you would like to view multiple images in sequence you can use the --wait option to specify the amount of time between the display of each image, creating a slideshow.  The command below will display each image for 5 seconds before displaying the next image.   

jiv --wait 5 [image1 image2 image3 ...]

For a full list of options, type

jiv --help

Further Reading

Additional information about JasPer can be found online at the JasPer Project Homepage.

From julialang.org:

"Julia is a high-level, high-performance dynamic programming language for numerical computing. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library. Julia’s Base library, largely written in Julia itself, also integrates mature, best-of-breed open source C and Fortran libraries for linear algebra, random number generation, signal processing, and string processing. In addition, the Julia developer community is contributing a number of external packages through Julia’s built-in package manager at a rapid pace. IJulia, a collaboration between the Jupyter and Julia communities, provides a powerful browser-based graphical notebook interface to Julia."

Interactive Julia Notebooks

If you are using OnDemand, you can simply work with Jupyter and the selection of the Julia kernel to use interactive notebooks to work on an Owens compute node!

Navigate to ondemand.osc.edu and select a Jupyter notebook:

Availability and Restrictions

Julia is available on Owens Clusters. The versions currently available at OSC are:

Feel free to contact OSC Help if you need other versions for your work.

Access

Julia is available for use by all OSC users.

The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a classical molecular dynamics code designed for high-performance simulation of large atomistic systems.  LAMMPS generally scales well on OSC platforms, provides a variety of modeling techniques, and offers GPU accelerated computation.

Availability and Restrictions

LAMMPS is available on Oakley, Ruby, and Owens Clusters. The following versions are currently available at OSC (S means serial executables, P means parallel, and C means CUDA, i.e., GPU enabled):

You can use module spider lammps to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

LAMMPS is available to all OSC users without restriction.

Usage on Oakley

lammps < input.file

module help lammps

qsub -I -l nodes=1:ppn=1 -l walltime=00:20:00

~srb/workshops/compchem/lammps/

#PBS -N chain  
#PBS -l nodes=2:ppn=12  
#PBS -l walltime=10:00:00  
#PBS -S /bin/bash  
#PBS -j oe  
module load lammps  
cd $PBS_O_WORKDIR  
pbsdcp chain.in $TMPDIR  
cd $TMPDIR  
lammps < chain.in  
pbsdcp -g '*' $PBS_O_WORKDIR

Usage on Ruby

lammps < input.file

module help lammps

qsub -I -l nodes=1:ppn=20:gpus=1 -l walltime=00:20:00 

~srb/workshops/compchem/lammps/

#PBS -N chain  
#PBS -l nodes=2:ppn=20  
#PBS -l walltime=10:00:00  
#PBS -S /bin/bash  
#PBS -j oe  
module load lammps  
cd $PBS_O_WORKDIR  
pbsdcp chain.in $TMPDIR  
cd $TMPDIR  
lammps < chain.in  
pbsdcp -g '*' $PBS_O_WORKDIR

Usage on Owens

lammps < input.file

module help lammps

qsub -I -l nodes=1:ppn=28:gpus=1 -l walltime=00:20:00 

~srb/workshops/compchem/lammps/

#PBS -N chain  
#PBS -l nodes=2:ppn=28  
#PBS -l walltime=10:00:00  
#PBS -S /bin/bash  
#PBS -j oe  
module load lammps  
cd $PBS_O_WORKDIR  
pbsdcp chain.in $TMPDIR  
cd $TMPDIR  
lammps < chain.in  
pbsdcp -g '*' $PBS_O_WORKDIR

Further Reading

• The LAMMPS Homepage

LS-DYNA is a general purpose finite element code for simulating complex structural problems, specializing in nonlinear, transient dynamic problems using explicit integration. LS-DYNA is one of the codes developed at Livermore Software Technology Corporation (LSTC).

Availability and Restrictions

LS-DYNA is available on Ruby and Oakley Clusters for both serial (smp solver for single node jobs) and parallel (mpp solver for multipe node jobs) versions. The versions currently available at OSC are:

Feel free to contact OSC Help if you need other versions for your work.

Access for Academic Users

OSC does not provide LS_DYNA license directly, however users with their own academic departmental license can use it on the OSC clusters.  Please contact OSC Help for further instruction.

Access for Commerical Users

Contact OSC Help for getting access to LS-DYNA if you are a commerical user.

Usage

Usage on Oakley

qsub -I -l nodes=1:ppn=12 -l walltime=00:20:00 

#PBS -N plate_test
#PBS -l walltime=5:00:00
#PBS -l nodes=1:ppn=12
#PBS -j oe
# The following lines set up the LSDYNA environment
module load ls-dyna/971_d_7.0.0
#
# Move to the directory where the input files are located
#
cd $PBS_O_WORKDIR
#
# Run LSDYNA (number of cpus > 1)
#
lsdyna I=explorer.k NCPU=12

#PBS -N plate_test
#PBS -l walltime=5:00:00
#PBS -l nodes=2:ppn=12
#PBS -j oe
# The following lines set up the LSDYNA environment
module swap mvapich2/1.7 intelmpi
module load mpp-dyna/971_d_R7.0.0
#
# Move to the directory where the input files are located
#
cd $PBS_O_WORKDIR
#
# Run LSDYNA (number of cpus > 1)
#
mpiexec mpp971 I=explorer.k NCPU=24

...
cd $TMPDIR
cp $PBS_O_WORKDIR/explorer.k .
... #launch the solver and execute
pbsdcp -g '*' $PBS_O_WORKDIR

Usage on Ruby

qsub -I -l nodes=1:ppn=20 -l walltime=00:20:00 

#PBS -N plate_test
#PBS -l walltime=5:00:00
#PBS -l nodes=1:ppn=20
#PBS -j oe
# The following lines set up the LSDYNA environment
module load ls-dyna/971_d_7.0.0
#
# Move to the directory where the input files are located
#
cd $PBS_O_WORKDIR
#
# Run LSDYNA (number of cpus > 1)
#
lsdyna I=explorer.k NCPU=20

#PBS -N plate_test
#PBS -l walltime=5:00:00
#PBS -l nodes=2:ppn=20
#PBS -j oe
# The following lines set up the LSDYNA environment
module swap mvapich2/1.7 intelmpi/5.0.1
module load mpp-dyna/971_d_R7.0.0
#
# Move to the directory where the input files are located
#
cd $PBS_O_WORKDIR
#
# Run LSDYNA (number of cpus > 1)
#
mpiexec mpp971 I=explorer.k NCPU=40

...
cd $TMPDIR
cp $PBS_O_WORKDIR/explorer.k .
... #launch the solver and execute
pbsdcp -g '*' $PBS_O_WORKDIR

Usage on Owens

qsub -I -l nodes=1:ppn=28 -l walltime=00:20:00 

#PBS -N plate_test
#PBS -l walltime=5:00:00
#PBS -l nodes=1:ppn=28
#PBS -j oe
# The following lines set up the LSDYNA environment
module load ls-dyna/971_d_9.0.1
#
# Move to the directory where the input files are located
#
cd $PBS_O_WORKDIR
#
# Run LSDYNA (number of cpus > 1)
#
lsdyna I=explorer.k NCPU=28

#PBS -N plate_test
#PBS -l walltime=5:00:00
#PBS -l nodes=2:ppn=28
#PBS -j oe
# The following lines set up the LSDYNA environment
module swap mvapich2/2.2 intelmpi
module load mpp-dyna/971_d_R9.0.1
#
# Move to the directory where the input files are located
#
cd $PBS_O_WORKDIR
#
# Run LSDYNA (number of cpus > 1)
#
mpiexec mpp971 I=explorer.k NCPU=56

...
cd $TMPDIR
cp $PBS_O_WORKDIR/explorer.k .
... #launch the solver and execute
pbsdcp -g '*' $PBS_O_WORKDIR

Further Reading

• The LSDYNA homepage
• The LSDYNA users manual (structural and keyword editions)
• The LSDYNA Theory Manual
• The LS-PREPOST Tutorial

See Also

MAGMA is a collection of next generation linear algebra (LA) GPU accelerated libraries designed and implemented by the team that developed LAPACK and ScaLAPACK. MAGMA is for heterogeneous GPU-based architectures, it supports interfaces to current LA packages and standards, e.g., LAPACK and BLAS, to allow computational scientists to effortlessly port any LA-relying software components. The main benefits of using MAGMA are that it can enable applications to fully exploit the power of current heterogeneous systems of multi/manycore CPUs and multi-GPUs, and deliver the fastest possible time to an accurate solution within given energy constraints.

Availability and Restrictions

MAGMA is available on Owens, and the following versions are currently available at OSC:

You can use module spider magma  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access for Academic Users

MAGMA is available without restriction to all OSC users. 

Usage on Owens

icc $MAGMA_CFLAGS example.c

ifort $MAGMA_F90FLAGS example.F90

qsub -I -l nodes=1:ppn=28 -l walltime=1:00:00

# MAGMA Example Batch Script for the Basic Tutorial in the MAGMA manual
#PBS -N 6pti
#PBS -l nodes=1:ppn=28
#PBS -l walltime=0:20:00
module load cuda
module load magma
# Use TMPDIR for best performance.
cd $TMPDIR
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cp $PBS_O_WORKDIR/example.c .
icc $MAGMA_CFLAGS example.c

Further Reading

• MAGMA Homepage

MATLAB is a technical computing environment for high-performance numeric computation and visualization. MATLAB integrates numerical analysis, matrix computation, signal processing, and graphics in an easy-to-use environment where problems and solutions are expressed just as they are written mathematically--without traditional programming.

Availability and Restrictions

MATLAB is available on Oakley, Ruby, and Owens Clusters. The versions currently available at OSC are:

You can use module spider matlab  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access to Academic Users

All academic users must be added to the license server before using MATLAB.  Please contact OSC Help to be granted access.

Another method to use MATLAB on OSC is to use the MATLAB Distributed Computing Server on Oakley via your local MATLAB client.  In order to use this feature, you should have your own MATLAB license, including the Parallel Computing Toolbox. See HOW-TO: Configure the MATLAB Parallel Computing Toolbox.

Usage on Oakley

matlab -nodisplay 

qsub -I -X -l nodes=1:ppn=12 -l walltime=00:20:00 

#PBS -N matlab_example
#PBS -l walltime=00:10:00
#PBS -l nodes=1:ppn=12
#PBS -j oe
module load matlab
matlab -nodisplay -nodesktop < hello.m
# end of example file

%Example M-file for Hello World
disp 'Hello World' 
exit   
% end of example file

qsub job.txt 

Bioinformatics_Toolbox
Communication_Toolbox
Control_Toolbox
Curve_Fitting_Toolbox
Data_Acq_Toolbox
Fuzzy_Toolbox
Image_Toolbox
Instr_Control_Toolbox
Neural_Network_Toolbox
Optimization_Toolbox
Distrib_Computing_Toolbox
PDE_Toolbox
RF_Toolbox
Robust_Toolbox
Signal_Toolbox
Statistics_Toolbox
Symbolic_Toolbox
Identification_Toolbox
Wavelet_Toolbox

#PBS -N disable_multithreading
#PBS -l walltime=00:10:00
#PBS -l nodes=1:ppn=1
#PBS -j oe
module load matlab
matlab -singleCompThread -nodisplay -nodesktop < hello.m
# end of example file

Usage on Ruby

matlab -nodisplay 

qsub -I -X -l nodes=1:ppn=20 -l walltime=00:20:00 

Bioinformatics_Toolbox
Communication_Toolbox
Control_Toolbox
Curve_Fitting_Toolbox
Data_Acq_Toolbox
Fuzzy_Toolbox
Image_Toolbox
Instr_Control_Toolbox
Neural_Network_Toolbox
Optimization_Toolbox
Distrib_Computing_Toolbox
PDE_Toolbox
RF_Toolbox
Robust_Toolbox
Signal_Toolbox
Statistics_Toolbox
Symbolic_Toolbox
Identification_Toolbox
Wavelet_Toolbox

#PBS -N disable_multithreading
#PBS -l walltime=00:10:00
#PBS -l nodes=1:ppn=20
#PBS -j oe
module load matlab
matlab -singleCompThread -nodisplay -nodesktop < hello.m
# end of example file

Usage on Owens

matlab -nodisplay 

qsub -I -X -l nodes=1:ppn=28 -l walltime=00:20:00 

Bioinformatics_Toolbox
Communication_Toolbox
Control_Toolbox
Curve_Fitting_Toolbox
Data_Acq_Toolbox
Fuzzy_Toolbox
Image_Toolbox
Instr_Control_Toolbox
Neural_Network_Toolbox
Optimization_Toolbox
Distrib_Computing_Toolbox
PDE_Toolbox
RF_Toolbox
Robust_Toolbox
Signal_Toolbox
Statistics_Toolbox
Symbolic_Toolbox
Identification_Toolbox
Wavelet_Toolbox

#PBS -N disable_multithreading
#PBS -l walltime=00:10:00
#PBS -l nodes=1:ppn=28
#PBS -j oe
module load matlab
matlab -singleCompThread -nodisplay -nodesktop < hello.m
# end of example file

MATLAB with a GPU

A GPU can be utilized for MATLAB. You can acquire a GPU by nodes=1:ppn=20;gpus=1 for Ruby or Owens (ppn=28 for Owens). For more detail, please read here.

You can check the GPU assigned to you using:

gpuDeviceCount  # show how many GPUs you have
gpuDevice       # show the details of the GPU

You can replace an array to gpuArray, for example:

A = gpuArray(A)

where A is a regular MATLAB array. This transfers the array data to the GPU memory. Then, you can use the gpuArray variable in GPU supported built-in functions. You can find the full list of GPU supported built-in functions from here. For more information about GPU programming for MATLAB, please read "GPU Computing" from Mathworks.

Further Reading

Official PDF documentation can be obtained from the MathWorks Website. 

MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.

Availability and Restrictions

The following versions of MIRA are available on OSC clusters:

You can use  module spider mira  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

MIRA is available to all OSC users without restriction.

Usage on Oakley

Usage on Owens

Further Reading

• The MIRA Official Webpage

High-performance, multithreaded mathematics libraries for linear algebra, fast Fourier transforms, vector math, and more.

Availability and Restrictions

OSC supports single-process use of MKL for LAPACK and BLAS levels one through three. For multi-process applications, we also support the ScaLAPACK, FFTW2, and FFTW3 MKL wrappers. MKL modules are available for the Intel, GNU, and PGI compilers. MKL is available on Oakley, Ruby, and Owens Clusters. The versions currently available at OSC are:

You can use module spider mkl to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

All OSC users may use the MKL for academic purposes.

Usage on Oakley

ifort -c my_prog.f
ifort -o my_prog my_prog.o $MKL_LIBS

icc -c my_prog.c
icc -o my_prog my_prog.o $MKL_LIBS

ifort -c my_prog.f95 $MKL_F95FLAGS
ifort -o my_prog my_prog.o $MKL_F95LIBS $MKL_LIBS

icc -c $MKL_FFTW_CFLAGS -DMKL_DOUBLE my_prog.c
icc -o my_prog my_prog.o $MKL_FFTW2_D_CLIBS $MKL_LIBS

ifort -c $MKL_FFTW_FFLAGS my_prog.f
ifort -o my_prog my_prog.o $MKL_FFTW2_S_FLIBS $MKL_LIBS

icc -c $MKL_FFTW_CFLAGS my_prog.c
icc -o my_prog my_prog.o $MKL_FFTW3_CLIBS $MKL_LIBS

ifort -c $MKL_FFTW_FFLAGS my_prog.f 
ifort -o my_prog my_prog.o $MKL_FFTW3_CLIBS $MKL_LIBS

Usage on Ruby

Usage on Owens

Further Reading

• Intel MKL Website
• Intel MKL Documentation
• FFTW

MPJ-Express is a Java library that provides message passing capabilities for parallel computing in Java applications.

MPJ-Express is available on Oakley.

Availability & Restrictions

MPJ-Express is available without restriction to all OSC users.

The following versions of MPJ-Express are available on OSC systems:

Note: We have modified MPJ-Express slightly from the default distribution to work nicely with our infrastructure. Installing your own copy of a newer version will not work. Please contact OSC Help if you need a newer version of this library.

Usage

Set-up

To set up your environment for using the MPJ-Express libraries, you must load the appropriate module. On Oakley this is pretty straightforward:

module load mpj-express

Building With MPJ-Express

When you load the MPJ-Express module, we will modify your CLASSPATH to ensure the JAR files are located.

Batch Usage

Programs built with MPJ-Express can only be run in the batch environment at OSC. For information on writing batch scripts, see Batch Processing at OSC.

If you have loaded a Java module when compiling, be sure to load that same module in your batch script to avoid version mismatches.

Here is a basic "Hello World" program, which needs to be in a file called "HelloWorld.java", which we use in our example batch script:

import mpi.*;
public class HelloWorld
{
     public static void main(String[] args) 
                     throws Exception
     {
          MPI.Init(args);
          int me = MPI.COMM_WORLD.Rank();
          int size = MPI.COMM_WORLD.Size();
          System.out.println
            ("Hi from " + me + " of " + size + "\n");
          MPI.Finalize();
     }
}

Below we have included a sample batch script:

#PBS -N mpj-world
#PBS -l walltime=0:05:00
#PBS -l nodes=2:ppn=12
#PBS -S /bin/bash

# Set environment
module load mpj-express/0.44

# Change to the directory you submitted the job from
cd $PBS_O_WORKDIR

# Set up the directory for the daemon logs to go in
export MPJ_LOG="$PBS_O_WORKDIR/log"
mkdir $MPJ_LOG

# Re-compile our application - not strictly necessary,
# if the source is unchanged.
javac HelloWorld.java

# Start MPJ
mpjboot $PBS_NODEFILE

# Launch your parallel program
mpjrun.sh -np $PBS_NP -dev native HelloWorld

# Shutdown MPJ
mpjhalt $PBS_NODEFILE

Further Reading

• http://mpj-express.org/index.html

See Also

• Batch Processing at OSC

MPI is a standard library for performing parallel processing using a distributed-memory model. 

Availability & Restrictions

MPI is available without restriction to all OSC users.

The following versions of MVAPICH2 are available on OSC systems.  To see which compilers a particular version of MVAPICH2 is available for, use, for example, module spider mvapich2/2.2.

Usage

Set-up

To set up your environment for using the MPI libraries, you must load the appropriate module:

module load mvapich2

You will get the default version for the compiler you have loaded.

Building With MPI

To build a program that uses MPI, you should use the compiler wrappers provided on the system. They accept the same options as the underlying compiler. The commands are shown in the following table.

For example, to build the code my_prog.c using the -O2 option, you would use:

mpicc -o my_prog -O2 my_prog.c

In rare cases you may be unable to use the wrappers. In that case you should use the environment variables set by the module.

For example, to build the code my_prog.c without using the wrappers you would use:

mpicc -c $MPI_CFLAGS my_prog.c

mpicc -o my_prog my_prog.o $MPI_LIBS

Batch Usage

Programs built with MPI can only be run in the batch environment at OSC. For information on starting MPI programs using the mpiexec command, see Batch Processing at OSC.

Be sure to load the same compiler and mvapich modules at execution time as at build time.

Further Reading

• The Message Passing Interface (MPI) Standard
• MPI Training Course

See Also

• Intel MPI
• OpenMPI

Apache Maven is a plugin-based build automation tool, similar in purpose to GNU Make or Apache Ant. It is most commonly used with Java projects, but also supports other languages such as .NET and C/C++.

Availability & Compatibility

Restrictions

There are no restrictions for this software; any OSC user may make use of the Apache Maven.

Usage

Set-up

To use Maven, load the the "maven" module with the following command.

module load maven

To test that the install worked correctly, run "mvn --version". You should see output similar to that shown below:

$ mvn --version
Apache Maven 3.0.4 (r1232337; 2012-01-17 03:44:56-0500)
Maven home: /usr/local/maven/3.0.4
Java version: 1.6.0_29, vendor: Sun Microsystems Inc.
Java home: /usr/lib/jvm/java-1.6.0-sun-1.6.0.29.x86_64/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "2.6.32-131.17.1.el6.x86_64", arch: "amd64", family: "unix"

Basic Usage

Once the module is loaded, you can use Maven just as you would on your local machine. For example, the session below illustrates initializing a new project call "my-app":

$ mvn archetype:generate -DgroupId=com.mycompany.app -DartifactId=my-app -DarchetypeArtifactId=maven-archetype-quickstart -DinteractiveMode=false
[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Maven Stub Project (No POM) 1
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] >>> maven-archetype-plugin:2.2:generate (default-cli) @ standalone-pom >>>
[INFO] 
[INFO] <<< maven-archetype-plugin:2.2:generate (default-cli) @ standalone-pom <<<
[INFO] 
[INFO] --- maven-archetype-plugin:2.2:generate (default-cli) @ standalone-pom ---
[INFO] Generating project in Batch mode
[INFO] ----------------------------------------------------------------------------
[INFO] Using following parameters for creating project from Old (1.x) Archetype: maven-archetype-quickstart:1.0
[INFO] ----------------------------------------------------------------------------
[INFO] Parameter: groupId, Value: com.mycompany.app
[INFO] Parameter: packageName, Value: com.mycompany.app
[INFO] Parameter: package, Value: com.mycompany.app
[INFO] Parameter: artifactId, Value: my-app
[INFO] Parameter: basedir, Value: /nfs/12/jmccance
[INFO] Parameter: version, Value: 1.0-SNAPSHOT
[INFO] project created from Old (1.x) Archetype in dir: /nfs/12/jmccance/my-app
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 4.429s
[INFO] Finished at: Fri Jun 08 14:30:57 EDT 2012
[INFO] Final Memory: 9M/361M
[INFO] ------------------------------------------------------------------------

Further Reading

• Official Apache Maven website

See Also

MrBayes is 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.

Availability & Restrictions

MrBayes is available without restriction to all OSC users.

The following versions of MrBayes are available:

Usage

Set-up

To load the MrBayes software on the Oakley system, use the following command:

module load mrbayes

Using MrBayes

Once mrbayes module is loaded, the commands are available for your use. The command for serial version is

mb

Parallel Mrbayes can only be used via batch system. The command is

mb-parallel

Batch Usage

Below is a sample batch script for running serial mrbayes job. It asks for 1 processor and 30 minutes of walltime.

#PBS -l walltime=30:00
#PBS -l nodes=1:ppn=1
#PBS -N mb
#PBS -j oe
set -x
date
cd $PBS_O_WORKDIR
cp ./primates.nex $TMPDIR
cp ./primates.nxs $TMPDIR
cd $TMPDIR
module load mrbayes/3.2.1
/usr/bin/time mb ./primates.nxs > mb.log
cp * $PBS_O_WORKDIR
date

#PBS -l walltime=30:00
#PBS -l nodes=2:ppn=12
#PBS -N mb-parallel
#PBS -j oe
set -x
date
cd $PBS_O_WORKDIR
pbsdcp ./primates.nex $TMPDIR
pbsdcp ./primates.nxs $TMPDIR
cd $TMPDIR
module load mrbayes
/usr/bin/time mpiexec mb-parallel ./primates.nxs > mb-paralllel.log
pbsdcp -g '*' $PBS_O_WORKDIR
date

Further Reading

• The MrBayes homepage

See Also

• Paup

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

Availability and Restrictions

The following versions of MuTect are available on OSC clusters:

You can use  module spider mutect  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access for Academic Users

MuTect is available to academic OSC users with proper validation. In order to obtain validation, please contact OSC Help for further instruction. 

Usage on Oakley

Usage on Owens

Further Reading

• The MuTect Official Webpage

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD generally scales well on OSC platforms and offers a variety of modelling techniques. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR.

Availability & Restrictions

NAMD is available without restriction to all OSC users.

The following versions of NAMD are available:

*: Current default version

Set-up

To load the NAMD software on the system, use the following command: module load namd/"version"  where "version" is the version of NAMD you require. The following will load the default or latest version of NAMD:  module load namd  

Using NAMD

NAMD is rarely executed interactively because preparation for simulations is typically performed with extraneous tools, such as, VMD.

Batch Usage

Sample batch scripts and input files are available here:

~srb/workshops/compchem/namd/