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 NQS Batch Queuing System @ UCL Theoretical Chemistry Group
 

Contents

    QUEUES CONFIGURATION ON ARGON
   Queue name
Memory Limit
# running jobs
User Run Limit
small
100 Mb
7
 2
medium
200 Mb
2
1
large
500 Mb
1
1

 
Global Limits
Total number of running jobs = 7
Maximum number of jobs per user = 2
CPU time unlimited for all the queues


 
    QUEUES CONFIGURATION ON NEON
   Queue name
Memory Limit
# running jobs
User Run Limit
small
100 Mb
9
 2
medium
300 Mb
2
1
large
600 Mb
2
1

 
Global Limits
Total number of running jobs = 9
Maximum number of jobs per user = 2
CPU time unlimited for all the queues


 
    SUBMITTING A JOB TO NQS
      prepare a batch script:
        cut and paste the following lines at the beginning of your script for interactive jobs (if you are not
        using a script to run your program then you just need to create a file with those lines) 
        # QSUB -eo
# QSUB -r (job_name)
# QSUB -q (queue_name)
cd (/working_directory)    # put the absolute path of the directory
(exec_name)                # name of the executable
      submit the job to the batch queuing system:
          qsub (script)
        where (script) is the file you have created/modified in the previous step.
       

      interaction with the queuing system: useful commands

        qstat -a    # give the list of all submitted jobs (running + queuing)
           
    example: ~> qstat -a
Request          I.D.   Owner    Queue   Start Time   Time Limit  Time Used   St
-------------- ------- -------- -------- -----------  ----------  ----------  --
job1             197    user1   medium    5/27 13:41    0  0:00   0  7:50:57   R
job2             152    user2   small     5/25 14:06    0  0:00   2  6:35:53   R
         
        qcat (job_I.D.)      # display the standard output of the job, (job_I.D.) is taken from the output of qstat.
           
        qstat -lx               # gives the complete configuration of the queues

     
      end of the job:
        when the job is finished, you will find the log file
                      (job_name).o(job_I.D)

        in the working directory, containing the standard output and the standard error of the job.

       
    COMMON PROBLEMS
      the queuing system doesn't give any special message if the job is not executed correctly;
      if you are sure that the job is running without problems in interactive mode then you need
      to submit the job to a queue with a larger memory limit
      the shell variable ENVIRONMENT, set by the batch system, can be used to bracket the part
      of the configuration files (.cshrc, .login,..) that must be executed only in interactive mode, as
      in the following example
          
        if (! $ENVIRONMENT) then
   set prompt="<%U%B%n@%m%b%u %~> "
endif
      in this way, you can eliminate some "warning messages" that you  find at the beginning
      of the log file of the job.
      man pages have also been installed on argon and neon.

Any problem?