From HPC

Please contact support if you need/what different software or libraries install. Appropriate licenses will need to be provide.

Contents 1 Compilers 1.1 Python 1.2 GNU 4.8 Compilers (DEFAULT) 1.2.1 Docs 1.2.2 C/C++ compiler options/tuning 1.2.3 Other GNU GCC Compilers (Newer) 1.3 R 1.4 Java 1.5 OpenMP 1.6 openMPI 1.7 Libraries 1.7.1 C 2 Software 2.1 Stata 2.2 JAGS 1.0.3 2.3 Winbugs/OpenBugs/Linbugs 2.4 Structure

Compilers

Listed below are the compilers currently installed and supported. If there is a language or compiler you would like, please speak to IT Services.

Python

Python versions 2.7 and 3.5 are available

Python 2.7 binaries/exectuables

python --version
python2 --version
pip
pip2

Python 3.5 binaries/exectuables

python3.5 --version
pip3.5

GNU 4.8 Compilers (DEFAULT)

• C/C++ (gcc/g++)
• Fortran (gfortran)

Docs

• GCC http://gcc.gnu.org/onlinedocs/gcc-4.1.2/gcc/
• GNU Fortran http://gcc.gnu.org/onlinedocs/gcc-4.1.2/gfortran/
• GCPP http://gcc.gnu.org/onlinedocs/gcc-4.1.2/cpp/

C/C++ compiler options/tuning

Note: You can also try optimization level 3, change -02 to -03

• i686 (32 bit)

CHOST="i686-pc-linux-gnu"
CFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer"
CXXFLAGS="${CFLAGS}"

• x86-64 (64 bit)

CHOST="x86_64-pc-linux-gnu"
CFLAGS="-march=nocona -O2 -pipe" 
CXXFLAGS="${CFLAGS}"

Improve make speed

MAKEOPTS="-j2"

Other GNU GCC Compilers (Newer)

Other custom versions of GCC are available via environment modules

module avail

To load a specific gcc module

module load gcc/7.4.0

R

R is a language and environment for statistical computing and graphics.

http://www.r-project.org/

R is available via environment modules

List all available versions

module avail

To load a specific version

module load R/3.4.2

Java

Versions JDK 7 and JDK 8 64bit

java -version (version 8)

/opt/java7/bin/java (version 7) 

OpenMP

OpenMP website http://openmp.org/wp/

Both the GNU and Intel compilers support OpenMP.

GNU

gcc -fopenmp
g++ -fopenmp
gfortran -fopenmp

Parallel Jobs

openMPI

Parallel Jobs

Libraries

C

• Xerces
• Boost
• CodeSynthesis XSD (/usr/local/bin/xsd /usr/local/include/libxsd/)

Software

For more details see Software Category

Stata

See Stata

Stata SE for use on cluster. Please note Stata has limited licenses on the HPC.

qstata jobscript

JAGS 1.0.3

See Jags

Bugs compile, similar to openbugs or winbugs http://www-fis.iarc.fr/~martyn/software/jags/

Manual http://www-fis.iarc.fr/~martyn/software/jags/jags_user_manual.pdf

jags

Winbugs/OpenBugs/Linbugs

See Linbugs ( aka Openbugs or Winbugs) for more information

You can run Openbugs/Winbugs jobs on the cluster using Linbugs.

linbugs < bugs.script > outputfile

This only runs the classic version i.e. no gui, so you should get everything ready on your workstation first.

Structure

See Structure (Software)

The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.

http://pritch.bsd.uchicago.edu/structure.html

Usage

You need to specify a main params file (can be created in the gui on you local workstation), an extra params file (this can be an empty text file, but must be specified), a data file and the location of the output

structure -m mainparams -e extraparams -i project_data -o results