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 Intel 10.1 Proffesional (2 concurrent licenses) 1.2 GNU 4.1 Compilers 1.2.1 Docs 1.2.2 C/C++ compiler options/tuning 1.3 R 1.4 Java 1.5 OpenMP 1.6 openMPI 1.7 Libraries 1.7.1 C 2 Software 2.1 Stata10 2.2 JAGS 1.0.3 2.3 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.

Intel 10.1 Proffesional (2 concurrent licenses)

The Intel compilers are highly optermized for the cpu's in the gecko cluster. They also include the Maths Kernel Library (BLAS, LAPACK, etc), please see Intel documentation for more information.

• C/C++ (icc/icpc)
• Fortran (ifort)

• Intel Fortran Information
• Intel Fortran Documentation
• Intel C/C++ Information
• Intel C/C++ Documentation

GNU 4.1 Compilers

• 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"

R

Version 2.7.2

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

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

Java

Versions 1.4, 1.5, 1.6 in 32bit and 64bit flavours, enabled/loaded via modules

OpenMP

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

Both the GNU and Intel compilers support OpenMP.

GNU

gcc -fopenmp
g++ -fopenmp
gfortran -fopenmp

Intel

icc -openmp
icpc -openmp
ifort -openmp

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

Stata10

Stata SE 32bit command line, for use on cluster

stata-se 

Stata SE 32bit GUI, for use only on head node to check/change do files etc

xstata-se

JAGS 1.0.3

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

Structure

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