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2026-01-06 16:40:15 +01:00
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docs/merlin7/03-Slurm-General-Documentation/interactive-jobs.md
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@@ -24,17 +24,17 @@ Is run is used to run parallel jobs in the batch system. It can be used within a
(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
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
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.
@@ -65,7 +65,7 @@ prompt a new shell on the first allocated node). However, this behaviour can be
a shell (`$SHELL`) at the end of the `salloc` command. In example:
```bash
# Typical 'salloc' call
# Typical 'salloc' call
salloc --clusters=merlin7 --partition=interactive -N 2 -n 2
# Custom 'salloc' call
@@ -111,20 +111,21 @@ salloc: Relinquishing job allocation 165
#### Graphical access
[NoMachine](../02-How-To-Use-Merlin/nomachine.md) 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}](../02-How-To-Use-Merlin/nomachine.md) for details about
[NoMachine](../02-How-To-Use-Merlin/nomachine.md) 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}](../02-How-To-Use-Merlin/nomachine.md) 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}](../02-How-To-Use-Merlin/connect-from-linux.md)
* For Windows clients, please follow [{How To Use Merlin -> Accessing from Windows Clients}](../02-How-To-Use-Merlin/connect-from-windows.md)
* For MacOS clients, please follow [{How To Use Merlin -> Accessing from MacOS Clients}](../02-How-To-Use-Merlin/connect-from-macos.md)
### 'srun' with x11 support
Merlin6 and merlin7 clusters allow running any windows based applications. For that, you need to
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
@@ -146,7 +147,7 @@ srun --clusters=merlin7 --partition=interactive --x11 --pty bash
<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
caubet_m@login001:~> srun --clusters=merlin7 --partition=interactive --x11 sview
caubet_m@login001:~>
caubet_m@login001:~>
caubet_m@login001:~> srun --clusters=merlin7 --partition=interactive --x11 --pty bash
@@ -162,7 +163,7 @@ exit
### 'salloc' with x11 support
**Merlin6** and **merlin7** clusters allow running any windows based applications. For that, you need to
**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
@@ -172,7 +173,7 @@ salloc --clusters=merlin7 --partition=interactive --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 to run just ``salloc --clusters=merlin7 --partition=interactive --x11``. Once resource is allocated, from
to add to run just ``salloc --clusters=merlin7 --partition=interactive --x11``. Once resource is allocated, from
there you can interactively run X11 and non-X11 based commands.
```bash
@@ -187,10 +188,10 @@ salloc: Granted job allocation 174
salloc: Nodes cn001 are ready for job
salloc: Relinquishing job allocation 174
caubet_m@login001:~> salloc --clusters=merlin7 --partition=interactive --x11
caubet_m@login001:~> salloc --clusters=merlin7 --partition=interactive --x11
salloc: Granted job allocation 175
salloc: Nodes cn001 are ready for job
caubet_m@cn001:~>
caubet_m@cn001:~>
caubet_m@cn001:~> sview