Index of /AMS_EPEAEK/the_elements

	Name	Last modified	Size	Description
	Parent Directory		-
	CDIGITAL/	02-May-1999 21:50	-
	CHP/	02-May-1999 21:50	-
	CSUN/	02-May-1999 21:50	-
	Ccompilers/	02-May-1999 21:50	-
	Cmemonet/	02-May-1999 21:50	-
	USERS/	07-Sep-2000 17:22	-
	articles/	20-Apr-2000 18:12	-
	doc/	21-Sep-2000 12:13	-
	flops/	04-Apr-2000 15:47	-
	information/	23-Feb-2001 16:05	-
	tc3mini.gif	29-Jul-2008 16:06	1.0K
	the_elements_profile.bak	29-Jul-2008 16:06	4.5K
	the_elements_profile.html_store	29-Jul-2008 16:06	4.9K
	the_elements_profile.html_original	29-Jul-2008 16:06	5.8K
	the_elements_profile.html.bak	29-Jul-2008 16:06	6.2K
	the_elements_profile.html	29-Jul-2008 16:06	8.8K
	the_elements.jpg	29-Jul-2008 16:06	16K
	mihani~4.jpg	29-Jul-2008 16:06	16K
	mihani~1.jpg	29-Jul-2008 16:06	20K
	the_elements_profile.ps	29-Jul-2008 16:06	26K
	hopper_input.gif	29-Jul-2008 16:06	71K
	earthnew.gif	29-Jul-2008 16:06	98K

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:

• Callable from Fortran or C.
• Runs on uniprocessors, parallel computers, and workstation networks.
• Binary-, integer-, real-, and character-valued native data types.
• Object-oriented data structure neutral design.
• Parameterized population replacement.
• Multiple choices for selection, crossover, and mutation operators.
• Easy integration of hill-climbing heuristics.
• Easy-to-use interface for novice and application users.
• Fully extensible to support custom operators and new data types.
• Extensive debugging facilities.
• A large set of example problems.

Further info

Comments:

• Details in the manual
• to view the man pages:  man 'routine-name'
• In linking add: -lpga0

---

Parmetis v2.0 and metis v.4.0

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

Homepage of metis.

Comments:

• Detais in the manual
• include file: parmetis.h
• In linking add: -lmetis -lparmetis

---

BLAS

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

Comments:

• Libraries for PII are under development.
• View a quick reference manual
• In linking add : -lblas or -lblas_single or -lblas_dual. Currently -lblas links blas_single.

---

PBLAS

Parallel version of Blas.

Comments:

• View a quick reference manual

  ---

Lapack, Lapack90

Lapack routines and Lapack90 interface to them.

Comments:

• Modules with interfaces are in /usr/local/include/lapack90_mod
• View a quick reference manual
• to view the man page : man lapack.

for a specific routine: man 'routine-name'
• In linking add : [/usr/local/lib/libllapack90] /usr/local/lib/liblapack.a /usr/local/lib/libblas_single.a

or : [/usr/local/lib/libllapack90] /usr/local/lib/liblapack.a /usr/local/lib/libblas_dual.a /usr/lib/lpthread.a

---

ScaLapack

The parallel version of lapack seems to be installed.

Comments:

• A lapack routine called 'name' is available in scalapack with 'Pname'
• View a quick reference manual

---

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:

• Details in the manual
• to view the man pages: man 'routine-name'
• include files in : /usr/local/include/BlockSolve95/
• In linking add: -lBS95
• examples available on request.

---

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:

• to view the man pages: man nagf95, man nagdbx90

---

CVODE

(stiff or not) ODE integrator.

Comments:

• written in C but callable from C or Fortran.
• Details in the manual
• include files in : /usr/local/include/cvode
• In linking add: -lcvode

---

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:

• Details in the manual in postscript or in the manual in HTML.
• Emacs Info file available.

---

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:

• Details in the manual in postscript for V2.0

---

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:

• in C : /usr/local/doc/Numerical_Recipes/C
• in Fortran 77 : /usr/local/doc/Numerical_Recipes/Fortran

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

contents of an electronic book for numerical algorithms.

(from the Computational Science Education Project)

F90

• Collected tutorials, courses, FAQ, etc. here
• Tutorial from the university of new mexico.
• see also /usr/local/doc/EBOOK/f90.ps.gz

HPF

• Manual for version 2.0.
• Collected tutorials, courses, FAQ, etc. here

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.