PBS

The first steps before running PBS



  •     Make sure you have all the computers: physerv,physdsk1,physdsk2 and eio05 to eio36 in
            the file  .rhosts  in  your  home  dir.,  like this:

    physerv         your_user_id
    physdsk1      your_user_id
    eio05             your_user_id
    ..
    eio36             your_user_id 

    and change it's attribute to read/write only for you:

    chmod 600 .rhosts

     

        Check your .login and/or .cshrc as it is explained in the manual:
      Modification of User shell initialization files

    A  user's  job  may  not  run  if  the user's start-up files
    (.cshrc, .login, or .profile) contain commands which attempt
    to  set  terminal characteristics.  Any such activity should
    be skipped by placing a test  of  the  environment  variable
    PBS_ENVIRONMENT  (or  for  NQS  compatibility, ENVIRONMENT).
    This can be done as shown in the following sample .login:
         setenv PRINTER printer_1
         setenv MANPATH /usr/man:/usr/local/man:/usr/new/man
         if ( ! $?PBS_ENVIRONMENT ) then
                 do terminal stuff here
         endif

    If the user's login shell is csh, the following message  may
    appear in the standard output of a job:
     

         Warning: no access to tty, thus no job control in this shell

    This message is produced by many csh versions when the shell
    determines that its input is not a terminal.  Short of modi-
    fying  csh, there is no way to eliminate the message.
    Fortunately, it is just  an  informative  message  and  has  no
    effect on the job.
     

       Enter the following lines in your .cshrc
    #######  PBS  ###########
            setenv PBS_HOME /usr/spool/PBS
            set path=( /usr/pbs/bin /usr/local/bin $path )
    ##############################

    In the directory from where you want to submit the job,
    prepare a script file (let's say: pbs_sub) of the following format:
    #!/bin/csh
    #
    #  Give the job a name
    #
    #PBS  -N test1
    #
    #  Join output log with error log
    #PBS  -j oe
    #
    #  A mail will be sent upon job abborting or ending
    #PBS -m ae
    #
    #  The user to which will be sent the mail
    #PBS  -M   fisrtname.lastname@weizmann.ac.il
    #
    # How many nodes and CPU's needed for this job
    #
    #PBS  -l nodes=1:ppn=1
    #
    # Define the queue
    #
    #PBS  -q X
    #
    # Change the DIRECTORY to the working dir
    # otherwise the PBS is keeping your module in your
    #  home directory !?
    # this PBS_O_WORKDIR is the directory from where you submit
    # the job and where you want to get  your results.
    # You can replace  $PBS_O_WORKDIR with a specific path.
    cd $PBS_O_WORKDIR
    echo `pwd`
    ############# Enter here your working requests ########
    your module to be executed
    etc.
    ################# END OF SCRIPT #######################
     

       Submit the job:
                        qsub  pbs_sub
            the job will get a name like:
                        416.eio09

    *****  If jobs are submitted from a script , please put a delay of 30 seconds at least
               sleep 30
    between one qsub  to another , otherwise most of your jobs will be sent to the same node !!

      qstat                   -- check the job status
        or
            qstat -n           -- a detailed status description
         or
           qstat -f  416         -- one job's full status description
     
     

         qdel  416             -- erase the job
     

       qstat -Q       --- see the queues

      qstat -Bf      --- see server status
    -----------------------------------------------------
            see 'man qsub' or 'man qstat' for more details.
    -----------------------------------------------------

    The queues are like this:
    X   --     20 min.
    S    --      8   hours  -- the default
    M   --    28  hours
    L    --    50  hours
    C   --     50  hours -- for jobs under RH-8 
    R   --  192   hours -- for huge productions (activated by head-group request)

    T   --      8   hours -- to run on physdsk1/2 when they are free


    activate 'qstat -q   or qstat -Q   or  qstat -Qf ' for more detailes
    --------------------------------------------------