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

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](job-submission-and-execution.html#PBSsaved). 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](../network.html) 
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](../hardware-overview.html) 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
--------------

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 64*38.41 = 2458.6 core hours. The
job3x already consumed 0.96*32 = 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

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
`

Job Execution
-------------

### Jobscript

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

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

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 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.

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

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

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

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

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

#exit
exit
`

In this example, some directory on the /home holds the input file input
and executable mympiprog.x . We create a 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 programm mympiprog.x and copy the output file back to the /home
directory. The mympiprog.x is executed as one process per node, on all
allocated nodes.

Consider preloading inputs and executables onto [shared
scratch](../storage.html) before the calculation starts.

In some cases, it may be impractical to copy the inputs to scratch and
outputs to home. 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 a case, it is users responsibility to
preload the input files on shared /scratch before the job submission and
retrieve the outputs manually, after all calculations are finished.

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

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
module load openmpi

# execute the calculation
mpiexec ./mympiprog.x

#exit
exit
`

In this example, input and executable files are assumed preloaded
manually in /scratch/$USER/myjob directory. Note the **mpiprocs** and
ompthreads** qsub options, controlling behavior of the MPI execution.
The 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 is found in the [Running
OpenMPI](../software/mpi-1/Running_OpenMPI.html) and
[Running MPICH2](../software/mpi-1/running-mpich2.html)
sections.

### Example Jobscript for Single Node Calculation

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

Example jobscript for single node calculation, using [local
scratch](../storage.html) 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, some directory on the 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 ($PBS_O_WORKDIR) to local
scratch /lscratch/$PBS_JOBID, execute the myprog.x and copy the output
file back to the /home directory. The myprog.x runs on one node only and
may use threads.

### Other Jobscript Examples

Further jobscript examples may be found in the
[Software](../software.1.html) section and the [Capacity
computing](capacity-computing.html) section.