218 lines
8.4 KiB
Markdown
218 lines
8.4 KiB
Markdown
# Running Interactive Jobs
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## Running interactive jobs
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There are two different ways for running interactive jobs in Slurm. This is possible by using
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the `salloc` and `srun` commands:
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* **`salloc`**: to obtain a Slurm job allocation (a set of nodes), execute command(s), and then release the allocation when the command is finished.
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* **`srun`**: is used for running parallel tasks.
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### srun
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Is run is used to run parallel jobs in the batch system. It can be used within a batch script
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(which can be run with `sbatch`), or within a job allocation (which can be run with `salloc`).
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Also, it can be used as a direct command (in example, from the login nodes).
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When used inside a batch script or during a job allocation, `srun` is constricted to the
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amount of resources allocated by the `sbatch`/`salloc` commands. In `sbatch`, usually
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these resources are defined inside the batch script with the format `#SBATCH <option>=<value>`.
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In other words, if you define in your batch script or allocation 88 tasks (and 1 thread / core)
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and 2 nodes, `srun` is constricted to these amount of resources (you can use less, but never
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exceed those limits).
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When used from the login node, usually is used to run a specific command or software in an
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interactive way. `srun` is a blocking process (it will block bash prompt until the `srun`
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command finishes, unless you run it in background with `&`). This can be very useful to run
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interactive software which pops up a Window and then submits jobs or run sub-tasks in the
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background (in example, **Relion**, **cisTEM**, etc.)
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Refer to `man srun` for exploring all possible options for that command.
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??? note "Running 'hostname' command on 3 nodes, using 2 cores (1 task/core) per node"
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```console
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(base) [caubet_m@merlin-l-001 ~]$ srun --clusters=merlin6 --ntasks=6 --ntasks-per-node=2 --nodes=3 hostname
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srun: job 135088230 queued and waiting for resources
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srun: job 135088230 has been allocated resources
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merlin-c-102.psi.ch
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merlin-c-102.psi.ch
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merlin-c-101.psi.ch
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merlin-c-101.psi.ch
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merlin-c-103.psi.ch
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merlin-c-103.psi.ch
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```
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### salloc
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**`salloc`** is used to obtain a Slurm job allocation (a set of nodes). Once job is allocated,
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users are able to execute interactive command(s). Once finished (`exit` or `Ctrl+D`),
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the allocation is released. **`salloc`** is a blocking command, it is, command will be blocked
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until the requested resources are allocated.
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When running **`salloc`**, once the resources are allocated, *by default* the user will get
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a ***new shell on one of the allocated resources*** (if a user has requested few nodes, it will
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prompt a new shell on the first allocated node). However, this behaviour can be changed by adding
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a shell (`$SHELL`) at the end of the `salloc` command. In example:
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```bash
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# Typical 'salloc' call
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# - Same as running:
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# 'salloc --clusters=merlin6 -N 2 -n 2 srun -n1 -N1 --mem-per-cpu=0 --gres=gpu:0 --pty --preserve-env --mpi=none $SHELL'
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salloc --clusters=merlin6 -N 2 -n 2
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# Custom 'salloc' call
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# - $SHELL will open a local shell on the login node from where ``salloc`` is running
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salloc --clusters=merlin6 -N 2 -n 2 $SHELL
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```
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??? note "Allocating 2 cores (1 task/core) in 2 nodes (1 core/node) - *default*"
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```console
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(base) [caubet_m@merlin-l-001 ~]$ salloc --clusters=merlin6 --ntasks=2 --nodes=2
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salloc: Pending job allocation 135171306
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salloc: job 135171306 queued and waiting for resources
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salloc: job 135171306 has been allocated resources
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salloc: Granted job allocation 135171306
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(base) [caubet_m@merlin-c-213 ~]$ srun hostname
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merlin-c-213.psi.ch
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merlin-c-214.psi.ch
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(base) [caubet_m@merlin-c-213 ~]$ exit
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exit
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salloc: Relinquishing job allocation 135171306
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(base) [caubet_m@merlin-l-001 ~]$ salloc --clusters=merlin6 -N 2 -n 2 srun -n1 -N1 --mem-per-cpu=0 --gres=gpu:0 --pty --preserve-env --mpi=none $SHELL
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salloc: Pending job allocation 135171342
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salloc: job 135171342 queued and waiting for resources
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salloc: job 135171342 has been allocated resources
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salloc: Granted job allocation 135171342
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(base) [caubet_m@merlin-c-021 ~]$ srun hostname
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merlin-c-021.psi.ch
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merlin-c-022.psi.ch
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(base) [caubet_m@merlin-c-021 ~]$ exit
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exit
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salloc: Relinquishing job allocation 135171342
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```
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??? note "Allocating 2 cores (1 task/core) in 2 nodes (1 core/node) - `$SHELL`"
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```console
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(base) [caubet_m@merlin-export-01 ~]$ salloc --clusters=merlin6 --ntasks=2 --nodes=2 $SHELL
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salloc: Pending job allocation 135171308
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salloc: job 135171308 queued and waiting for resources
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salloc: job 135171308 has been allocated resources
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salloc: Granted job allocation 135171308
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(base) [caubet_m@merlin-export-01 ~]$ srun hostname
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merlin-c-218.psi.ch
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merlin-c-117.psi.ch
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(base) [caubet_m@merlin-export-01 ~]$ exit
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exit
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salloc: Relinquishing job allocation 135171308
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```
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## Running interactive jobs with X11 support
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### Requirements
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#### Graphical access
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[NoMachine](/merlin6/nomachine.html) is the official supported service for graphical
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access in the Merlin cluster. This service is running on the login nodes. Check the
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document [{Accessing Merlin -> NoMachine}](/merlin6/nomachine.html) for details about
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how to connect to the **NoMachine** service in the Merlin cluster.
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For other non officially supported graphical access (X11 forwarding):
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* For Linux clients, please follow [{How To Use Merlin -> Accessing from Linux Clients}](/merlin6/connect-from-linux.html)
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* For Windows clients, please follow [{How To Use Merlin -> Accessing from Windows Clients}](/merlin6/connect-from-windows.html)
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* For MacOS clients, please follow [{How To Use Merlin -> Accessing from MacOS Clients}](/merlin6/connect-from-macos.html)
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### 'srun' with x11 support
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Merlin5 and Merlin6 clusters allow running any windows based applications. For that, you need to
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add the option ``--x11`` to the ``srun`` command. In example:
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```bash
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srun --clusters=merlin6 --x11 xclock
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```
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will popup a X11 based clock.
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In the same manner, you can create a bash shell with x11 support. For doing that, you need
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to add the option ``--pty`` to the ``srun --x11`` command. Once resource is allocated, from
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there you can interactively run X11 and non-X11 based commands.
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```bash
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srun --clusters=merlin6 --x11 --pty bash
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```
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??? note "Using 'srun' with X11 support"
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```console
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(base) [caubet_m@merlin-l-001 ~]$ srun --clusters=merlin6 --x11 xclock
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srun: job 135095591 queued and waiting for resources
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srun: job 135095591 has been allocated resources
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(base) [caubet_m@merlin-l-001 ~]$
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(base) [caubet_m@merlin-l-001 ~]$ srun --clusters=merlin6 --x11 --pty bash
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srun: job 135095592 queued and waiting for resources
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srun: job 135095592 has been allocated resources
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(base) [caubet_m@merlin-c-205 ~]$ xclock
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(base) [caubet_m@merlin-c-205 ~]$ echo "This was an example"
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This was an example
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(base) [caubet_m@merlin-c-205 ~]$ exit
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exit
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```
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### 'salloc' with x11 support
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**Merlin5** and **Merlin6** clusters allow running any windows based applications. For that, you need to
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add the option ``--x11`` to the ``salloc`` command. In example:
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```bash
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salloc --clusters=merlin6 --x11 xclock
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```
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will popup a X11 based clock.
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In the same manner, you can create a bash shell with x11 support. For doing that, you need
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to add to run just ``salloc --clusters=merlin6 --x11``. Once resource is allocated, from
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there you can interactively run X11 and non-X11 based commands.
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```bash
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salloc --clusters=merlin6 --x11
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```
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??? note "Using 'salloc' with X11 support examples"
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```console
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(base) [caubet_m@merlin-l-001 ~]$ salloc --clusters=merlin6 --x11 xclock
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salloc: Pending job allocation 135171355
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salloc: job 135171355 queued and waiting for resources
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salloc: job 135171355 has been allocated resources
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salloc: Granted job allocation 135171355
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salloc: Relinquishing job allocation 135171355
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(base) [caubet_m@merlin-l-001 ~]$ salloc --clusters=merlin6 --x11
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salloc: Pending job allocation 135171349
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salloc: job 135171349 queued and waiting for resources
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salloc: job 135171349 has been allocated resources
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salloc: Granted job allocation 135171349
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salloc: Waiting for resource configuration
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salloc: Nodes merlin-c-117 are ready for job
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(base) [caubet_m@merlin-c-117 ~]$ xclock
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(base) [caubet_m@merlin-c-117 ~]$ echo "This was an example"
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This was an example
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(base) [caubet_m@merlin-c-117 ~]$ exit
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exit
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salloc: Relinquishing job allocation 135171349
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```
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