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The Quarry Cluster

Available Software

The following table contains all of the macros and keywords available for use with the SoftEnv system on Quarry. If you need a software package that is not listed in this table, please submit a Research Systems Software Request.

In addition to the packages available via SoftEnv, there are several utilities and applications included in the Red Hat Linux Enterprise Server distribution. Your default path should be configured to allow use of the distribution software. Please contact the High Performance Systems group, hps-admin@iu.edu, if you feel there's a problem with your environment, or software that should be available in the distribution.

(A table of keywords sorted by type is also available)

Macro	Description
@Molpro	A system for molecular electronic structure calculations
@Siesta	Spanish Initiative for Electronic Simulations with Thousands of Atoms
@amber10	AMBER 10, 64-bit, Intel, Serial & openmpi/1.2.6/intel-64
@default	Standard site-specific settings
@intel-32-v10.1	Intel(R) compiler suite, 32-bit
@intel-64-v10.1	Intel(R) compiler suite, 64-bit
@lam	A MPI implementation before OpenMPI, still in use
@mpich-idp-intel-32	MPICH1 for iDP (compiled with Intel compilers)
@mpich-idp-intel-64	MPICH1 for iDP (compiled with Intel compilers)
@mpich1	Default MPICH1 (compiled with Intel compilers)
@openmpi	Default openmpi (compiled with Intel compilers)
@quarry	Default environment for Quarry users

Keyword	Description
+CDO-64	NetCDF aware Common Data Operators, 64-bit
+Gauss	Gauss - system default version
+Gauss-9.0	Gauss Version 9.0
+ITK-3.4.0	InsightToolKit-3.4.0
+Lisrel	Lisrel Structural Equation Modelling - system default version
+Lisrel-8.7	Lisrel Structural Equation Modelling Version 8.7
+MDCE	The MATLAB Distributed Computing Environment, system default version
+MDCE-2007a	The MATLAB Distributed Computing Environment, version 2007a
+MDCS	The MATLAB Distributed Computing Server, system default version
+MDCS-2008b	The MATLAB Distributed Computing Server, version 2008b
+Maple	Maple mathematical software, system default version
+Maple-11	Maple mathematical software, version 11
+Mathematica	Mathematica computational environment
+Mathematica-6.0	Mathematica computational environment, version 6.0
+Matlab	The MATLAB computational environment, system default version
+Matlab-2007a	The MATLAB computational environment, version 2007a
+Matlab-2008b	The MATLAB computational environment, version 2008b
+Mesa-7.2-32	OpenGL and GLUT libraries, 32 bit
+Mesa-7.2-64	OpenGL and GLUT libraries, 64 bit
+NetCDF-64	Network Common Data Form for array oriented data, 64-bit
+OpenCV-1.0.0	OpenCV-1.0.0
+Oracle	Oracle client, system default version
+PGarli	Parallel version of Garli
+Pblast	Parallel NCBI Blast
+Pphast	Parallel Phast, (reqs. +openmpi-1.2.5-intel-32)
+R	The R Project for Statistical Computing
+R-2.7.0	A free software environment for statistical computing
+Splus	The S-Plus statistical analysis system, system default version
+Splus-8.0.4	The S-Plus statistical analysis system
+StarP	StarP, system default version
+StarP-2.6.0	StarP, version 2.6.0
+StarP-2.6.1	StarP, version 2.6.1
+StatTransfer	Stat/Transfer, system default version
+StatTransfer9	Stat/Transfer, version 9
+Timbl	Tilberg Memory Based Learner GCC-4.1.1
+VTK-5.0.3-64	VTK 5.0.3, 64-bit
+VampirTrace-gcc-32	Vampir Tracing v.5.4.4 32-bit gcc compilers
+VampirTrace-gcc-64	Vampir Tracing v.5.4.4 64-bit gcc compilers
+VampirTrace-intel-32	Vampir Tracing v.5.4.4 32-bit intel compilers
+VampirTrace-intel-64	Vampir Tracing v.5.4.4 64-bit intel compilers
+WGRIB-64	Manipulate, inventory and decode GRIB files
+Weeder-1.3.1	transcription factor binding sites (TFBS) in DNA regulatory region
+ansys	Ansys, Inc. Solutions, latest stable version
+ansys.v110	Ansys, Inc. Solutions, version 11.0
+autodoc-4	Autodoc-4 suite, Intel compilers, 64-bit
+binutils	binary utilities
+binutils-2.18	binary utilities 2.18
+blat	BLAT
+blat-34	BLAT-34
+cern	cernlib binaries and libraries
+cmake-32	CMake: Cross-platform 'make' 32-bit
+cmake-64	CMake: Cross-platform 'make' 64-bit
+ctl-idp-intel-i64	Control Language Library
+curl-7.18	A command line tool for transferring files with URL syntax
+ds9	DS9 image display
+emacs	The GNU Emacs text editor, system default version
+emacs-22.1	The GNU Emacs text editor, version 22.1
+emboss	EMBOSS (Molecular Biology analysis package)
+emboss-6.0.1	EMBOSS (Current Version)
+fftw-3.1.2	Fast Fourier Transforms
+fftw3_idp_32_omp	Fast Fourier Transforms
+fluent	Fluent, latest stable version
+fluent64-6.3.26	Fluent, version 6.3.26
+ga-4.0.8-openmpi-1.2.4	Global Array with Openmpi-1.2.4
+gambit	Gambit, latest stable version
+gambit64-2.4.6	Gambit, version 2.4.6
+gamess	general ab initio quantum chemistry package
+garli	Garli
+garli0.942	Garli0.942
+garli0.951	Garli0.951
+garli0.96b8	Garli0.96b8
+gcc-4.1.1	GNU compiler suite, version 4.1.1
+gcc-4.2.2	GNU compiler suite, version 4.2.2
+genomethreader-1.0.4-32bit	GenomeThreader gth-1.0.4-Linux_x86-64-32bit
+genomethreader32	GenomeThreader 32 bit
+gnuplot	Portable data and function plotting utility, system default version
+gnuplot-4.2.2	Portable data and function plotting utility 4.2.2
+graphviz-2.12	Graphviz software for representing structural information as graphs
+gsl-1.10	GNU Scientific Library, version 1.10
+hadoop	HADOOP; system default currently 0.17.0
+hadoop-0.17.0	HADOOP 0.17.0
+harminv-idp-intel-i32	Wave model FFT solver Intel 32bit OpenMPI
+harminv-idp-intel-i64	Wave model FFT solver Intel 64bit OpenMPI
+hdf5-idp-intel-i32	HDF5 Intel 32bit OpenMPI
+hdf5-idp-intel-i64	HDF5 Intel i64bit OpenMPI
+hpss	Applications to access HPSS.
+intel-cmkl-10.0.2.018	Intel Math kernel Library 10.0.2.018
+intel-mkl	Intel Cluster Math kernel Library, system default version
+iraf	Image Reduction and Analysis Facility
+local-utils	Local Quarry utilities
+log4j	The Log4j Java runtime logging system, system default version:
+log4j-1.2.15	The Log4j Java runtime logging system, system default version:
+ls-dyna.971.dp	LS-DYNA Double Precision, Version 971
+ls-dyna.971.sp	LS-DYNA Single Precision, Version 971
+ls-dyna.dp	LS-DYNA Double Precision
+ls-dyna.sp	LS-DYNA Single Precision
+lynx	text-based web browser, system default version
+lynx-2.8.6	text-based web browser, version 2.8.6
+mcmccoal	likelihood and Bayesian Markov chain Monte Carlo for estimating species divergence times
+migrate	Migrate; default; 2.4.4; serial; icc
+migrate-2.3-s-serial-icc	Migrate 2.3; serial; icc
+migrate-2.4.4-p-smp	Migrate 2.4.4; Open MPI-SMP; icc
+migrate-2.4.4-s-icc	Migrate 2.4.4; serial; icc
+mimar	estimate the demographic parameter of an isolation-migration model from recombining loci
+moab	Moab Workload Manager, system default version
+moab-5.2.4.s11388	Moab Workload Manager 5.2.4
+moab-5.2.5	Moab Workload Manager 5.2.5
+nano	pico substitute, system default version
+nano-1.2.5	pico substitute
+netlib-idp-intel-i32	Intel 32bit BLACS, LAPACK, BLAS, ScaLapack
+netlib-idp-intel-i64	Intel 64bit BLACS, LAPACK, BLAS, ScaLapack
+ns	ns: network simulator; system default version
+ns.2.33	ns: network simulator v 2.33
+ns.2.33-test-2	ns: network simulator v 2.33; geo test 2
+ns2	ns: network simulator; geo test 2
+openafs	OpenAFS file system
+openmpi-1.2.6-gcc-32	Openmpi-1.2.6 GCC compilers 32-bit
+openmpi-1.2.6-gcc-64	Openmpi-1.2.6 GCC compilers 64-bit
+openmpi-1.2.6-intel-32	Openmpi-1.2.6 Intel compilers 32-bit
+openmpi-1.2.6-intel-64	Openmpi-1.2.6 Intel compilers 64-bit
+oracle_10g_rel2	Oracle client, version 10g, release 2
+pari	for fast computations in number theory
+paup	Phylogenetic Analysis Using Parsimony
+pgi	Portland Group Compilers 7.0-3
+pgi-6.1-6	Portland Group compilers 6.1-6
+pgi-7.0-3	Portland Group compilers 7.0-3
+pgi-7.2-4	Portland Group compilers 7.2-4
+phylip	PHYLogeny Inference Package
+pvm3	pvm3.4.5 gcc 64-bit compiled
+python	The python interpreter, lastest stable version
+python-2.5.1	The python interpreter, version 2.5.1
+python-2.6	The python interpreter, version 2.6
+python32	The python interpreter, 32-bit i386 version
+python32-2.3.4	The python interpreter, 32-bit i386 version 2.3.4
+qt4	Qt4 default version
+qt4-4.3.2	Qt4
+rats	RATS Econometric software package
+rats7	RATS econometric software package
+ray	analysis and visualization of lighting in design
+rfs	Research File System.
+sas	The SAS system for data analysis
+sas913	SAS version 9.1.3
+scheme	Chez Scheme, default system version
+scheme-7.3	Chez Scheme, version 7.3
+softenv	Software Environment Management System
+softenv-1.6.2	SoftEnv 1.6.2
+sqlite-3.5.6	SQLite an embedded SQL database engine
+starcd	StarCD, latest stable version
+starcd_4.02.001	CD Adapco StarCD, version 4.02.001
+stata	A statistical package for data analysis, management, graphics
+stata-mp	A statistical package for data analysis, management, graphics
+stata10	Stata version 10
+structure	Structure
+structure-2.2	Structure 2.2
+structure-2.2.3	Structure 2.2.3
+svn	Subversion version control system
+swig	Simplified Wrapper and Interface Generator, system default version
+swig-1.3.31	Simplified Wrapper and Interface Generator, 1.3.31
+tcl-tk	Tcl 8.4.16, Tk 8.4.16
+teTeX	the teTeX distribution of TeX/LaTeX, version 3.0
+teTeX-3.0	the teTeX distribution of TeX/LaTeX, version 3.0
+totalview	TotalView Parallel Debugger. system default version
+totalview-8.3.0-1	TotalView 8.3.0-1 Parallel Debugger
+totalview-8.6.2-0	TotalView 8.6.2-0 Parallel Debugger
+trilinos	multi-physics engineering and scientific tools
+twisted	The Twisted Python server framework: system default version
+twisted-8.0.1	The Twisted Python server framework: version 8.0.1
+user	Default user owned paths
+user-paths	Standard user-owned paths
+valgrind	Valgrind Debugger, System default version
+valgrind-3.3.1	Valgrind Debugger, v3.3.1
+vampirserver-1.10.0	Vampir trace viewer server
+xemacs	XEmacs text editor, system default version
+xemacs-21.4.20	XEmacs 21.4.20 Double Solitaire release
+xerces-c++	The Xerces C++ XML parser, system default version
+xerces-c++-2.8.0	The Xerces C++ XML parser, version 2.8.0

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