ADD: interactive-jobs.md

_data/sidebars/merlin7_sidebar.yml

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         folderitems:
           - title: Merlin7 Infrastructure
             url: /merlin7/slurm-configuration.html
+          - title: Running Slurm Interactive Jobs
+            url: /merlin7/interactive-jobs.html
           - title: Slurm Batch Script Examples
             url: /merlin7/slurm-examples.html
       - title: Software Support

pages/merlin7/03-Slurm-General-Documentation/interactive-jobs.md

@@ -0,0 +1,202 @@
+---
+title: Running Interactive Jobs
+#tags:
+keywords: interactive, X11, X, srun, salloc, job, jobs, slurm, nomachine, nx
+last_updated: 07 August 2024
+summary: "This document describes how to run interactive jobs as well as X based software."
+sidebar: merlin7_sidebar
+permalink: /merlin7/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">
+caubet_m@login001:~> srun --clusters=merlin7 --ntasks=6 --ntasks-per-node=2 --nodes=3 hostname
+cn001.merlin7.psi.ch
+cn001.merlin7.psi.ch
+cn002.merlin7.psi.ch
+cn002.merlin7.psi.ch
+cn003.merlin7.psi.ch
+cn003.merlin7.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 
+salloc --clusters=merlin7 -N 2 -n 2
+
+# Custom 'salloc' call
+#   - $SHELL will open a local shell on the login node from where ``salloc`` is running
+salloc --clusters=merlin7 -N 2 -n 2 $SHELL
+```
+
+<details>
+<summary>[Show 'salloc' example]: Allocating 2 cores (1 task/core) in 2 nodes (1 core/node) - <i>Default</i></summary>
+<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
+caubet_m@login001:~> salloc --clusters=merlin7 -N 2 -n 2
+salloc: Granted job allocation 161
+salloc: Nodes cn[001-002] are ready for job
+
+caubet_m@login001:~> srun hostname
+cn002.merlin7.psi.ch
+cn001.merlin7.psi.ch
+
+caubet_m@login001:~> exit
+exit
+salloc: Relinquishing job allocation 161
+</pre>
+</details>
+
+<details>
+<summary>[Show 'salloc' example]: Allocating 2 cores (1 task/core) in 2 nodes (1 core/node) - <i>$SHELL</i></summary>
+<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
+caubet_m@login001:~> salloc --clusters=merlin7 --ntasks=2 --nodes=2 $SHELL
+salloc: Granted job allocation 165
+salloc: Nodes cn[001-002] are ready for job
+caubet_m@login001:~> srun hostname
+cn001.merlin7.psi.ch
+cn002.merlin7.psi.ch
+caubet_m@login001:~> exit
+exit
+salloc: Relinquishing job allocation 165
+</pre>
+</details>
+
+## Running interactive jobs with X11 support
+
+### Requirements
+
+#### Graphical access
+
+[NoMachine](/merlin7/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}](/merlin7/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}](/merlin7/connect-from-linux.html)
+* For Windows clients, please follow [{How To Use Merlin -> Accessing from Windows Clients}](/merlin7/connect-from-windows.html)
+* For MacOS clients, please follow [{How To Use Merlin -> Accessing from MacOS Clients}](/merlin7/connect-from-macos.html)
+
+### 'srun' with x11 support
+
+Merlin6 and merlin7 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=merlin7 --x11 sview
+```
+
+will popup a X11 based slurm view of the cluster.
+
+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=merlin7 --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">
+caubet_m@login001:~> srun --clusters=merlin7 --x11 sview
+
+caubet_m@login001:~> 
+
+caubet_m@login001:~> srun --clusters=merlin7 --x11 --pty bash
+
+caubet_m@cn003:~> sview
+
+caubet_m@cn003:~> echo "This was an example"
+This was an example
+
+caubet_m@cn003:~> exit
+exit
+</pre>
+</details>
+
+### 'salloc' with x11 support
+
+**Merlin6** and **merlin7** 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=merlin7 --x11 sview
+```
+
+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=merlin7 --x11``. Once resource is allocated, from 
+there you can interactively run X11 and non-X11 based commands.
+
+```bash
+salloc --clusters=merlin7 --x11
+```
+
+<details>
+<summary>[Show 'salloc' with X11 support examples]</summary>
+<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
+caubet_m@login001:~> salloc --clusters=merlin7 --x11 sview
+salloc: Granted job allocation 174
+salloc: Nodes cn001 are ready for job
+salloc: Relinquishing job allocation 174
+
+caubet_m@login001:~> salloc --clusters=merlin7 --x11 
+salloc: Granted job allocation 175
+salloc: Nodes cn001 are ready for job
+caubet_m@cn001:~> 
+
+caubet_m@cn001:~> sview
+
+caubet_m@cn001:~> echo "This was an example"
+This was an example
+
+caubet_m@cn001:~> exit
+exit
+salloc: Relinquishing job allocation 175
+</pre>
+</details>