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Cluster System Usage Tips

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Measuring resource usage (e.g. memory usage)

Resources (e.g. memory) used by the processes can be viewed by using the GNU time command (/usr/bin/time). Specifying the option -v displays the resource details used by the process, such as follows (see time command man page).

-bash-4.1$ /usr/bin/time --version
GNU time 1.7

-bash-4.1$ /usr/bin/time -v whoami
my016
        Command being timed: "whoami"
        User time (seconds): 0.00
        System time (seconds): 0.00
        Percent of CPU this job got: 0%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.00
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 3088
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 0
        Minor (reclaiming a frame) page faults: 243
        Voluntary context switches: 3
        Involuntary context switches: 1
        Swaps: 0
        File system inputs: 0
        File system outputs: 0
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0

Maximum resident set size shows the memory usage. Note that the GNU time command V. 1.7 shows this figure 4 times greater than the actual memory usage, which is a known bug (see Massive bug in GNU time (Japanese)).

You can run the GNU time command on a calculation node, however, the result is output as the standard error.

Batch Deletion of Submitted Jobs

End users are not permitted to use the -all option for qdel command, and qdel -t does not function correctly. For this reason, use the following script to perform batch deletion of multiple submitted jobs.

   1 #!/bin/bash
   2 
   3 if [ $# -ne 1 -a $# -ne 2 ]; then
   4     echo "Usage: bash $0 [ 'all' | firstId lastId | lastId ]"
   5     exit
   6 fi
   7 
   8 # Is the first argument a numerical value?
   9 if expr "$1" : '[0-9]*' > /dev/null ; then
  10     ids=`seq $1 $2`
  11 else
  12     ids=`qstat | cut -d . -f 1 | tail -n +3 | column`
  13 fi
  14 
  15 echo qdel $ids
  16 qdel $ids

Specifying all as the first argument deletes all the submitted jobs (regardless of whether they are being executed or not). It is also possible to delete a range of jobs by specifying the starting job ID as the first argument and the ending job ID as the second argument. To execute a script called qdel.sh, write the code such as follows:

-bash-4.1$ bash qdel.sh all

-bash-4.1$ bash qdel.sh 100 200

Script to Submit Specified Command as a Job

The qsub command with the -v option can pass an environment variable to a script. The following script uses this function to execute the specified command as a job on a calculation node. In this script, the standard error is output with the standard output (-j oe), and the script also includes commands to log the execution time and the node where the calculation took place (date and hostname).

   1 #!/bin/bash
   2 #PBS -l nodes=1:ppn=1
   3 #PBS -q wLrchq
   4 #PBS -j oe
   5 
   6 cd $PBS_O_WORKDIR
   7 
   8 date
   9 hostname
  10 echo "$JOB_CMD"
  11 eval "$JOB_CMD"
  12 date

To execute a script called qsub.sh, specify the command to execute as the argument of JOB_CMD. Executing this script submits the command as a job.

-bash-4.1$ qsub -v JOB_CMD="/usr/bin/time -v perl i_love_cats.pl" qsub.sh

-bash-4.1$ qsub -v JOB_CMD="perl catching_cats.pl | perl counting_cats.pl" qsub.sh

List of All Users' Jobs in the Queue

A list of all jobs including other users' jobs in the queue can be checked using the /usr/local/maui/bin/showq command.

Displaying Job Status Repeatedly

It is useful to use the watch command to display the execution status of a submitted job. The code examples below run the watch command every 5 seconds, displaying the latest job execution status. Option -d highlights the difference from the last status. Note that an alias cannot be specified to a command that is executed repeatedly.

-bash-4.1$ watch -n 5 qstat -a

-bash-4.1$ watch -n 5 qstat -Q

-bash-4.1$ watch -n 5 -d qstat -Q

Limitation by ulimit -t (the CPU time)

The development node has a limitation on the CPU time as specified by the ulimit command. This limit value seems to apply to the value that are not shown by time command (hidden values). If a job is aborted due to an unknown reason, this limitation could be the cause. For example, synchronizing a large volume of data using the rsync command generates an error such as follows.

-bash-4.1$ rsync --progress -avh /tmp/source /destination/
sending incremental file list

...

rsync: writefd_unbuffered failed to write 4 bytes to socket [sender]: Broken pipe (32)
rsync: connection unexpectedly closed (96 bytes received so far) [sender]
rsync error: error in rsync protocol data stream (code 12) at io.c(600) [sender=3.0.6]

The CPU time consumed by rsync appears to be determined by the transmitted data volume regardless of whether --bwlimit has been specified or not. As remote synchronization involves transport encryption using ssh, it consumes approximately twice as much CPU time as local synchronization.

Job Scheduling Order

The Wide-Area Coordinated Cluster System for Education and Research

The job scheduler allocates jobs in descending order of host number of the calculation nodes such as wsnd30, wsnd29, ..., and wsnd00.