Packages Installed

  • How to use various programs
  • LessTif
  • Xmpi
  • PGAPack
  • BlockSolve95
  • Parmetis and Metis
  • BLAS
  • PBLAS
  • Lapack, Lapack90
  • Scalapack
  • NAG f95 compiler and debugger
  • CVODE
  • FFTW
  • PETSc
  • GNU Plotutils
  • Various Tutorials, Manuals...
  • Various Utilities

  • Some entries are incomplete. Last update in 5/02/1999.


    How to use various programs

    mpi

    To compile and link {F77 | F90 | C} programs calling MPI routines use {mpif77 | mpif90 | mpicc} as the compiler. They accept all options of  {pgf77 | pgf90 | pgcc} in addition to a few others. Check the respective man pages.

        Example : mpif77 -O2 -tp p6 test.f -o test

    To run programs using MPI routines use mpirun. The necessary option is -np; it defines the number of processes. For the others consult the man pages.

        Example :  mpirun -np 4 test 

    To view the man pages you can use mpiman.

    queues

     The queuing system was reconfigured as following:

      LIMITS
    queue Memory CPU time nice jobs
    fast 60 MB 1 h 5 2
    medium 60 MB 8 h 10 2
    large 250 MB unlimited 15 4
    mlarge 250 MB unlimited 15 1
    interactive unlimited unlimited 0 unlimited

    to submit a job:
             > qsub -q queue
            where queue: the queue name, eg. fast, medium ...

        batch file example:

        cd /home/myname/programs/executables
        program_in_the_above_directory.exe


        to check the jobs:
          > qstat -da

        to delete a job:
          > qdel -k  ID.fire@machine

       where:
                     ID :  the ID shown in qstat
                machine:  the machine where the job is running

           eg.  :  qdel -k 19.fire@water


    LessTif 0.87.0

    A free Motif clone. Necessary to build Xmpi. Visit the Homepage of Lesstif.

    Xmpi

    XMPI is a graphical user interface for running MPI programs, monitoring MPI processes and messages, and viewing execution trace files. It exploits the debugging capabilities of LAM, a parallel computing environment for UNIX clusters. XMPI is constructed from the Motif widget set.

    Further info

    PGapack v1.0

    PGAPack is a general-purpose, data-structure-neutral, parallel genetic algorithm library being developed at Argonne National Laboratory.

    Key features are:

    Further info

    Comments:


    Parmetis v2.0 and metis v.4.0

    Parallel Library for Unstructured Mesh (Re)Partitioning and Sparse Matrix Ordering.

    Homepage of metis.

    Comments:


    BLAS

    The BLAS library for single and dual proccesor Pentium Pro machines.

    Comments:


    PBLAS

    Parallel version of Blas.

    Comments:

    Lapack, Lapack90

    Lapack routines and Lapack90 interface to them.

    Comments:


    ScaLapack

    The parallel version of lapack seems to be installed.

    Comments:


    BlockSolve95 v3.0

    The BlockSolve95 package contains routines for solving large sparse symmetric systems of linear equations on massively parallel distributed memory systems and networks of workstations.

    Comments:


    NAG f95 compiler and debugger (dbx90)

    The NAGWare f95 Compiler is a full Fortran 95 compiler for a range of Unix platforms. Derived from the NAGWare f90 Compiler, the world's first Fortran 90 compiler, f95 provides robust, well tested, widely ported compiler capabilities for the Fortran 95 language. The f95 Compiler accepts fixed or free format Fortran 95 input and a number of common Fortran 77 extensions. HPF code is also compiled and checked though only single processor output is generated.

    Comments:


    CVODE

    (stiff or not) ODE integrator.

    Comments:


    FFTW v2.0

    THE FFT package (reference for all others). Uniprocessor version. MPI version has not been tried, yet. Written in C, can be called from Fortran as every C routine.

    Homepage of FFTW.

    Comments:


    GNU Plotting utilities

    Release 2.1.5 of the GNU plotutils (plotting utilities) package, including release 1.5 of GNU libplot: a function library for two-dimensional device-independent vector graphics, including vector graphics animations under the X Window System.

    Comments:


    PETSc

    PETSc the Portable Extensible Toolkit for Scientific computation is a suite of uni- and parallel processor codes that are intended for the solution of large scale problems modeled by partial differential equations. PETSc employs the MPI standard for all message passing communication. The code is written in a data-structure-neutral manner to enable easy reuse and flexibility.

    PETSc is easy to use for beginners. Moreover, its careful design allows advanced users to have detailed control over the solution process. PETSc includes an expanding suite of parallel linear and nonlinear equation solvers that are easily used in application codes written in C, C++, and Fortran. PETSc provides many of the mechanisms needed within parallel application codes, such as simple parallel matrix and vector assembly routines that allow the overlap of communication and computation. In addition, PETSc includes growing support for distributed arrays. PETSc integrates a hierarchy of components, thus enabling the user to employ the level of abstraction that is most natural for a particular problem. Some of the components are

    Mat -
    a suite of data structures and code for the manipulation of parallel sparse matrices,
    PC -
    a collection of preconditioners,
    KSP -
    data-structure-neutral implementations of many popular Krylov subspace iterative methods,
    SLES -
    a higher-level interface for the solution of large-scale linear systems and,
    SNES -
    data-structure-neutral implementations of Newton-like methods for nonlinear systems,
    TS -
    timestepping code for scalably solving nonlinear ODEs arising from applying general "methods of lines", techniques to time-dependent PDEs. Includes support for pseudo-timestepping.
    Manual: /usr/local/doc/PETSc.ps.gz 

    Various Tutorials

    Numerical Recipes (the text).

    The full text of Numerical Recipes is available is ps files:

    EBOOK (in /usr/local/doc/EBOOK).

    contents of an electronic book for numerical algorithms.

    (from the Computational Science Education Project)

    F90

    HPF

    G77.

    Manual of the g77 compiler is /usr/local/doc/g77.ps.gz.

    MPI (in /usr/local/doc/MPI).

    Various documents about MPI. See /usr/local/doc/MPI/README

    Various Utilities

    f2f90

    A program to convert FORTRAN 77 fixed source form to FORTRAN 90 free source form. Consult the man page for more information. Does not accept command line arguments; use the program prompt to pass them.

    For any problems, comments or requests send an e-mail to: Stamatis