Available Software
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==Winbugs/OpenBugs/Linbugs== | ==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. | You can run Openbugs/Winbugs jobs on the cluster using Linbugs. | ||
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- | [[Category:Getting Started]][[Category:About]] | + | [[Category:Getting Started]][[Category:About]][[Category:Software]] |
Revision as of 09:50, 7 May 2009
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.
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.
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
openMPI
Libraries
C
- Xerces
- Boost
- CodeSynthesis XSD (/usr/local/bin/xsd /usr/local/include/libxsd/)
Software
For more details see Software Category
Stata 10
See Stata 10
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
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
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