Hans-Nikolai Viessmann
bde174b726
refactor CSCS and Meg content add merlin6 quick start update merlin6 nomachine docs give the userdoc its own color scheme we use the Materials default one refactored slurm general docs merlin6 add merlin6 JB docs add software support m6 docs add all files to nav vibed changes #1 add missing pages further vibing #2 vibe #3 further fixes
205 lines
8.4 KiB
Markdown
205 lines
8.4 KiB
Markdown
# Running Interactive Jobs
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### The Merlin7 'interactive' partition
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On the **`merlin7`** cluster, it is recommended to always run interactive jobs on the **`interactive`** partition.
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This partition allows CPU oversubscription (up to four users may share the same CPU) and **has the highest scheduling priority**. Access to this partition is typically quick, making it a convenient extension of the login nodes for interactive workloads.
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On the **`gmerlin7`** cluster, additional interactive partitions are available, but these are primarily intended for CPU-only workloads (such like compiling GPU-based software, or creating an allocation for submitting jobs to Grace-Hopper nodes).
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!!! warning
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Because **GPU resources are scarce and expensive**, interactive allocations on GPU nodes that use GPUs should only be submitted when strictly necessary and well justified.
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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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<details>
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<summary>[Show 'srun' example]: Running 'hostname' command on 3 nodes, using 2 cores (1 task/core) per node</summary>
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<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
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caubet_m@login001:~> srun --clusters=merlin7 --partition=interactive --ntasks=6 --ntasks-per-node=2 --nodes=3 hostname
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cn001.merlin7.psi.ch
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cn001.merlin7.psi.ch
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cn002.merlin7.psi.ch
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cn002.merlin7.psi.ch
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cn003.merlin7.psi.ch
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cn003.merlin7.psi.ch
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</pre>
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</details>
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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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salloc --clusters=merlin7 --partition=interactive -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=merlin7 --partition=interactive -N 2 -n 2 $SHELL
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```
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<details>
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<summary>[Show 'salloc' example]: Allocating 2 cores (1 task/core) in 2 nodes (1 core/node) - <i>Default</i></summary>
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<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
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caubet_m@login001:~> salloc --clusters=merlin7 --partition=interactive -N 2 -n 2
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salloc: Granted job allocation 161
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salloc: Nodes cn[001-002] are ready for job
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caubet_m@login001:~> srun hostname
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cn002.merlin7.psi.ch
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cn001.merlin7.psi.ch
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caubet_m@login001:~> exit
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exit
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salloc: Relinquishing job allocation 161
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</pre>
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</details>
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<details>
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<summary>[Show 'salloc' example]: Allocating 2 cores (1 task/core) in 2 nodes (1 core/node) - <i>$SHELL</i></summary>
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<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
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caubet_m@login001:~> salloc --clusters=merlin7 --partition=interactive --ntasks=2 --nodes=2 $SHELL
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salloc: Granted job allocation 165
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salloc: Nodes cn[001-002] are ready for job
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caubet_m@login001:~> srun hostname
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cn001.merlin7.psi.ch
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cn002.merlin7.psi.ch
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caubet_m@login001:~> exit
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exit
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salloc: Relinquishing job allocation 165
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</pre>
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</details>
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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](../02-How-To-Use-Merlin/nomachine.md) 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}](../02-How-To-Use-Merlin/nomachine.md) 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}](../02-How-To-Use-Merlin/connect-from-linux.md)
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* For Windows clients, please follow [{How To Use Merlin -> Accessing from Windows Clients}](../02-How-To-Use-Merlin/connect-from-windows.md)
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* For MacOS clients, please follow [{How To Use Merlin -> Accessing from MacOS Clients}](../02-How-To-Use-Merlin/connect-from-macos.md)
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### 'srun' with x11 support
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Merlin6 and merlin7 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=merlin7 --partition=interactive --x11 sview
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```
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will popup a X11 based slurm view of the cluster.
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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=merlin7 --partition=interactive --x11 --pty bash
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```
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<details>
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<summary>[Show 'srun' with X11 support examples]</summary>
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<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
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caubet_m@login001:~> srun --clusters=merlin7 --partition=interactive --x11 sview
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caubet_m@login001:~>
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caubet_m@login001:~> srun --clusters=merlin7 --partition=interactive --x11 --pty bash
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caubet_m@cn003:~> sview
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caubet_m@cn003:~> echo "This was an example"
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This was an example
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caubet_m@cn003:~> exit
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exit
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</pre>
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</details>
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### 'salloc' with x11 support
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**Merlin6** and **merlin7** 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=merlin7 --partition=interactive --x11 sview
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```
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will popup a X11 based slurm view of the cluster.
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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=merlin7 --partition=interactive --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=merlin7 --partition=interactive --x11
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```
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<details>
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<summary>[Show 'salloc' with X11 support examples]</summary>
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<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
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caubet_m@login001:~> salloc --clusters=merlin7 --partition=interactive --x11 sview
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salloc: Granted job allocation 174
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salloc: Nodes cn001 are ready for job
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salloc: Relinquishing job allocation 174
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caubet_m@login001:~> salloc --clusters=merlin7 --partition=interactive --x11
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salloc: Granted job allocation 175
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salloc: Nodes cn001 are ready for job
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caubet_m@cn001:~>
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caubet_m@cn001:~> sview
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caubet_m@cn001:~> echo "This was an example"
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This was an example
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caubet_m@cn001:~> exit
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exit
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salloc: Relinquishing job allocation 175
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</pre>
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</details>
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