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Comment: updated software list


Using software

Research Computing has a number of third-party software packages installed (both with restricted licenses and open source). We use the modules package to mitigate any conflicts between the environments and installations of these different tools.

To see what software is available, you can use the module avail command. For example:

[abc1234@brodie ~ []]$ module avail

---------------------------------- /etc/modulefiles ----------------------------------
mpich2-i386   mpich2-x86_64

----------------------------- /tools/Modules/modulefiles -----------------------------
ampl/20091123 cuda/2.3 condor/7.4.1 MapSplice/1.15.2
ampl/20091123-stu(default) cuda/4.0.17 lumerical/6.5.11 SpliceMap/ mathematica/10.0
ampl/20130226 cuda/4.1.28 cuda/2.3 matlab/2011b
ansoft/12 lumericalcufflinks/62.5.8(default) ampl/200911230.2b matlab/2012b
ansys/15.0.7 cuda eigen/43.0.174 lumerical/7.5.4 ampl/20091123-stu(default) maya/2012
boost/1.48.0 envi/6.3 maple/15 ansoft/12 module_archive
bowtie/0.12.5 envi/8.0 fluent/13.0.0 mathematica omnetpp/6.0 bowtie/
cadence/5.1.41 fluent/613.3.26(default)0.0 mathematica/7.0(default) cadence/5(default) font_serverpcl/1.4.0
cadence/6.210 matlab/2007b cadence/6 fluent/15.0.0 g95 R/0.902.15.3
cadence/6.13 font_server/1.0.2 matlab/2009a(default) R/3.0.0
caldb/caldb-413 glpkg95/40.4590 matlab/2011a R/3.0.1
casava/1.7.0 gurobigcc/2.0.1(default)4.4 python/2.6.4 R/3.0.2
ciao/ciao-412 gurobiglpk/34.0.145 python/2.7.1 comsol/cheme-35a R/3.1.1
cmake/2.8.7 gurobi/4.06.01 samtools/0.1.17
comsol/mechecheme-3435a gurobi/ sentaurus/E-2010.12
comsol/meche-35a34 harpoon/3.2a6a silvaco/multi
comsol/microsystemsmeche-3335a harpoon/3.6a(default) system_defaults comsol/smfl-40aIntelClusterSuite/2013xe SpliceMap/
comsol/microsystems-33 knitro/7.0.0 knitro/6.0.1 system_defaults
comsol/smfl-40a lumerical/8.11.318(default) tophat/1.3.1
comsol/smfl-41 knitrolumerical/78.0.0 condor/
cplex/12.4 lumerical/6.0.4 maple/15


We no longer run CentOS 5.5, the following, while vaild, isn't 100% accurate

For instance, the operating system we run (CentOS 5.5) comes with python 2.4 by default (which is pretty old). Many users need access to the latest version of python. You can check which version of python is available in your $PATH and load the newest version with the following:

[abc1234@brodie ~ []]$ python -V
Python 2.4.3
[abc1234@brodie ~ []]$ which python
[abc1234@brodie ~ []]$ module load python/2.7.1
[abc1234@brodie ~ []]$ python -V
Python 2.7.1
[abc1234@brodie ~ []]$ which python

Some packages are a little trickier. For instance, many imaging scientists need access to the idl programming environment. Our module avail command doesn’t list idl explicitly, but it is contained with the envi package. The following example demonstrates this:

[abc1234@brodie ~ []]$ which idl
/usr/bin/which: no idl in (/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/tools/condor/7.4.1/bin:/tools/bin:/tools/bin:/home/abc1234/bin)
[abc1234@brodie ~ []]$ module load envi
[abc1234@brodie ~ []]$ which idl
[abc1234@brodie ~ []]$ idl
IDL Version 6.3 (linux x86_64 m64). (c) 2006, Research Systems, Inc.
Installation number: 214968-1.
Licensed for use by: Rochester Institute of Technol