---
title: Running Interactive Jobs
#tags:
keywords: interactive, X11, X, srun
last_updated: 23 January 2020
summary: "This document describes how to run interactive jobs as well as X based software."
sidebar: merlin6_sidebar
permalink: /merlin6/interactive-jobs.html
---

## Running interactive jobs

There are two different ways for running interactive jobs in Slurm. This is possible by using
the ``salloc`` and ``srun`` commands:

* **``salloc``**: to obtain a Slurm job allocation (a set of nodes), execute command(s), and then release the allocation when the command is finished.
* **``srun``**: is used for running parallel tasks.

### srun

Is run is used to run parallel jobs in the batch system. It can be used within a batch script
(which can be run with ``sbatch``), or within a job allocation (which can be run with ``salloc``).
Also, it can be used as a direct command (in example, from the login nodes).

When used inside a batch script or during a job allocation, ``srun`` is constricted to the 
amount of resources allocated by the ``sbatch``/``salloc`` commands. In ``sbatch``, usually 
these resources are defined inside the batch script with the format ``#SBATCH <option>=<value>``. 
In other words, if you define in your batch script or allocation 88 tasks (and 1 thread / core) 
and 2 nodes, ``srun`` is constricted to these amount of resources (you can use less, but never 
exceed those limits).

When used from the login node, usually is used to run a specific command or software in an 
interactive way. ``srun`` is a blocking process (it will block bash prompt until the ``srun`` 
command finishes, unless you run it in background with ``&``). This can be very useful to run 
interactive software which pops up a Window and then submits jobs or run sub-tasks in the 
background (in example, **Relion**, **cisTEM**, etc.)

Refer to ``man srun`` for exploring all possible options for that command.

<details>
<summary>[Show 'srun' example]: Running 'hostname' command on 3 nodes, using 2 cores (1 task/core) per node</summary>
<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
(base) [caubet_m@merlin-l-001 ~]$ srun --clusters=merlin6 --ntasks=6 --ntasks-per-node=2 --nodes=3 hostname
srun: job 135088230 queued and waiting for resources
srun: job 135088230 has been allocated resources
merlin-c-102.psi.ch
merlin-c-102.psi.ch
merlin-c-101.psi.ch
merlin-c-101.psi.ch
merlin-c-103.psi.ch
merlin-c-103.psi.ch
</pre>
</details>

### salloc

**``salloc``** is used to obtain a Slurm job allocation (a set of nodes). Once job is allocated,
users are able to execute interactive command(s). Once finished (``exit`` or ``Ctrl+D``), 
the allocation is released. **``salloc``** is a blocking command, it is, command will be blocked 
until the requested resources are allocated. 

When running **``salloc``**, once the resources are allocated, *by default* the user will get 
a ***new shell on one of the allocated resources*** (if a user has requested few nodes, it will 
prompt a new shell on the first allocated node). However, this behaviour can be changed by adding
a shell (`$SHELL`) at the end of the `salloc` command. In example:

```bash
# Typical 'salloc' call
#   - Same as running:
#    'salloc --clusters=merlin6 -N 2 -n 2 srun -n1 -N1 --mem-per-cpu=0 --gres=gpu:0 --pty --preserve-env --mpi=none $SHELL' 
salloc --clusters=merlin6 -N 2 -n 2

# Custom 'salloc' call
#   - $SHELL will open a local shell on the login node from where ``salloc`` is running
salloc --clusters=merlin6 -N 2 -n 2 $SHELL
```

<details>
<summary>[Show 'salloc' example]: Allocating 2 cores (1 task/core) in 2 nodes (1 core/node) - <i>Default</i></summary>
<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
(base) [caubet_m@merlin-l-001 ~]$ salloc --clusters=merlin6 --ntasks=2 --nodes=2
salloc: Pending job allocation 135171306
salloc: job 135171306 queued and waiting for resources
salloc: job 135171306 has been allocated resources
salloc: Granted job allocation 135171306

(base) [caubet_m@merlin-c-213 ~]$ srun hostname
merlin-c-213.psi.ch
merlin-c-214.psi.ch

(base) [caubet_m@merlin-c-213 ~]$ exit
exit
salloc: Relinquishing job allocation 135171306

(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
salloc: Pending job allocation 135171342
salloc: job 135171342 queued and waiting for resources
salloc: job 135171342 has been allocated resources
salloc: Granted job allocation 135171342

(base) [caubet_m@merlin-c-021 ~]$ srun hostname
merlin-c-021.psi.ch
merlin-c-022.psi.ch

(base) [caubet_m@merlin-c-021 ~]$ exit
exit
salloc: Relinquishing job allocation 135171342
</pre>
</details>

<details>
<summary>[Show 'salloc' example]: Allocating 2 cores (1 task/core) in 2 nodes (1 core/node) - <i>$SHELL</i></summary>
<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
(base) [caubet_m@merlin-export-01 ~]$ salloc --clusters=merlin6 --ntasks=2 --nodes=2 $SHELL
salloc: Pending job allocation 135171308
salloc: job 135171308 queued and waiting for resources
salloc: job 135171308 has been allocated resources
salloc: Granted job allocation 135171308

(base) [caubet_m@merlin-export-01 ~]$ srun hostname
merlin-c-218.psi.ch
merlin-c-117.psi.ch

(base) [caubet_m@merlin-export-01 ~]$ exit
exit
salloc: Relinquishing job allocation 135171308
</pre>
</details>

## Running interactive jobs with X11 support

### Requirements

#### Graphical access

[NoMachine](/merlin6/nomachine.html) is the official supported service for graphical 
access in the Merlin cluster. This service is running on the login nodes. Check the 
document [{Accessing Merlin -> NoMachine}](/merlin6/nomachine.html) for details about 
how to connect to the **NoMachine** service in the Merlin cluster.

For other non officially supported graphical access (X11 forwarding):

* For Linux clients, please follow [{How To Use Merlin -> Accessing from Linux Clients}](/merlin6/connect-from-linux.html)
* For Windows clients, please follow [{How To Use Merlin -> Accessing from Windows Clients}](/merlin6/connect-from-windows.html)
* For MacOS clients, please follow [{How To Use Merlin -> Accessing from MacOS Clients}](/merlin6/connect-from-macos.html)

### 'srun' with x11 support

Merlin5 and Merlin6 clusters allow running any windows based applications. For that, you need to 
add the option ``--x11`` to the ``srun`` command. In example:

```bash
srun --clusters=merlin6 --x11 xclock
```

will popup a X11 based clock.

In the same manner, you can create a bash shell with x11 support. For doing that, you need
to add the option ``--pty`` to the ``srun --x11`` command. Once resource is allocated, from
there you can interactively run X11 and non-X11 based commands.

```bash
srun --clusters=merlin6 --x11 --pty bash
```

<details>
<summary>[Show 'srun' with X11 support examples]</summary>
<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
(base) [caubet_m@merlin-l-001 ~]$ srun --clusters=merlin6 --x11 xclock
srun: job 135095591 queued and waiting for resources
srun: job 135095591 has been allocated resources

(base) [caubet_m@merlin-l-001 ~]$ 

(base) [caubet_m@merlin-l-001 ~]$ srun --clusters=merlin6 --x11 --pty bash
srun: job 135095592 queued and waiting for resources
srun: job 135095592 has been allocated resources

(base) [caubet_m@merlin-c-205 ~]$ xclock

(base) [caubet_m@merlin-c-205 ~]$ echo "This was an example"
This was an example

(base) [caubet_m@merlin-c-205 ~]$ exit
exit
</pre>
</details>

### 'salloc' with x11 support

**Merlin5** and **Merlin6** clusters allow running any windows based applications. For that, you need to 
add the option ``--x11`` to the ``salloc`` command. In example:

```bash
salloc --clusters=merlin6 --x11 xclock
```

will popup a X11 based clock.

In the same manner, you can create a bash shell with x11 support. For doing that, you need
to add to run just ``salloc --clusters=merlin6 --x11``. Once resource is allocated, from 
there you can interactively run X11 and non-X11 based commands.

```bash
salloc --clusters=merlin6 --x11
```

<details>
<summary>[Show 'salloc' with X11 support examples]</summary>
<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
(base) [caubet_m@merlin-l-001 ~]$ salloc --clusters=merlin6 --x11 xclock
salloc: Pending job allocation 135171355
salloc: job 135171355 queued and waiting for resources
salloc: job 135171355 has been allocated resources
salloc: Granted job allocation 135171355
salloc: Relinquishing job allocation 135171355

(base) [caubet_m@merlin-l-001 ~]$ salloc --clusters=merlin6 --x11 
salloc: Pending job allocation 135171349
salloc: job 135171349 queued and waiting for resources
salloc: job 135171349 has been allocated resources
salloc: Granted job allocation 135171349
salloc: Waiting for resource configuration
salloc: Nodes merlin-c-117 are ready for job

(base) [caubet_m@merlin-c-117 ~]$ xclock

(base) [caubet_m@merlin-c-117 ~]$ echo "This was an example"
This was an example

(base) [caubet_m@merlin-c-117 ~]$ exit
exit
salloc: Relinquishing job allocation 135171349
</pre>
</details>