The  following software is available on the PC_Farm :

CERNLIB

All the CERN libraries and binaries are in /cern/
/cern/pro/  points to 99
/cern/new/ points to 2000
 new software for RH7.2 has been added:
/cern/2001/
 

Please add the following lines to the end of your private files:
in   .cshrc:

set path=( $path /cern/pro/bin)
setenv CERN_ROOT /cern/pro

or, in   .profile:

PATH=$PATH:/cern/pro/bin
export PATH
CERN_ROOT=/cern/pro
export CERN_ROOT
 
 

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NAGLIB

 
 

The NAG libraries and utilities are in /usr/local/fllux18dg

Please read and use /usr/local/bin/nagexample  in order to test the system.
 
 

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MpiCH

 
 

       MPICH   developed at the Argonne National Laboratory, is an open source implementation of the
Message-Passing Interface (MPI) standard.
MPI-CH is a full implementation of MPI.
It is available and in use on a wide variety of parallel systems.
To be able to use the MPICH commands, the user should have the following files in his/her home directory:
1.    .rhosts
physerv.weizmann.ac.il       userid
physdsk1.weizmann.ac.il       userid
physdsk2.weizmann.ac.il       userid
eio05.weizmann.ac.il       userid
....................       ......
eio36.weizmann.ac.il       userid

.rhosts should be available for the user only , so please change it's attributes to r/w for you alone , by typing:
chmod 600 .rhosts

2.    .alias
alias ls 'ls -F '
alias rm 'rm -i '

3.  enter   /mpi/bin  in your path , in .cshrc or .profile
 

To check if the system works correctly , please activate the command
/mpi/bin/tstmachines

One can use the command mpiman to see the MPI man pages,
or follow this link to browse the html version.

To run some examples, you can copy the following files from /mpi/examples
Makefile    *.c*    *.f*   to your disk

make cpi
mpirun -np 4 cpi
 
 
 
 
 


 
 

PGI compilers

 
 

The latest release of The Portland Group, Inc. (PGI)  of high quality parallelizing
Fortran, C, and C++ compilers and tools.
The 3.1 release includes native PGHPF®, PGF90®, PGF77®, and PGCC® compilers,
full native OpenMP user-directed parallelization for F77 and F90 and
full native OpenMP pragma-based parallelization for C/C++, on Linux, Solaris86 and Windows® NT,
automatic usage of Pentium III SSE instructions, byte-swapping I/O for interoperability with RISC workstations,
enhanced debugging support using gdb, the PGDBG® debugger and PGPROF® profiler.

Please add the following lines to the end of your   private files:
in   .cshrc:
#  Environement setup for PGI users #
setenv PGI /usr/local/pgi
set path = ( $PGI/linux86/bin $path )
# --- for the MAN pages ----
if ( $?MANPATH) then
setenv MANPATH "$MANPATH":$PGI/man
else
setenv MANPATH .:/usr/local/man:$PGI/man
endif
#
or
in   .profile:
#  Environement setup for PGI users #
PGI=/usr/local/pgi
export PGI
PATH=/usr/local/pgi/linux86/bin:$PATH
export PATH
# --- for the MAN pages ---
MANPATH=$MANPATH:$PGI/man
export MANPATH
#
 
 

Using the PGI compilers

The license for the PGI software is for eio02 .
In order to use the PGI  from other computers
in the PC_Farm one should use command  ssh eio02  , for example:
rsh  eio02    pgf77  logo.f
.
The online documentation is available at  /usr/local/pgi/doc/pgi.index.html

or  take a look at    http://www.pgroup.com/ppro_docs/pgiws_rel/pgiwsr.htm
 

 
 

  AFS

ANDREW FILE SYSTEM (AFS)
 
 

The ANDREW FILE SYSTEM (AFS) and the KERBEROS authentication system
are installed now on all PC-farm computers.
Each computer from the farm is configured as an AFS client for three AFS Cells = cern.ch , desy.de and rhic.
The software installed is from the ARLA project.
Kerberos KRB-4 is used for security and authentication.

Each user can see from any PC-farm computer the /afs tree for cern.ch ,desy.de and rhic cells.

In order to get read/write permission on his directory/files from each /afs cell, one should follow the steps :

1)     Add in .cshrc
           set path=($path /usr/athena/bin /usr/arla/bin)
        or in .profile
           export PATH=$PATH:/usr/athena/bin:/usr/arla/bin

2) Run:

    a) kauth user_id@Cell_name and provide your afs-passwd from that cell

Examples

  • kauth levinson@cern.ch and levinson's passwd for afslog into cern or
  • kauth ravini@rhic and ravini's passwd for afslog into rhic cell

    •  

     
     
     
     
     

        b) afslog

        c) klist -To  check if user got a ticket for the afs cell.

    If a user wants to live his afs cell before his ticket expires,
     he should run :

            kdestroy     and his ticket will be removed.

    As of now there are 3 groups  of dedicated computers ,
    each one of them for each AFS-cell.
    The list of those computers is :
     

            eio02 and eio32                        are dedicated to desy.de   realm,   rhic, cern.ch       realm -  rafsX.rcf.bnl.gov
          eio02 and eio32    are dedicated to cern.ch  realm
     

    To submit a job that uses /afs files directly with PBS one should do:

  • 1) login into the computer dedicated to your needed cell;
  • 2) get /afs login (like desribed beyond);
  • 3) submit from that computer your job ;

    •  

     
     
     
     
     
     
     

    PBS knows how to pass your authentication ticket to other computers that have free resources for your job.

    It is highly recomended to avoid this form of work because your job can run more time
    that was accorded to your authentication ticket
    and if the ticket expires your job will crash.
    It is better and safer to copy from /afs cells libraries, or binaries
    that you want to include in your jobs and after that to submit to the batch system your jobs.

    For any information or malfunction in the afs/kerberos system please contact
    Camelia at 3288 or send mail to camelia@wicc.weizmann.ac.il.
     
     

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     ROOT


    Root is a graphical interface program from Cern.





    #### ---- Environment setup for root users. -----
    setenv ROOTSYS /Local/root
    set path=($path $ROOTSYS/bin)
    if ( $?LD_LIBRARY_PATH) then
        setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${ROOTSYS}/lib
    else
         setenv LD_LIBRARY_PATH  $ROOTSYS/lib
    endif
     
     

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     PVM

    PVM is a software system that enables a collection of heterogeneous
    computers to be used as a coherent and flexible concurrent computational
    resource.





    #### ---- Environment setup for PVM users. ----
         setenv PVM_ROOT /usr/share/pvm3
         source $PVM_ROOT/lib/cshrc.stub
     
     


     
     

     

     

    FFTW is a collection of fast C routines to compute the
    Discrete Fourier Transform in one or more dimensions.








       The libraries are in /usr/local/lib and
    the include files , in /usr/local/include

       Type   info fftw   to read the manual.
     
     


     
     

      PVFS

     
     
     

    PVFS is a parallel file system. It allows applications, both serial and parallel,
    to store and retrieve file data which is distributed across a set of I/O servers.

    This is done through traditional file I/O semantics, which is to say that you can open, close,
    read, write, and seek in PVFS files just as in files stored in your home directory.

       Please visit http://parlweb.parl.clemson.edu/pvfs/user-guide.html
    to learn more about it.



     
     
     
     
     


     

     LINDA


    Linda Gauss98 is a parralel programming language based on C and Fortran.
       In order to use Linda , please enter the following lines into your
    .cshrc or .login file:








    ##### For LINDA #######
    set path=($path /usr/sca/linda-5.0rh6.0/linux-2.2/bin)
    setenv LINDA_CLC cds
    setenv LINDA_FLC cds
    #####
     
     


    MTX


    MTX is a set of low level driver programs to control features of SCSI backup related devices
    such as autoloaders, tape changers, media jukeboxes, and tape drives.

    It can also report much data, including serial numbers, maximum block sizes, and
    TapeAlert(tm) messages that most modern tape drives implement .

    For usage, type 'man mtx' or see mtx.pdf

                                           For more details visit http://mtx.sourceforge.net/
     



    (1)   Gmemusage


      Gmemusage graphically  displays the contents of memory on a running system,
    broken  up  by individual processes.
    The display is a stacked bar graph with the height of an area representing the  RSS
           size  of  the corresponding process.
    In addition, the process name, number of processes with that name and the size
           (in kilobytes) are shown.

    For syntax, type 'man gmemusage'


     Xosview  is a monitor which displays the status of several  system based parameters.
    These include  CPU  usage,  load average,  memory  usage,  swap space usage, network usage,
           interrupts, and serial port status.
    Each of these is displayed  as  a horizontal bar which is separated into color coded regions.
    Each region represents a percentage of the resource which is being put to a particular use.

    For syntax, type 'man xosview'
     
     

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    (1)   DDD


           DDD  is  a  graphical front-end for GDB and other command-line debuggers.
           Using DDD, you can see what is  going  on "inside"   another  program  while  it  executes,
           or  what another program was doing at the moment it crashed.

    In order to use it, please add the following to your .cshrc file:

    #### ---- Environment setup for DDD  users. -----
    if ( $?LD_LIBRARY_PATH) then
       setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/Local/cern/2000/lib:/usr/X11R6/lib:/usr/local/lib
    else
       setenv LD_LIBRARY_PATH "/Local/cern/2000/lib:/usr/X11R6/lib:/usr/local/lib"
    endif
    ####-----

    Type 'man ddd'   or   'info ddd'  to read more about it.
     
     

    (2)   JCC

          JCC is a text editor and UNIX development environment.

    In order to use it, please add the following to your .cshrc file:

    ####---- Environment setup for  JCC ----
    set path=( $path /Local/CodeCrusader )
    ####----

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    Helen Katz  - Aug.  9 1999        Last update:  02 June  02