job-submission-and-execution.md

Job submission and execution

Job Submission

When allocating computational resources for the job, please specify

1. suitable queue for your job (default is qprod)
2. number of computational nodes required
3. number of cores per node required
4. maximum wall time allocated to your calculation, note that jobs exceeding maximum wall time will be killed
5. Project ID
6. Jobscript or interactive switch

!!! Note "Note" Use the qsub command to submit your job to a queue for allocation of the computational resources.

Submit the job using the qsub command:

$ qsub -A Project_ID -q queue -l select=x:ncpus=y,walltime=[[hh:]mm:]ss[.ms] jobscript

The qsub submits the job into the queue, in another words the qsub command creates a request to the PBS Job manager for allocation of specified resources. The resources will be allocated when available, subject to above described policies and constraints. After the resources are allocated the jobscript or interactive shell is executed on first of the allocated nodes.

Job Submission Examples

$ qsub -A OPEN-0-0 -q qprod -l select=64:ncpus=16,walltime=03:00:00 ./myjob

In this example, we allocate 64 nodes, 16 cores per node, for 3 hours. We allocate these resources via the qprod queue, consumed resources will be accounted to the Project identified by Project ID OPEN-0-0. Jobscript myjob will be executed on the first node in the allocation.

$ qsub -q qexp -l select=4:ncpus=16 -I

In this example, we allocate 4 nodes, 16 cores per node, for 1 hour. We allocate these resources via the qexp queue. The resources will be available interactively

$ qsub -A OPEN-0-0 -q qnvidia -l select=10:ncpus=16 ./myjob

In this example, we allocate 10 nvidia accelerated nodes, 16 cores per node, for 24 hours. We allocate these resources via the qnvidia queue. Jobscript myjob will be executed on the first node in the allocation.

$ qsub -A OPEN-0-0 -q qfree -l select=10:ncpus=16 ./myjob

In this example, we allocate 10 nodes, 16 cores per node, for 12 hours. We allocate these resources via the qfree queue. It is not required that the project OPEN-0-0 has any available resources left. Consumed resources are still accounted for. Jobscript myjob will be executed on the first node in the allocation.

All qsub options may be saved directly into the jobscript. In such a case, no options to qsub are needed.

$ qsub ./myjob

By default, the PBS batch system sends an e-mail only when the job is aborted. Disabling mail events completely can be done like this:

$ qsub -m n

Advanced job placement

Placement by name

Specific nodes may be allocated via the PBS

qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16:host=cn171+1:ncpus=16:host=cn172 -I

In this example, we allocate nodes cn171 and cn172, all 16 cores per node, for 24 hours. Consumed resources will be accounted to the Project identified by Project ID OPEN-0-0. The resources will be available interactively.

Placement by CPU type

Nodes equipped with Intel Xeon E5-2665 CPU have base clock frequency 2.4GHz, nodes equipped with Intel Xeon E5-2470 CPU have base frequency 2.3 GHz (see section Compute Nodes for details). Nodes may be selected via the PBS resource attribute cpu_freq .

CPU Type	base freq.	Nodes	cpu_freq attribute
Intel Xeon E5-2665	2.4GHz	cn[1-180], cn[208-209]	24
Intel Xeon E5-2470	2.3GHz	cn[181-207]	23

$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16:cpu_freq=24 -I

In this example, we allocate 4 nodes, 16 cores, selecting only the nodes with Intel Xeon E5-2665 CPU.

Placement by IB switch

Groups of computational nodes are connected to chassis integrated Infiniband switches. These switches form the leaf switch layer of the Infiniband network fat tree topology. Nodes sharing the leaf switch can communicate most efficiently. Sharing the same switch prevents hops in the network and provides for unbiased, most efficient network communication.

Nodes sharing the same switch may be selected via the PBS resource attribute ibswitch. Values of this attribute are iswXX, where XX is the switch number. The node-switch mapping can be seen at Hardware Overview section.

We recommend allocating compute nodes of a single switch when best possible computational network performance is required to run the job efficiently:

    qsub -A OPEN-0-0 -q qprod -l select=18:ncpus=16:ibswitch=isw11 ./myjob

In this example, we request all the 18 nodes sharing the isw11 switch for 24 hours. Full chassis will be allocated.

Advanced job handling

Selecting Turbo Boost off

Intel Turbo Boost Technology is on by default. We strongly recommend keeping the default.

If necessary (such as in case of benchmarking) you can disable the Turbo for all nodes of the job by using the PBS resource attribute cpu_turbo_boost

    $ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16 -l cpu_turbo_boost=0 -I

More about the Intel Turbo Boost in the TurboBoost section

Advanced examples

In the following example, we select an allocation for benchmarking a very special and demanding MPI program. We request Turbo off, 2 full chassis of compute nodes (nodes sharing the same IB switches) for 30 minutes:

    $ qsub -A OPEN-0-0 -q qprod
    -l select=18:ncpus=16:ibswitch=isw10:mpiprocs=1:ompthreads=16+18:ncpus=16:ibswitch=isw20:mpiprocs=16:ompthreads=1
    -l cpu_turbo_boost=0,walltime=00:30:00
    -N Benchmark ./mybenchmark

The MPI processes will be distributed differently on the nodes connected to the two switches. On the isw10 nodes, we will run 1 MPI process per node 16 threads per process, on isw20 nodes we will run 16 plain MPI processes.

Although this example is somewhat artificial, it demonstrates the flexibility of the qsub command options.

Job Management

!!! Note "Note" Check status of your jobs using the qstat and check-pbs-jobs commands

$ qstat -a
$ qstat -a -u username
$ qstat -an -u username
$ qstat -f 12345.srv11

Example:

$ qstat -a

srv11:
                                                            Req'd  Req'd   Elap
Job ID          Username Queue    Jobname    SessID NDS TSK Memory Time  S Time
--------------- -------- --  |---|---| ------ --- --- ------ ----- - -----
16287.srv11     user1    qlong    job1         6183   4  64    --  144:0 R 38:25
16468.srv11     user1    qlong    job2         8060   4  64    --  144:0 R 17:44
16547.srv11     user2    qprod    job3x       13516   2  32    --  48:00 R 00:58

In this example user1 and user2 are running jobs named job1, job2 and job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each. The job1 already runs for 38 hours and 25 minutes, job2 for 17 hours 44 minutes. The job1 already consumed 6438.41 = 2458.6 core hours. The job3x already consumed 0.9632 = 30.93 core hours. These consumed core hours will be accounted on the respective project accounts, regardless of whether the allocated cores were actually used for computations.

Check status of your jobs using check-pbs-jobs command. Check presence of user's PBS jobs' processes on execution hosts. Display load, processes. Display job standard and error output. Continuously display (tail -f) job standard or error output.

$ check-pbs-jobs --check-all
$ check-pbs-jobs --print-load --print-processes
$ check-pbs-jobs --print-job-out --print-job-err

$ check-pbs-jobs --jobid JOBID --check-all --print-all

$ check-pbs-jobs --jobid JOBID --tailf-job-out

Examples:

$ check-pbs-jobs --check-all
JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165
Check session id: OK
Check processes
cn164: OK
cn165: No process

In this example we see that job 35141.dm2 currently runs no process on allocated node cn165, which may indicate an execution error.

$ check-pbs-jobs --print-load --print-processes
JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165
Print load
cn164: LOAD: 16.01, 16.01, 16.00
cn165: LOAD:  0.01,  0.00,  0.01
Print processes
       %CPU CMD
cn164:  0.0 -bash
cn164:  0.0 /bin/bash /var/spool/PBS/mom_priv/jobs/35141.dm2.SC
cn164: 99.7 run-task
...

In this example we see that job 35141.dm2 currently runs process run-task on node cn164, using one thread only, while node cn165 is empty, which may indicate an execution error.

$ check-pbs-jobs --jobid 35141.dm2 --print-job-out
JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165
Print job standard output:
======================== Job start  ==========================
Started at    : Fri Aug 30 02:47:53 CEST 2013
Script name   : script
Run loop 1
Run loop 2
Run loop 3

In this example, we see actual output (some iteration loops) of the job 35141.dm2

!!! Note "Note" Manage your queued or running jobs, using the qhold, qrls, qdel, qsig or qalter commands

You may release your allocation at any time, using qdel command

$ qdel 12345.srv11

You may kill a running job by force, using qsig command

$ qsig -s 9 12345.srv11

Learn more by reading the pbs man page

$ man pbs_professional