pbs-job-submission-and-execution.md

!!!warning
    This page has not been updated yet. The page does not reflect the transition from PBS to Slurm.

# 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)
1. the number of computational nodes (required)
1. the number of cores per node (not required)
1. the maximum wall time allocated to your calculation, note that jobs exceeding the maximum wall time will be killed
1. your Project ID
1. a Jobscript or interactive switch

Submit the job using the `qsub` command:

```console
$ 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. it 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
    `ncpus=y` is usually not required, because the smallest allocation unit is an entire node. The exception are corner cases for `qviz` and `qfat` on Karolina.

### Job Submission Examples

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

In this example, we allocate 64 nodes, 36 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.

```console
$ qsub -q qexp -l select=4 -I
```

In this example, we allocate 4 nodes, 36 cores per node, for 1 hour. We allocate these resources via the `qexp` queue. The resources will be available interactively.

```console
$ qsub -A OPEN-0-0 -q qnvidia -l select=10 ./myjob
```

In this example, we allocate 10 NVIDIA accelerated nodes, 24 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.

```console
$ qsub -A OPEN-0-0 -q qfree -l select=10 ./myjob
```

In this example, we allocate 10 nodes, 24 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][1]. In such cases, it is not necessary to specify any options for `qsub`.

```console
$ qsub ./myjob
```

By default, the PBS batch system sends an email only when the job is aborted. Disabling mail events completely can be done as follows:

```console
$ qsub -m n
```

#### Dependency Job Submission

To submit dependent jobs in sequence, use the `depend` function of `qsub`.

First submit the first job in a standard manner:

```console
$ qsub -A OPEN-0-0 -q qprod -l select=64,walltime=02:00:00 ./firstjob
123456[].isrv1
```

Then submit the second job using the `depend` function:

```console
$ qsub -W depend=afterok:123456 ./secondjob
```

Both jobs will be queued, but the second job won't start until the first job has finished successfully.

Below is the list of arguments that can be used with `-W depend=dependency:jobid`:

| Argument    | Description                                                     |
| ----------- | --------------------------------------------------------------- |
| after       | This job is scheduled after `jobid` begins execution.       |
| afterok     | This job is scheduled after `jobid` finishes successfully.  |
| afternotok  | This job is scheduled after `jobid` finishes unsucessfully. |
| afterany    | This job is scheduled after `jobid` finishes in any state.  |
| before      | This job must begin execution before `jobid` is scheduled.  |
| beforeok    | This job must finish successfully before `jobid` begins.        |
| beforenotok | This job must finish unsuccessfully before `jobid` begins.      |
| beforeany   | This job must finish in any state before `jobid` begins.        |

### Useful Tricks

All `qsub` options may be [saved directly into the jobscript][1]. In such a case, no options to `qsub` are needed.

```console
$ qsub ./myjob
```

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

```console
$ qsub -m n
```

<!--- NOT IMPLEMENTED ON KAROLINA YET

## Advanced Job Placement

### Salomon - Placement by Network Location

The network location of allocated nodes in the [InfiniBand network][3] influences efficiency of network communication between nodes of job. Nodes on the same InfiniBand switch communicate faster with lower latency than distant nodes. To improve communication efficiency of jobs, PBS scheduler on Salomon is configured to allocate nodes (from currently available resources), which are as close as possible in the network topology.

For communication intensive jobs, it is possible to set stricter requirement - to require nodes directly connected to the same InfiniBand switch or to require nodes located in the same dimension group of the InfiniBand network.

### Salomon - Placement by InfiniBand Switch

Nodes directly connected to the same InfiniBand switch can communicate most efficiently. Using the same switch prevents hops in the network and provides for unbiased, most efficient network communication. There are 9 nodes directly connected to every InfiniBand switch.

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

Nodes directly connected to the one InfiniBand switch can be allocated using node grouping on the PBS resource attribute `switch`.

In this example, we request all 9 nodes directly connected to the same switch using node grouping placement.

```console
$ qsub -A OPEN-0-0 -q qprod -l select=9 -l place=group=switch ./myjob
```

-->

## Advanced Job Handling

### Selecting Turbo Boost Off

!!! note
    For Barbora only.

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 Turbo for all nodes of the job by using the PBS resource attribute `cpu_turbo_boost`:

```console
$ qsub -A OPEN-0-0 -q qprod -l select=4 -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:

```console
$ qsub -A OPEN-0-0 -q qprod
    -l select=18:ibswitch=isw10:mpiprocs=1:ompthreads=16+18: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 the status of your jobs using the `qstat` and `check-pbs-jobs` commands

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

Example:

```console
$ 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`. `job1` and `job2` are using 4 nodes, 128 cores per node each. `job1` has already run for 38 hours and 25 minutes, and `job2` for 17 hours 44 minutes. So `job1`, for example, has already consumed `64 x 38.41 = 2,458.6` core-hours. `job3x` has already consumed `32 x 0.96 = 30.93` core-hours. These consumed core-hours will be [converted to node-hours][10] and 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, and continuously display (`tail -f`) job standard or error output.

```console
$ 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:

```console
$ 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:

```console
$ 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.

```console
$ 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 the 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

```console
$ qdel 12345.srv11
```

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

```console
$ qsig -s 9 12345.srv11
```

Learn more by reading the PBS man page

```console
$ 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.

```console
$ qsub -q qexp -l select=4 -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   4 128    --  01:00 R 00:00
   cn17/0*32+cn108/0*32+cn109/0*32+cn110/0*32
```

In this example, the nodes `cn17`, `cn108`, `cn109`, and `cn110` were allocated for 1 hour via the qexp queue. The `myjob` jobscript 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:

```console
$ qsub -q qexp -l select=4 -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

```console
$ qsub -q qexp -l select=4 -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` were 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.

```bash
#!/bin/bash

cd $PBS_O_WORKDIR

SCRDIR=/scratch/project/open-00-00/${USER}/myjob
mkdir -p $SCRDIR

# change to scratch directory, exit on failure
cd $SCRDIR || exit

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

# load the MPI module
# (Always specify the module's name and version in your script;
# for the reason, see https://docs.it4i.cz/software/modules/lmod/#loading-modules.)
ml OpenMPI/4.1.1-GCC-10.2.0-Java-1.8.0_221

# 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 the `mympiprog.x` executable. We create the `myjob` directory 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][6] 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 the 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 the `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:

```bash
#!/bin/bash
#PBS -q qprod
#PBS -N MYJOB
#PBS -l select=100:mpiprocs=1:ompthreads=16
#PBS -A OPEN-00-00

# job is run using project resources; here ${PBS_ACCOUNT,,} translates to "open-00-00"
SCRDIR=/scratch/project/${PBS_ACCOUNT,,}/${USER}/myjob

# change to scratch directory, exit on failure
cd $SCRDIR || exit

# load the MPI module
# (Always specify the module's name and version in your script;
# for the reason, see https://docs.it4i.cz/software/modules/lmod/#loading-modules.)
ml OpenMPI/4.1.1-GCC-10.2.0-Java-1.8.0_221

# execute the calculation
mpirun ./mympiprog.x

#exit
exit
```

In this example, input and executable files are assumed to be preloaded manually in the `/scratch/project/open-00-00/$USER/myjob` directory. Because we used the `qprod` queue, we had to specify which project's resources we want to use, and our `PBS_ACCOUNT` variable will be set accordingly (OPEN-00-00). `${PBS_ACCOUNT,,}` uses one of the bash's built-in functions to translate it into lower case.

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.

### 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][6] memory on the node:

```bash
#!/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 the executable `myprog.x`. We copy input and executable files from the `/home` directory where the `qsub` was invoked (`$PBS_O_WORKDIR`) to the local `/scratch` memory `/lscratch/$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][9] section.

[1]: #example-jobscript-for-mpi-calculation-with-preloaded-inputs
[2]: resources-allocation-policy.md
[3]: ../salomon/network.md
[5]: ../salomon/7d-enhanced-hypercube.md
[6]: ../salomon/storage.md
[9]: capacity-computing.md
[10]: resources-allocation-policy.md#resource-accounting-policy