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docs.it4i/general/capacity-computing.md
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@@ -10,8 +10,7 @@ However, executing a huge number of jobs via the PBS queue may strain the system
Follow one of the procedures below, in case you wish to schedule more than 100 jobs at a time.
* Use [Job arrays][1] when running a huge number of [multithread][2] (bound to one node only) or multinode (multithread across several nodes) jobs.
* Use [GNU parallel][3] when running single core jobs.
* Combine [GNU parallel with Job arrays][4] when running huge number of single core jobs.
* Use [HyperQueue][3] when running single core jobs.
## Policy
@@ -151,162 +150,47 @@ $ qstat -u $USER -tJ
For more information on job arrays, see the [PBSPro Users guide][6].
## GNU Parallel
## HyperQueue
!!! note
Use GNU parallel to run many single core tasks on one node.
GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. GNU parallel is most useful when running single core jobs via the queue systems.
For more information and examples, see the parallel man page:
```console
$ module add parallel
$ man parallel
```
### GNU Parallel Jobscript
The GNU parallel shell executes multiple instances of the jobscript using all cores on the node. The instances execute different work, controlled by the `$PARALLEL_SEQ` variable.
Example:
Assume we have 101 input files with each name beginning with "file" (e.g. file001, ..., file101). Assume we would like to use each of these input files with the myprog.x program executable, each as a separate single core job. We call these single core jobs tasks.
First, we create a tasklist file listing all tasks - all input files in our example:
```console
$ find . -name 'file*' > tasklist
```
Then we create a jobscript:
```bash
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
#PBS -l select=1:ncpus=16,walltime=02:00:00
[ -z "$PARALLEL_SEQ" ] &&
{ module add parallel ; exec parallel -a $PBS_O_WORKDIR/tasklist $0 ; }
# change to local scratch directory
SCR=/lscratch/$PBS_JOBID/$PARALLEL_SEQ
mkdir -p $SCR ; cd $SCR || exit
# get individual task from tasklist
TASK=$1
# copy input file and executable to scratch
cp $PBS_O_WORKDIR/$TASK input
# execute the calculation
cat input > output
# copy output file to submit directory
cp output $PBS_O_WORKDIR/$TASK.out
```
In this example, tasks from the tasklist are executed via the GNU parallel. The jobscript executes multiple instances of itself in parallel, on all cores of the node. Once an instace of the jobscript is finished, a new instance starts until all entries in the tasklist are processed. Currently processed entries of the joblist may be retrieved via the `$1` variable. The `$TASK` variable expands to one of the input filenames from the tasklist. We copy the input file to the local scratch memory, execute myprog.x, and copy the output file back to the submit directory under the $TASK.out name.
### Submit the Job
To submit the job, use the `qsub` command. The 101 task job of the [example above][7] may be submitted as follows:
HyperQueue lets you build a computation plan consisting of a large amount of tasks and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs and distributes them to fully utilize allocated notes. You thus do not have to manually aggregate your tasks into SLURM/PBS jobs. See the [project repository][a].
```console
$ qsub -N JOBNAME jobscript
12345.dm2
```
In this example, we submit a job of 101 tasks. 16 input files will be processed in parallel. The 101 tasks on 16 cores are assumed to complete in less than 2 hours.
!!! hint
Use #PBS directives at the beginning of the jobscript file, do not forget to set your valid `PROJECT_ID` and the desired queue.
## Job Arrays and GNU Parallel
!!! note
Combine the Job arrays and GNU parallel for the best throughput of single core jobs
While job arrays are able to utilize all available computational nodes, the GNU parallel can be used to efficiently run multiple single-core jobs on a single node. The two approaches may be combined to utilize all available (current and future) resources to execute single core jobs.
!!! note
Every subjob in an array runs GNU parallel to utilize all cores on the node
### GNU Parallel, Shared jobscript
A combined approach, very similar to job arrays, can be taken. A job array is submitted to the queuing system. The subjobs run GNU parallel. The GNU parallel shell executes multiple instances of the jobscript using all of the cores on the node. The instances execute different work, controlled by the `$PBS_JOB_ARRAY` and the `$PARALLEL_SEQ` variables.
Example:
Assume we have 992 input files with each name beginning with "file" (e. g. file001, ..., file992). Assume we would like to use each of these input files with the myprog.x program executable, each as a separate single core job. We call these single core jobs tasks.
First, we create a tasklist file listing all tasks - all input files in our example:
```console
$ find . -name 'file*' > tasklist
```
### Installation
Next we create a file, controlling how many tasks will be executed in one subjob:
To install/compile HyperQueue, follow the steps on the [official webpage][b].
```console
$ seq 32 > numtasks
```
### Submiting a simple task
Then we create a jobscript:
* Start server (e.g. on a login node or in a cluster partition)
```bash
#!/bin/bash
#PBS -A PROJECT_ID
#PBS -q qprod
#PBS -l select=1:ncpus=16,walltime=02:00:00
``$ hq server start &``
[ -z "$PARALLEL_SEQ" ] &&
{ module add parallel ; exec parallel -a $PBS_O_WORKDIR/numtasks $0 ; }
* Submit a job (command ``echo 'Hello world'`` in this case)
# change to local scratch directory
SCR=/lscratch/$PBS_JOBID/$PARALLEL_SEQ
mkdir -p $SCR ; cd $SCR || exit
``$ hq submit echo 'Hello world'``
# get individual task from tasklist with index from PBS JOB ARRAY and index form Parallel
IDX=$(($PBS_ARRAY_INDEX + $PARALLEL_SEQ - 1))
TASK=$(sed -n "${IDX}p" $PBS_O_WORKDIR/tasklist)
[ -z "$TASK" ] && exit
* Ask for computing resources
# copy input file and executable to scratch
cp $PBS_O_WORKDIR/$TASK input
* Start worker manually
# execute the calculation
cat input > output
``$ hq worker start &``
# copy output file to submit directory
cp output $PBS_O_WORKDIR/$TASK.out
```
* Automatic resource request
In this example, the jobscript executes in multiple instances in parallel, on all cores of a computing node. The `$TASK` variable expands to one of the input filenames from the tasklist. We copy the input file to local scratch memory, execute myprog.x and copy the output file back to the submit directory, under the $TASK.out name. The numtasks file controls how many tasks will be run per subjob. Once a task is finished, a new task starts, until the number of tasks in the numtasks file is reached.
[Not implemented yet]
!!! note
Select the subjob walltime and the number of tasks per subjob carefully
* Manual request in PBS
When deciding these values, keep in mind the following guiding rules:
- Start worker on the first node of a PBS job
1. Let n=N/16. Inequality (n+1) \* T < W should hold. N is the number of tasks per subjob, T is the expected single task walltime and W is subjob walltime. A short subjob walltime improves scheduling and job throughput.
1. The number of tasks should be modulo 16.
1. These rules are valid only when all tasks have similar task walltimes T.
``$ qsub <your-params-of-qsub> -- hq worker start``
### Submit the Job Array (-J)
- Start worker on all nodes of a PBS job
To submit the job array, use the `qsub -J` command. The 992 task jobs of the [example above][8] may be submitted like this:
``$ qsub <your-params-of-qsub> -- `which pbsdsh` hq worker start``
```console
$ qsub -N JOBNAME -J 1-992:32 jobscript
12345[].dm2
```
* Monitor the state of jobs
In this example, we submit a job array of 31 subjobs. Note the -J 1-992:**32**, this must be the same as the number sent to numtasks file. Each subjob will run on one full node and process 16 input files in parallel, 32 in total per subjob. Every subjob is assumed to complete in less than 2 hours.
!!! hint
Use #PBS directives at the beginning of the jobscript file, do not forget to set your valid PROJECT_ID and desired queue.
``$ hq jobs``
## Examples
@@ -321,10 +205,10 @@ $ cat README
[1]: #job-arrays
[2]: #shared-jobscript-on-one-node
[3]: #gnu-parallel
[4]: #job-arrays-and-gnu-parallel
[3]: #hyperqueue
[5]: ##shared-jobscript
[6]: ../pbspro.md
[7]: #gnu-parallel-jobscript
[8]: #gnu-parallel-shared-jobscript
[9]: capacity.zip
[a]: https://github.com/It4innovations/hyperqueue
[b]: https://it4innovations.github.io/hyperqueue/install/