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Software on Linux Systems

Issue rpm -qa on a linux login node to list all the RPMs installed.

Package

Version		 Location On
login
nodes		 On
batch
nodes
ABAQUS
6.7-1		 /opt/abaqus yes yes
Ant
1.6.5 (default)		 /opt/rocks/bin yes yes
Ant /opt/apache-ant-1.7.1 yes yes
APPSPACK /cac/contrib/appspack-5.0.1 yes yes
BLAS /usr/lib64
(or use Intel MKL) 		yes yes
Boost
1.33.1		 /usr/lib64 yes yes
Clustalw
2.0.5		 /opt/Bio/clustalw yes yes
Eclipse
3.4.0 (Ganymede)		 /opt/eclipse yes no
EMBOSS
5.0.0		 /opt/Bio/EMBOSS yes yes
Fasta
35.03		 /opt/Bio/fasta yes yes
FFTW2 /cac/contrib/fftw-2.1.5 yes yes
FFTW3
3.1.2		 /usr/lib64 yes yes
Firefox
3		 /usr/local/bin yes no
GIMP
2.2.13		 /usr/bin yes no
Glimmer
3.02		 /opt/Bio/glimmer yes yes
Globus client tools
4.2.1		 /opt/globus yes no
GNU C/C++ compiler
(gcc, default)
4.1.2		 /usr/bin yes yes
GNU C/C++ compiler
(gcc)		 /opt/gcc-4.3.1/bin yes yes
GNU Fortran 95 compiler
(gfortran, default)
4.1.2		 /usr/bin yes yes
GNU Fortran 95 compiler
(gfortran)		 /opt/gcc-4.3.1/bin yes yes
GSL /cac/contrib/gsl-1.11 yes yes
Gromacs
3.3.1		 /opt/Bio/gromacs yes yes
Hmmer
2.3.2		 /opt/Bio/hmmer yes yes
Intel C/C++ compiler
(icc)		 /opt/intel/cce/10.1.017 yes runtime
Intel Fortran compiler
(ifort)		 /opt/intel/fce/10.1.017 yes runtime
Intel MKL /opt/intel/mkl/10.0.3.020 yes no
Intel MPI libraries /opt/intel/impi/3.1 yes runtime
Java SDK
1.6.0_07		 /usr/java/default yes yes
LAPACK
3.0.3		 /usr/lib64
(or use Intel MKL)		 yes yes
MATLAB
R2007b		 /opt/matlab-7.5 yes runtime
Moab client tools /usr/local/bin yes no
mpiBLAST
1.4.0		 /opt/Bio/mpiblast yes yes
mpich2 /opt/mpich2 yes yes
MrBayes
3.1.2		 /opt/Bio/mrbayes yes yes
mysql
5.0.22		 /usr/bin yes yes
NCBI Software Development Toolkit
6.1		 /opt/Bio/ncbi yes yes
Octave
3.0.0		 /usr/bin yes yes
OpenOffice /opt/openoffice.org2.4 yes no
Perl
5.8.8		 /usr/bin yes yes
Phylip
3.67		 /opt/Bio/phylip yes yes
Python
2.4.3 (default)		 /usr/bin yes yes
Python2.5
2.5.2		 /usr/local/bin yes yes
R
2.7.1		 /usr/bin yes yes
Subversion client tools
1.5.0 (svn, svnversion)		 /usr/local/bin yes yes
t_coffee
5.65		 /opt/Bio/t_coffee yes yes

last updated 9/10/08