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Merge branch 'slurm-batch-system' into 'preview' 

Updated "Batch System Slurm" (slurm.md)

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# Batch System Slurm
ZIH uses the batch system Slurm for resource management and job scheduling. Compute nodes are not
accessed directly, but addressed through Slurm. You specify the needed resources
(cores, memory, GPU, time, ...) and Slurm will schedule your job for execution.
When logging in to ZIH systems, you are placed on a login node. There, you can manage your
[data life cycle](../data_lifecycle/overview.md),
setup experiments, and
edit and prepare jobs. The login nodes are not suited for computational work! From the login nodes,
you can interact with the batch system, e.g., submit and monitor your jobs.
A typical workflow would look like this:
```mermaid
sequenceDiagram
user ->>+ login node: run programm
login node ->> login node: kill after 5 min
login node ->>- user: Killed!
user ->> login node: salloc [...]
login node ->> Slurm: Request resources
Slurm ->> user: resources
user ->>+ allocated resources: srun [options] [command]
allocated resources ->> allocated resources: run command (on allocated nodes)
allocated resources ->>- user: program finished
user ->>+ allocated resources: srun [options] [further_command]
allocated resources ->> allocated resources: run further command
allocated resources ->>- user: program finished
user ->>+ allocated resources: srun [options] [further_command]
allocated resources ->> allocated resources: run further command
Slurm ->> allocated resources: Job limit reached/exceeded
allocated resources ->>- user: Job limit reached
```
??? note "Batch System"
The batch system is the central organ of every HPC system users interact with its compute
......@@ -36,6 +18,28 @@ sequenceDiagram
for your job, the batch system allocates and connects to these resources, transfers runtime
environment, and starts the job.
A workflow could look like this:
```mermaid
sequenceDiagram
user ->>+ login node: run programm
login node ->> login node: kill after 5 min
login node ->>- user: Killed!
user ->> login node: salloc [...]
login node ->> Slurm: Request resources
Slurm ->> user: resources
user ->>+ allocated resources: srun [options] [command]
allocated resources ->> allocated resources: run command (on allocated nodes)
allocated resources ->>- user: program finished
user ->>+ allocated resources: srun [options] [further_command]
allocated resources ->> allocated resources: run further command
allocated resources ->>- user: program finished
user ->>+ allocated resources: srun [options] [further_command]
allocated resources ->> allocated resources: run further command
Slurm ->> allocated resources: Job limit reached/exceeded
allocated resources ->>- user: Job limit reached
```
??? note "Batch Job"
At HPC systems, computational work and resource requirements are encapsulated into so-called
......@@ -50,10 +54,6 @@ sequenceDiagram
Moreover, the [runtime environment](../software/overview.md) as well as the executable and
certain command-line arguments have to be specified to run the computational work.
ZIH uses the batch system Slurm for resource management and job scheduling.
Just specify the resources you need in terms
of cores, memory, and time and your Slurm will place your job on the system.
This page provides a brief overview on
* [Slurm options](#options) to specify resource requirements,
......@@ -74,31 +74,40 @@ information:
There are three basic Slurm commands for job submission and execution:
1. `srun`: Submit a job for execution or initiate job steps in real time.
1. `srun`: Run a parallel application (and, if necessary, allocate resources first).
1. `sbatch`: Submit a batch script to Slurm for later execution.
1. `salloc`: Obtain a Slurm job allocation (a set of nodes), execute a command, and then release the
allocation when the command is finished.
1. `salloc`: Obtain a Slurm job allocation (i.e., resources like CPUs, nodes and GPUs) for
interactive use. Release the allocation when finished.
Using `srun` directly on the shell will be blocking and launch an
[interactive job](#interactive-jobs). Apart from short test runs, it is recommended to submit your
jobs to Slurm for later execution by using [batch jobs](#batch-jobs). For that, you can conveniently
put the parameters directly in a [job file](#job-files), which you can submit using `sbatch
put the parameters in a [job file](#job-files), which you can submit using `sbatch
[options] <job file>`.
At runtime, the environment variable `SLURM_JOB_ID` is set to the id of your job. The job
id is unique. The id allows you to [manage and control](#manage-and-control-jobs) your jobs.
After submission, your job gets a unique job ID, which is stored in the environment variable
`SLURM_JOB_ID` at job runtime. The command `sbatch` outputs the job ID to stderr. Furthermore, you
can find it via `squeue --me`. The job ID allows you to
[manage and control](#manage-and-control-jobs) your jobs.
!!! warning "srun vs. mpirun"
On ZIH systems, `srun` is used to run your parallel application. The use of `mpirun` is provenly
broken on partitions `ml` and `alpha` for jobs requiring more than one node. Especially when
using code from github projects, double-check it's configuration by looking for a line like
'submit command mpirun -n $ranks ./app' and replace it with 'srun ./app'.
## Options
The following table contains the most important options for `srun/sbatch/salloc` to specify resource
requirements and control communication.
The following table contains the most important options for `srun`, `sbatch`, `salloc` to specify
resource requirements and control communication.
??? tip "Options Table"
??? tip "Options Table (see `man sbatch`)"
| Slurm Option | Description |
|:---------------------------|:------------|
| `-n, --ntasks=<N>` | Number of (MPI) tasks (default: 1) |
| `-N, --nodes=<N>` | Number of nodes; there will be `--ntasks-per-node` processes started on each node |
| `-n, --ntasks=<N>` | Total number of (MPI) tasks (default: 1) |
| `-N, --nodes=<N>` | Number of compute nodes |
| `--ntasks-per-node=<N>` | Number of tasks per allocated node to start (default: 1) |
| `-c, --cpus-per-task=<N>` | Number of CPUs per task; needed for multithreaded (e.g. OpenMP) jobs; typically `N` should be equal to `OMP_NUM_THREADS` |
| `-p, --partition=<name>` | Type of nodes where you want to execute your job (refer to [partitions](partitions_and_limits.md)) |
......@@ -140,11 +149,11 @@ Interactive activities like editing, compiling, preparing experiments etc. are n
the login nodes. For longer interactive sessions, you can allocate cores on the compute node with
the command `salloc`. It takes the same options as `sbatch` to specify the required resources.
`salloc` returns a new shell on the node, where you submitted the job. You need to use the command
`salloc` returns a new shell on the node where you submitted the job. You need to use the command
`srun` in front of the following commands to have these commands executed on the allocated
resources. If you allocate more than one task, please be aware that `srun` will run the command on
each allocated task by default! To release the allocated resources, invoke the command `exit` or
`scancel <jobid`.
`scancel <jobid>`.
```console
marie@login$ salloc --nodes=2
......@@ -188,12 +197,14 @@ taurusi6604.taurus.hrsk.tu-dresden.de
The [module commands](../software/modules.md) are made available by sourcing the files
`/etc/profile` and `~/.bashrc`. This is done automatically by passing the parameter `-l` to your
shell, as shown in the example above. If you missed adding `-l` at submitting the interactive
session, no worry, you can source this files also later on manually.
session, no worry, you can source this files also later on manually (`source /etc/profile`).
!!! note "Partition `interactive`"
A dedicated partition `interactive` is reserved for short jobs (< 8h) with not more than one job
per user. Please check the availability of nodes there with `sinfo --partition=interactive`.
A dedicated partition `interactive` is reserved for short jobs (< 8h) with no more than one job
per user. An interactive partition is available for every regular partition, e.g.
`alpha-interactive` for `alpha`. Please check the availability of nodes there with
`sinfo |grep 'interactive\|AVAIL' |less`
### Interactive X11/GUI Jobs
......@@ -222,18 +233,18 @@ marie@login$ srun --ntasks=1 --cpus-per-task=8 --time=1:00:00 --pty --x11=first
## Batch Jobs
Working interactively using `srun` and `salloc` is a good starting point for testing and compiling.
But, as soon as you leave the testing stage, we highly recommend you to use batch jobs.
But, as soon as you leave the testing stage, we highly recommend to use batch jobs.
Batch jobs are encapsulated within [job files](#job-files) and submitted to the batch system using
`sbatch` for later execution. A job file is basically a script holding the resource requirements,
environment settings and the commands for executing the application. Using batch jobs and job files
has multiple advantages:
has multiple advantages*:
* You can reproduce your experiments and work, because all steps are saved in a file.
* You can easily share your settings and experimental setup with colleagues.
* You can submit your job file to the scheduling system for later execution. In the meanwhile, you can
grab a coffee and proceed with other work (e.g., start writing a paper).
!!! hint "The syntax for submitting a job file to Slurm is"
*) If job files are version controlled or environment `env` is saved along with Slurm output.
!!! hint "Syntax: Submitting a batch job"
```console
marie@login$ sbatch [options] <job_file>
......@@ -247,15 +258,15 @@ Job files have to be written with the following structure.
#!/bin/bash
# ^Batch script starts with shebang line
#SBATCH --ntasks=24 # All #SBATCH lines have to follow uninterrupted
#SBATCH --time=01:00:00 # after the shebang line
#SBATCH --account=<KTR> # Comments start with # and do not count as interruptions
#SBATCH --job-name=fancyExp
#SBATCH --output=simulation-%j.out
#SBATCH --error=simulation-%j.err
#SBATCH --ntasks=24 # #SBATCH lines request resources and
#SBATCH --time=01:00:00 # specify Slurm options
#SBATCH --account=<KTR> #
#SBATCH --job-name=fancyExp # All #SBATCH lines have to follow uninterrupted
#SBATCH --output=simulation-%j.out # after the shebang line
#SBATCH --error=simulation-%j.err # Comments start with # and do not count as interruptions
module purge # Set up environment, e.g., clean modules environment
module load <modules> # and load necessary modules
module purge # Set up environment, e.g., clean/switch modules environment
module load <module1 module2> # and load necessary modules
srun ./application [options] # Execute parallel application with srun
```
......@@ -361,9 +372,10 @@ On the command line, use `squeue` to watch the scheduling queue.
Invoke `squeue --me` to list only your jobs.
The command `squeue` will tell the reason, why a job is not running (job status in the last column
of the output). More information about job parameters can also be determined with `scontrol -d show
job <jobid>`. The following table holds detailed descriptions of the possible job states:
In it's last column, the `squeue` command will also tell why a job is not running.
Possible reasons and their detailed descriptions are listed in the following table.
More information about job parameters can be obtained with `scontrol -d show
job <jobid>`.
??? tip "Reason Table"
......@@ -384,8 +396,6 @@ job <jobid>`. The following table holds detailed descriptions of the possible jo
| `TimeLimit` | The job exhausted its time limit. |
| `InactiveLimit` | The job reached the system inactive limit. |
In addition, the `sinfo` command gives you a quick status overview.
For detailed information on why your submitted job has not started yet, you can use the command
```console
......@@ -394,7 +404,7 @@ marie@login$ whypending <jobid>
### Editing Jobs
Jobs that have not yet started can be altered. Using `scontrol update timelimit=4:00:00
Jobs that have not yet started can be altered. By using `scontrol update timelimit=4:00:00
jobid=<jobid>`, it is for example possible to modify the maximum runtime. `scontrol` understands
many different options, please take a look at the
[scontrol documentation](https://slurm.schedmd.com/scontrol.html) for more details.
......@@ -404,62 +414,70 @@ many different options, please take a look at the
The command `scancel <jobid>` kills a single job and removes it from the queue. By using `scancel -u
<username>`, you can send a canceling signal to all of your jobs at once.
### Accounting
### Evaluating Jobs
The Slurm command `sacct` provides job statistics like memory usage, CPU time, energy usage etc.
as table-formatted output on the command line.
The job monitor [PIKA](../software/pika.md) provides web-based graphical performance statistics
at no extra cost.
!!! hint "Learn from old jobs"
We highly encourage you to use `sacct` to learn from you previous jobs in order to better
We highly encourage you to inspect your previous jobs in order to better
estimate the requirements, e.g., runtime, for future jobs.
With PIKA, it is e.g. easy to check whether a job is hanging, idling,
or making good use of the resources.
`sacct` outputs the following fields by default.
??? tip "Using sacct (see also `man sacct`)"
`sacct` outputs the following fields by default.
```console
# show all own jobs contained in the accounting database
marie@login$ sacct
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
[...]
```
```console
# show all own jobs contained in the accounting database
marie@login$ sacct
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
[...]
```
We'd like to point your attention to the following options to gain insight in your jobs.
We'd like to point your attention to the following options to gain insight in your jobs.
??? example "Show specific job"
??? example "Show specific job"
```console
marie@login$ sacct --jobs=<JOBID>
```
```console
marie@login$ sacct --jobs=<JOBID>
```
??? example "Show all fields for a specific job"
??? example "Show all fields for a specific job"
```console
marie@login$ sacct --jobs=<JOBID> --format=All
```
```console
marie@login$ sacct --jobs=<JOBID> --format=All
```
??? example "Show specific fields"
??? example "Show specific fields"
```console
marie@login$ sacct --jobs=<JOBID> --format=JobName,MaxRSS,MaxVMSize,CPUTime,ConsumedEnergy
```
```console
marie@login$ sacct --jobs=<JOBID> --format=JobName,MaxRSS,MaxVMSize,CPUTime,ConsumedEnergy
```
The manual page (`man sacct`) and the [sacct online reference](https://slurm.schedmd.com/sacct.html)
provide a comprehensive documentation regarding available fields and formats.
The manual page (`man sacct`) and the [sacct online reference](https://slurm.schedmd.com/sacct.html)
provide a comprehensive documentation regarding available fields and formats.
!!! hint "Time span"
!!! hint "Time span"
By default, `sacct` only shows data of the last day. If you want to look further into the past
without specifying an explicit job id, you need to provide a start date via the option
`--starttime` (or short: `-S`). A certain end date is also possible via `--endtime` (or `-E`).
By default, `sacct` only shows data of the last day. If you want to look further into the past
without specifying an explicit job id, you need to provide a start date via the option
`--starttime` (or short: `-S`). A certain end date is also possible via `--endtime` (or `-E`).
??? example "Show all jobs since the beginning of year 2021"
??? example "Show all jobs since the beginning of year 2021"
```console
marie@login$ sacct -S 2021-01-01 [-E now]
```
```console
marie@login$ sacct -S 2021-01-01 [-E now]
```
## Jobs at Reservations
Within a reservation, you have privileged access to HPC resources.
How to ask for a reservation is described in the section
[reservations](overview.md#exclusive-reservation-of-hardware).
After we agreed with your requirements, we will send you an e-mail with your reservation name. Then,
......
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