Job submit/management commands

Job submission

qsub : Job submit command


Submit command places a job on the job queue of the supercomputer.
Submitting options also can be described in the execution script.

attention!

Please submit job to appropriate queue with qsub command, not to execute your program on the front end node directly.
If you execute a program on the front end node, it may be canceled by the administrator because it has effects on other users.


Usage

$ qsub [-q queue name] [-l select=number of nodes] [-N job name] [-M e-mail address] [-m mail point] [-l walltime=limit of walltime] [-l license name=number of use licenses] [execution script file]


List of options

Option Value
-q queue name Set the queue name.
As for details of queue, see a List of queues.
-l select=number of nodes Specify number of the nodes to be used.
No this option means default.(see List of queues.)
-N job name Set the job name.
The name of job is up to 236 characters.
The real-time job reference system displays up to 64 characters.
If no ‘-N’ option is specified, the system assign the default job name.
-M e-mail address Set e-mail address to be received.
To receive an e-mail, ‘-m’ option is required.
-m mail point Specify the set of events that causes mailing to be sent to the list of users specified in the ‘-M’ option.
To receive an e-mail, ‘-m’ option is required.
-l walltime=walltime Specify the limit of walltime.
If no this option is specified, the walltime is default value specified in the queue. (see List of queues.)
Appropriate value makes a queued job running frequently.
-l license name=number of use licenses Specify the number of licenses when you use applications that requires managed licenses.
If no this options specified, the job is regarded not to use applications that licenses are managed.
As for specifying licenses, see how to execute applications.


Example
Execute following jobs

・queue: DP_002, number of nodes: 2, limit of walltime: 10 minutes, script file:hello.sh 

$ qsub -q DP_002 -l select=2 -l walltime=00:10:00 hello.sh


Description in the execution script. 

#!/bin/sh
#PBS -q DP_002
#PBS -l select=2
#PBS -l walltime=00:10:00
...


・queue: P_016, script file:hello.sh, recipient address: userA@test.com
Mail is sent when the job begins execution (option is ‘-m b’) and terminates (option is ‘-m e’). 

$ qsub -q P_016 -M userA@test.com -m be hello.sh


Description in the execution script. 

#!/bin/sh
#PBS -q P_016
#PBS -M userA@test.com
#PBS -m be
...


・queue: DP_002, application: QuantumATK, script file: atk.sh 

$ qsub -q DP_002 -l atk=1 -l atkdp=35 atk.sh


Description in the execution script. 

#!/bin/sh
#PBS -q DP_002
#PBS -l atk=1 -l atkdp=35
...

aprun : Program execution command


To execute a program, use the aprun command.

attention!

Be sure to use the aprun command to execute a program.
If executed without using aprun, the program will be executed on the I/O node, which will be annoying to other users.


Usage

$ aprun [-n MPI total tasks] [-d OpenMP threads][-N MPI tasks per node] [-S MPI tasks per CPU socket] [-j 0|1|N] [--cc placement method] program


List of options

Option Description
-n MPI total tasks Set the total number of MPI tasks.
-d OpenMP threads Set the number of OpenMP threads.
(Set OMP_NUM_THREADS together.)
-N MPI tasks per node Set the number of MPI tasks per node.
-S MPI tasks per CPU socket Set the number of MPI tasks per CPU socket.
-j 0|1|N| Set the number of thread per CPU core.
0: Use HyperThreading (default)
1: No use HyperThreading
N: Use HyperThreading, place N threads per core.
–cc placement method Set the tasks / threads placement method.
depth: Bind the threads so that the process is close to the allocated CPU core
(useful when executing OpenMP, MPI + OpenMP programs).
*To improve job performance, specify values so that:
[MPI total tasks(the value of “-n”)] = [Number of nodes(the value of “#PBS -l select=”)] × [MPI tasks per node(the value of “-N”)]

Format of an execution script


This section describes the format of execution script files to run programs on the supercomputer.
To execute the application that requires an execution script file, create the file in advance.
/work area have better I/O performance than /home area, so copy your data to the /work area, execute it, and move the result to the source directory with reference to the following example.

Execute a non MPI program

#!/bin/sh
#PBS -l select=1
#PBS -q queue
#PBS -N jobname

# Copy the job input directory to /work area and move there
DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

# Execute your program
aprun program >output file 2>error file

# Move the result to the source directory after execution
cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi


・Example To execute a program ‘a.out’. 

#!/bin/sh
#PBS -l select=1
#PBS -q P_016
#PBS -N sample

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

aprun ./a.out > result.out 2> result.err

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi


Execute a MPI program using ESM mode of Cray XC

#!/bin/sh
#PBS -l select=nodes
#PBS -q queue
#PBS -N jobname

# Copy the job input directory to /work area and move there
DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

# Execute your program
aprun [ -n MPI total tasks ] [ -N MPI tasks per node ] program > output file 2> error file

# Move the result to the source directory after execution
cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi


・Example To run a program on 1 node and 2 MPI processes. 

#!/bin/sh
#PBS -l select=1
#PBS -q P_016
#PBS -N mpi1

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

aprun -n 2 -N 2 ./a.out > result.out 2> result.err

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi


・Example To run a program on 2 node and 2 MPI processes. 

#!/bin/sh
#PBS -l select=2
#PBS -q P_016
#PBS -N mpi2

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

aprun -n 2 -N 1 ./a.out > result.out 2> result.err

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

Interactive mode


Submit a job with interactive mode.
Add option -I (uppercase i) to the qsub command and specify IP_001 for the queue.

Important

Be sure to use the aprun command to execute a program.

Usage

$ qsub -I -q IP_001


Example

$ qsub -I -q IP_001
qsub: waiting for job 220331.sdb to start
qsub: job 220331.sdb ready

Directory: /home/userA
Mon Sep 23 01:03:04 JST 2019

userA@mom1:~> cd $PBS_O_WORKDIR
userA@mom1: /work/userA/testdir> aprun -n 32 -j 1 ./a.out


Job management commands

statj : Display your own job information


Display your own job information on the supercomputer.

Usage

$ statj [-x] [ [job_identifier | destination] ...]


List of options

Option Value
-x Displays status of finished, queued, and running jobs.


Example

userA@super2:~> statj
                                                            Req'd  Req'd   Elap
Job ID          Username Queue    Jobname    SessID NDS TSK Memory Time  S Time
--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
3413.sdb        userA    P_016    STDIN      231503   1  36  690gb 24:00 R 00:00

qstat : Display job information


Display information of the jobs on the supercomputer.

Usage

Default format:
qstat [-a] [-p] [-J] [-t] [-x] [ [job_identifier | destination] ...]
Long format:
qstat -f [-p] [-J] [-t] [-x] [ [job_identifier | destination] ...]


List of options

Option Value
-a Display memory usage, elapsed time, status of jobs, etc.
-p Display the percentage of the job completion.
-J Display limits status of job array.
-t Displays status of jobs.
-x Displays status of finished, queued, and running jobs.
-f Display status in long format.


Example

userA@super2:~> qstat -a
                                                            Req'd  Req'd   Elap
Job ID          Username Queue    Jobname    SessID NDS TSK Memory Time  S Time
--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
3390.sdb        userA    P_016    abinit     193347   4 144 2760gb 72:00 R 47:28
3401.sdb        userA    P_016    prog9_1    121974   4 144 2760gb 72:00 R 47:26

userA@super2:~> qstat -p
Job id           Name             User             % done   S Queue
---------------- ---------------- ---------------- -------- - -----
3390.sdb         abinit           userA                  2  R P_016
3401.sdb         prog9_1          userA                  0  R P_016

userA@super2:~> qstat -t
Job id           Name             User             Time Use S Queue
---------------- ---------------- ---------------- -------- - -----
3390.sdb         abinit           userA            00:00:01 R P_016
3401.sdb         prog9_1          userA            00:00:01 R P_016

userA@super2:~ > qstat -x
Job id           Name             User             Time Use S Queue
---------------- ---------------- ---------------- -------- - -----
2235.sdb         prog9_2          userA            00:00:03 F P_016
2236.sdb         vasp4            userA            00:00:01 F P_016
2237.sdb         prog9_1          userA            00:00:01 F P_016
...

userA@super2:~> qstat -f 3390.sdb
Job Id: 3390.sdb
 Job_Name = abinit
 Job_Owner = userA@nid00204
 resources_used.cpupercent = 10
 resources_used.cput = 00:00:01
 resources_used.mem = 12836kb
 resources_used.ncpus = 72
...

statq : Display queue status


Display information about queues on the supercomputer.

Usage

Default format:
statq [destination ...]
Long format:
statq -f [destination ...]


List of options

Option Value
-f Display status in long format.


Example

userA@super2:~> statq
Queue            Max   Tot   Ena Str Que   Run   Hld   Wat   Trn   Ext   Type
---------------- ----- ----- --- --- ----- ----- ----- ----- ----- ----- ----
workq                0     0 no  yes     0     0     0     0     0     0 Exec
DP_002               0     0 yes yes     0     0     0     0     0     0 Exec
P_016                0     1 yes yes     0     1     0     0     0     0 Exec
P_032                0     0 yes yes     0     0     0     0     0     0 Exec
P_064                0     0 yes yes     0     0     0     0     0     0 Exec
LP_032               0     0 yes yes     0     0     0     0     0     0 Exec
LP_064               0     0 yes yes     0     0     0     0     0     0 Exec
...

userA@super2:~> statq -f
Queue: workq
     queue_type = Execution
     total_jobs = 0
     state_count = Transit:0 Queued:0 Held:0 Waiting:0 Running:0 Exiting:0 Begun
         :0
     enabled = False
     started = True
...

qstat -B : Display server status


Display information about servers of the supercomputer.

Usage

Default format:
qstat -B [destination ...]
Long format:
qstat -B -f [destination ...]


List of options

Option Value
-B Display server status.
-f Display status in long format.

Example

userA@super2:~> qstat -B
Server           Max   Tot   Que   Run   Hld   Wat   Trn   Ext   Status
---------------- ----- ----- ----- ----- ----- ----- ----- ----- -----------
sdb                  0  1155     0     1     0     0     0     0 Active
userA@super2:~> qstat -Bf
Server: sdb
    server_state = Active
    server_host = sdb
    scheduling = True
    max_queued = [u:PBS_GENERIC=200]
...

qdel : Cancel the job before the job finished


Use qdel command for cancelling the job on the supercomputer.

Usage

qdel [ -x ] [ -Wsuppress_email=<N> ] job_identifier [job_identifier ...]


List of options

Option Value
-x Delete job and job history of the specified job.
-Wsuppress_email Set limit on number of e-mails sent on deleting jobs.

Example 

userA@super2:~/work/20180712_sample> statj
                                                       Req'd  Req'd   Elap
Job ID     Username Queue    Jobname    SessID NDS TSK Memory Time  S Time
---------- -------- -------- ---------- ------ --- --- ------ ----- - -----
3413.sdb   userA    P_016    abinit       3710   3 216 2304gb 72:00 R 00:00
3414.sdb   userA    DP_002   STDIN       13588   1  72  768gb 00:10 R 00:00

userA@super2:~/work/20180712_sample> qdel 3414.sdb

userA@super2:~/work/20180712_sample> statj
                                                       Req'd  Req'd   Elap
Job ID     Username Queue    Jobname    SessID NDS TSK Memory Time  S Time
---------- -------- -------- ---------- ------ --- --- ------ ----- - -----
3413.sdb   userA    P_016    abinit       3710   3 216 2304gb 72:00 R 00:00


Display information about used and remained time of job execution

jobtime : Display information about used and remained time of job execution


Usage

$ jobtime


Information

Section Details
Last Updated updated time
User user ID
Total available time of job execution
Used used time
Remained remained time


Example

userA@super2:~ > jobtime
# Last Updated: 2018/10/01 13:45
# User Total Used Remained (H)
username 500 222.32 277.68


References for submitting job and script

Specify the parameters affecting performance of job


Specifying number of processes per core by apron command, performance of the job can be improved, because Hyper-Threading is enabled on the supercomputer.

Usage
Specify 1 thread per physical core. 

aprun -j 1 program


Example

#!/bin/bash
#PBS -j oe
#PBS -l select=1
#PBS -q P_016

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

aprun -n 36 -N 36 -j 1 ./xhpl_skl_diag_cray_opt > result.out 2> result.err

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf$WORKDIR; fi


  • user_manual/supercomputer/job_submission_management.txt
  • Last modified: 2023/04/11 05:26
  • (external edit)