Available Software

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Listed below are the compilers currently installed and supported. If there is a language or compiler you would like, please speak to IT Services.
Listed below are the compilers currently installed and supported. If there is a language or compiler you would like, please speak to IT Services.
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==Intel 10.1 Proffesional (2 concurrent licenses)==
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===Python===
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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.
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Python versions 2.7 and 3.5 are available
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* C/C++ (icc/icpc)
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Python 2.7 binaries/exectuables
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* Fortran (ifort)
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*[http://www.intel.com/cd/software/products/asmo-na/eng/compilers/282048.htm Intel Fortran Information]
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python --version
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*[http://www.intel.com/software/products/compilers/docs/flin/main_for/index.htm Intel Fortran Documentation]
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python2 --version
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*[http://www.intel.com/cd/software/products/asmo-na/eng/compilers/277618.htm Intel C/C++ Information]
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pip
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*[http://www.intel.com/software/products/compilers/docs/clin/main_cls/index.htm Intel C/C++ Documentation]
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pip2
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==GNU 4.1 Compilers==
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Python 3.5 binaries/exectuables
 +
 
 +
python3.5 --version
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pip3.5
 +
 
 +
==GNU 4.8 Compilers (DEFAULT)==
*C/C++ (gcc/g++)
*C/C++ (gcc/g++)
Line 48: Line 52:
  MAKEOPTS="-j2"
  MAKEOPTS="-j2"
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==R==
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===Other GNU GCC Compilers (Newer)===
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Version 2.7.2
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Other custom versions of GCC are available via environment modules
 +
 
 +
module avail
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 +
To load a specific gcc module
 +
 
 +
module load gcc/7.4.0
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 +
==R==
R is a language and environment for statistical computing and graphics.
R is a language and environment for statistical computing and graphics.
http://www.r-project.org/
http://www.r-project.org/
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 +
R is available via environment modules
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 +
List all available versions
 +
 +
module avail
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 +
To load a specific version
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module load R/3.4.2
==Java==
==Java==
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Versions 1.4, 1.5, 1.6 in 32bit and 64bit flavours, enabled/loaded via [[modules]]
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Versions JDK 7 and JDK 8 64bit
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 +
java -version (version 8)
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 +
/opt/java7/bin/java (version 7)
==OpenMP==
==OpenMP==
Line 72: Line 98:
  gfortran -fopenmp
  gfortran -fopenmp
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Intel
 
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icc -openmp
 
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icpc -openmp
 
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ifort -openmp
 
[[Parallel Jobs]]
[[Parallel Jobs]]
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=Software=
=Software=
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==Stata10==
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For more details see [[:Category:Software|Software Category]]
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stata-se (Stata SE 32bit command line, for use on cluster)
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==Stata==
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xstata-se (Stata SE 32bit GUI, for use only on head node to check/change do files etc)
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See [[Stata]]
 +
 
 +
Stata SE for use on cluster. Please note Stata has limited licenses on the HPC.
 +
 
 +
qstata jobscript
==JAGS 1.0.3==
==JAGS 1.0.3==
 +
 +
See [[Jags]]
Bugs compile, similar to openbugs or winbugs http://www-fis.iarc.fr/~martyn/software/jags/
Bugs compile, similar to openbugs or winbugs http://www-fis.iarc.fr/~martyn/software/jags/
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Manual http://www-fis.iarc.fr/~martyn/software/jags/jags_user_manual.pdf
Manual http://www-fis.iarc.fr/~martyn/software/jags/jags_user_manual.pdf
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/user/local/jags-1.0.3/bin/jags
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jags
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 +
==Winbugs/OpenBugs/Linbugs==
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 +
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==
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 +
See [[Structure (Software)]]
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 +
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
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[[Category:Getting Started]][[Category:About]]
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[[Category:Getting Started]][[Category:About]][[Category:Software]]

Current revision as of 07:49, 3 April 2019

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

Contents

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

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
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