Available Software
From HPC
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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. | ||
- | == | + | ===Python=== |
- | + | Python versions 2.7 and 3.5 are available | |
- | + | Python 2.7 binaries/exectuables | |
- | + | ||
- | + | python --version | |
- | + | python2 --version | |
- | + | pip | |
- | + | pip2 | |
- | ==GNU Compilers== | + | Python 3.5 binaries/exectuables |
+ | |||
+ | python3.5 --version | ||
+ | pip3.5 | ||
+ | |||
+ | ==GNU 4.8 Compilers (DEFAULT)== | ||
*C/C++ (gcc/g++) | *C/C++ (gcc/g++) | ||
*Fortran (gfortran) | *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=== | ===C/C++ compiler options/tuning=== | ||
Line 42: | Line 52: | ||
MAKEOPTS="-j2" | 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. | R is a language and environment for statistical computing and graphics. | ||
http://www.r-project.org/ | 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== | ==Java== | ||
- | Versions | + | Versions JDK 7 and JDK 8 64bit |
+ | |||
+ | java -version (version 8) | ||
+ | |||
+ | /opt/java7/bin/java (version 7) | ||
==OpenMP== | ==OpenMP== | ||
Line 66: | Line 98: | ||
gfortran -fopenmp | gfortran -fopenmp | ||
- | |||
- | + | ||
- | + | [[Parallel Jobs]] | |
- | + | ||
==openMPI== | ==openMPI== | ||
+ | |||
+ | [[Parallel Jobs]] | ||
+ | |||
+ | ==Libraries== | ||
+ | |||
+ | ===C=== | ||
+ | |||
+ | *Xerces | ||
+ | *Boost | ||
+ | *CodeSynthesis XSD (/usr/local/bin/xsd /usr/local/include/libxsd/) | ||
=Software= | =Software= | ||
- | == | + | For more details see [[:Category:Software|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 | ||
- | |||
- | |||
- | [[Category:Getting Started]][[Category:About]] | + | [[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
- 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.
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
openMPI
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
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