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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 -----------------------------
MapSplice/1.15.2

-
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/3.3.5.2            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/0.12.54.6
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/4.5.1.0                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/3.3.5.2
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/7.2.29.269
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
/usr/bin/python
[abc1234@brodie ~ []]$ module load python/2.7.1
[abc1234@brodie ~ []]$ python -V
Python 2.7.1
[abc1234@brodie ~ []]$ which python
/tools/python/2.7.1/bin/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
/tools/rsi/idl_6.3/bin/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

IDL>

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Using software