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Software tools available on the cluster

• Version: version number of software
• Path: path of the software
• Variables: Relevant shell variables that are pre-set or need to be set
• Documentation: Location of documentation
• Function: Description of the software's purpose/function

PVM

• Version: 3.4.5
• Path: Standard system paths
• Variables:
  Set automatically: PVM_ROOT=/usr/share/pvm3
  Set automatically: PVM_ARCH=`$PVM_ROOT/lib/pvmgetarch`
  Set automatically: PVM_RSH=/usr/bin/ssh
• Documentation: /usr/share/doc/pvm-3.4.5
• Description: PVM3 (Parallel Virtual Machine) is a library and daemon that allows distributed processing environments to be constructed on heterogeneous machines and architectures.

LAM

• Version: 7.1.2
• Path: Binaries are in system paths; Libraries are in /usr/lib64/lam ; Include files are in /usr/include/lam and /usr/include/lam/64
• Variables:
  Set automatically: LAMRSH=/usr/bin/ssh
• Documentation:
  /usr/share/doc/lam-7.1.2
  http://www.lam-mpi.org/
• Description: LAM (Local Area Multicomputer) is an Message-Passing Interface (MPI) programming environment and development system for heterogeneous computers on a network. With LAM/MPI, a dedicated cluster or an existing network computing infrastructure can act as one parallel computer to solve one problem. LAM/MPI is considered to be "cluster friendly" because it offers daemon-based process startup/control as well as fast client-to-client message passing protocols. LAM/MPI can use TCP/IP and/or shared memory for message passing (different RPMs are supplied for this -- see the main LAM website at http://www.lam-mpi.org/ for details).

  LAM features a full implementation of MPI version 1 (with the exception that LAM does not support cancelling of sends), and much of version 2. Compliant applications are source code portable between LAM and any other implementation of MPI. In addition to meeting the standard, LAM/MPI offers extensive monitoring capabilities to support debugging. Monitoring happens on two levels: On one level, LAM/MPI has the hooks to allow a snapshot of a process and message status to be taken at any time during an application run. The status includes all aspects of synchronization plus datatype map/signature, communicator group membership and message contents (see the XMPI application on the main LAM website). On the second level, the MPI library can produce a cumulative record of communication, which can be visualized either at runtime or post-mortem.

MVAPICH2

• Version: 1.4
• Path: /usr/lib64/mvapich2/
• Variables: User set: Run "mpi-selector --set mvapich2-1.4-gcc-x86_64" in order to set 64-bit mvapich2 as the default MPI environment.
• Documentation:
  /usr/lib64/mvapich2/1.4-gcc/man
  /usr/lib64/mvapich2/1.4-gcc/www/
  http://mvapich.cse.ohio-state.edu/
• Description: This is an MPI-2 implementation which includes all MPI-1 features. It is based on MPICH2 and MVICH.

OpenMPI

• Version: 1.4
• Path: /usr/lib64/openmpi/
• Variables: User set: Run "mpi-selector --set openmpi-1.4-gcc-x86_64" in order to set 64-bit OpenMPI as the default MPI environment.
• Documentation:
  /usr/lib64/openmpi/1.4-gcc/man
  http://www.open-mpi.org/
• Description: Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

Intel 64 bit C/C++ Compiler

• 11.1
• /cluster/intel-11
• Set automatically
  
• /cluster/intel-11/Documentation
• C/C++ Compiler

Intel 32 bit C/C++ Compiler

• 11.1
• /cluster/intel-11
• User set: source /cluster/intel-11/bin/iccvars.csh ia32
  
• /cluster/intel-11/Documentation
• C/C++ Compiler

Intel 64 bit Fortran Compiler

• 11.1
• /cluster/intel-11
• Set automatically: source /cluster/intel-11/bin/iccvars.csh intel64
• /cluster/intel-11/Documentation
• Fortran Compiler

Intel 32 bit Fortran Compiler

• 11.1
• /cluster/intel_fc_386
• User set: source /cluster/intel-11/bin/ifortvars.csh ia32
• /cluster/intel-11/Documentation
• Fortran Compiler

Intel Debugger

• 11.1
• /cluster/intel-11
• Set automatically: source /cluster/intel-11/bin/ifortvars.csh intel64
• Set automatically: source /cluster/intel-11/bin/iccvars.csh intel64
• /cluster/intel-11/Documentation
• The debugger provides support (at various levels, depending on the compiler version) for debugging programs written in C, C++, and Fortran (77, 90 and 95).

Java

• 1.6
• /usr/java/default
• At the least, the PATH will need to be set, the other variables that may need to be set will be dependent on the software using them (JAVA_HOME is a common one).
  User set: PATH=/usr/java/default/bin:$PATH
• http://java.sun.com/docs/index.html
• This is the Sun Java Software Development Kit for 1.6

R

• 2.10.1
• /usr/bin/R
• Automatically set: R_LIBS=/cluster/statsoft/Rlibs64
  Automatically set: PATH="$PATH:/cluster/statsoft/bin"
• /usr/share/doc/R-2.10.1
  /usr/share/doc/R-devel-2.10.1
  
• R is a free software environment for statistical computing and graphics.

Ox

• 5.10
• /usr/bin/oxl64
• None that I am aware of
• Please see http://www.doornik.com/ox/index.html for documentation
• Ox is an object-oriented matrix programming language with a comprehensive mathematical and statistical function library.The Console (command line) versions may be used freely for academic research and teaching purposes only...Failure to cite the use of Ox in published work may result in loss of the right to use the free version, and an invoice at the full commercial price. Please see http://www.doornik.com/ox/index.html?content=/ox/oxcite.html for further requirements.

TeX/LaTeX

• TeX (Web2C 7.4.5) 3.14159
  kpathsea version 3.4.5
• System paths
• No custom environment variables are needed for running the installed TeX/LaTeX environment
• There are a variety of sources for learning/using TeX/LaTex
• TeX, and associated programs such as LaTeX, form a system for computer typesetting, for placing text on a page. (Pronounce the name "tech".) It is well known for its abilities with the most difficult typesetting jobs: mathematical and scientific text, long and intricate documents, and multilingual works.