Job Submission and Execution

Job Submission

When allocating computational resources for the job, specify:

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

Note

Use the qsub command to submit your job to a queue for allocation of 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 command submits the job to the queue, i.e. 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 the above described policies and constraints. After the resources are allocated, the jobscript or interactive shell is executed on the first of the allocated nodes.

Note

PBS statement nodes (qsub -l nodes=nodespec) are not supported on the Anselm cluster.

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. The 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. the 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. The jobscript myjob will be executed on the first node in the allocation.

All qsub options may be saved directly into the jobscript. In such cases, it is not necessary to specify any options for qsub.

$ 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 as follows:

$ 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 an Intel Xeon E5-2665 CPU have a base clock frequency of 2.4GHz, nodes equipped with an Intel Xeon E5-2470 CPU have a base frequency of 2.3 GHz (see the 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 per node, 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 facilitates unbiased, highly 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 in the Hardware Overview section.

We recommend allocating compute nodes to 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 of the 18 nodes sharing the isw11 switch for 24 hours. a 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 the 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 information about the Intel Turbo Boost can be found 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, and 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 with 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

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. job1 has already run for 38 hours and 25 minutes, and job2 for 17 hours 44 minutes. job1 has already consumed 64 x 38.41 = 2458.6 core hours. job3x has already consumed 0.96 x 32 = 30.93 core hours. These consumed core hours will be accounted for on the respective project accounts, regardless of whether the allocated cores were actually used for computations.

The following commands allow you to; check the status of your jobs using the check-pbs-jobs command; check for the presence of user's PBS jobs' processes on execution hosts; display load and 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 is not currently running any processes on the 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 is currently running a 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

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

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

$ qdel 12345.srv11

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

$ qsig -s 9 12345.srv11

Learn more by reading the pbs man page

$ man pbs_professional

Job Execution

Jobscript

Note

Prepare the jobscript to run batch jobs in the PBS queue system

The Jobscript is a user made script controlling a sequence of commands for executing the calculation. It is often written in bash, though other scripts may be used as well. The jobscript is supplied to the PBS qsub command as an argument, and is executed by the PBS Professional workload manager.

Note

The jobscript or interactive shell is executed on first of the allocated nodes.

$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob
$ qstat -n -u username

srv11:
                                                            Req'd Req'd   Elap
Job ID          Username Queue    Jobname    SessID NDS TSK Memory Time S Time
--------------- -------- --  |---|---| ------ --- --- ------ ----- - -----
15209.srv11     username qexp     Name0        5530   4 64    --  01:00 R 00:00
   cn17/0*16+cn108/0*16+cn109/0*16+cn110/0*16

In this example, the nodes cn17, cn108, cn109, and cn110 were allocated for 1 hour via the qexp queue. The jobscript myjob will be executed on the node cn17, while the nodes cn108, cn109, and cn110 are available for use as well.

The jobscript or interactive shell is by default executed in the home directory

$ qsub -q qexp -l select=4:ncpus=16 -I
qsub: waiting for job 15210.srv11 to start
qsub: job 15210.srv11 ready

$ pwd
/home/username

In this example, 4 nodes were allocated interactively for 1 hour via the qexp queue. The interactive shell is executed in the home directory.

Note

All nodes within the allocation may be accessed via ssh. Unallocated nodes are not accessible to the user.

The allocated nodes are accessible via ssh from login nodes. The nodes may access each other via ssh as well.

Calculations on allocated nodes may be executed remotely via the MPI, ssh, pdsh or clush. You may find out which nodes belong to the allocation by reading the $PBS_NODEFILE file

qsub -q qexp -l select=4:ncpus=16 -I
qsub: waiting for job 15210.srv11 to start
qsub: job 15210.srv11 ready

$ pwd
/home/username

$ sort -u $PBS_NODEFILE
cn17.bullx
cn108.bullx
cn109.bullx
cn110.bullx

$ pdsh -w cn17,cn[108-110] hostname
cn17: cn17
cn108: cn108
cn109: cn109
cn110: cn110

In this example, the hostname program is executed via pdsh from the interactive shell. The execution runs on all four allocated nodes. The same result would be achieved if the pdsh is called from any of the allocated nodes or from the login nodes.

Example Jobscript for MPI Calculation

Note

Production jobs must use the /scratch directory for I/O

The recommended way to run production jobs is to change to the /scratch directory early in the jobscript, copy all inputs to /scratch, execute the calculations and copy outputs to the home directory.

#!/bin/bash

# change to scratch directory, exit on failure
SCRDIR=/scratch/$USER/myjob
mkdir -p $SCRDIR
cd $SCRDIR || exit

# copy input file to scratch
cp $PBS_O_WORKDIR/input .
cp $PBS_O_WORKDIR/mympiprog.x .

# load the MPI module
ml OpenMPI

# execute the calculation
mpirun -pernode ./mympiprog.x

# copy output file to home
cp output $PBS_O_WORKDIR/.

#exit
exit

In this example, a directory in /home holds the input file input and executable mympiprog.x . We create the directory myjob on the /scratch filesystem, copy input and executable files from the /home directory where the qsub was invoked ($PBS_O_WORKDIR) to /scratch, execute the MPI program mympiprog.x and copy the output file back to the /home directory. mympiprog.x is executed as one process per node, on all allocated nodes.

Note

Consider preloading inputs and executables onto shared scratch memory before the calculation starts.

In some cases, it may be impractical to copy the inputs to the scratch memory and the outputs to the home directory. This is especially true when very large input and output files are expected, or when the files should be reused by a subsequent calculation. In such cases, it is the users' responsibility to preload the input files on shared /scratch memory before the job submission, and retrieve the outputs manually after all calculations are finished.

Note

Store the qsub options within the jobscript. Use mpiprocs and ompthreads qsub options to control the MPI job execution.

Example Jobscript for MPI Calculation With Preloaded Inputs

Example jobscript for an MPI job with preloaded inputs and executables, options for qsub are stored within the script:

#!/bin/bash
#PBS -q qprod
#PBS -N MYJOB
#PBS -l select=100:ncpus=16:mpiprocs=1:ompthreads=16
#PBS -A OPEN-0-0

# change to scratch directory, exit on failure
SCRDIR=/scratch/$USER/myjob
cd $SCRDIR || exit

# load the MPI module
ml OpenMPI

# execute the calculation
mpirun ./mympiprog.x

#exit
exit

In this example, input and executable files are assumed to be preloaded manually in the /scratch/$USER/myjob directory. Note the mpiprocs and ompthreads qsub options controlling the behavior of the MPI execution. mympiprog.x is executed as one process per node, on all 100 allocated nodes. If mympiprog.x implements OpenMP threads, it will run 16 threads per node.

More information can be found in the Running OpenMPI and Running MPICH2 sections.

Example Jobscript for Single Node Calculation

Note

The local scratch directory is often useful for single node jobs. Local scratch memory will be deleted immediately after the job ends.

Example jobscript for single node calculation, using local scratch memory on the node:

#!/bin/bash

# change to local scratch directory
cd /lscratch/$PBS_JOBID || exit

# copy input file to scratch
cp $PBS_O_WORKDIR/input .
cp $PBS_O_WORKDIR/myprog.x .

# execute the calculation
./myprog.x

# copy output file to home
cp output $PBS_O_WORKDIR/.

#exit
exit

In this example, a directory in /home holds the input file input and executable myprog.x . We copy input and executable files from the home directory where the qsub was invoked (PBS_O_WORKDIR) to local scratch memory /lscratch/PBS_JOBID, execute myprog.x and copy the output file back to the /home directory. myprog.x runs on one node only and may use threads.

Other Jobscript Examples

Further jobscript examples may be found in the software section and the Capacity computing section.