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213 lines
8.4 KiB
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---
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title: Running Interactive Jobs
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#tags:
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keywords: interactive, X11, X, srun, salloc, job, jobs, slurm, nomachine, nx
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last_updated: 07 August 2024
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summary: "This document describes how to run interactive jobs as well as X based software."
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sidebar: merlin7_sidebar
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permalink: /merlin7/interactive-jobs.html
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---
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### The Merlin7 'interactive' partition
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On `merlin7`, is recommended to always run interactive jobs on the `interactive` partition. This partition oversubscribe
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CPUs (up to 4 users can use the same CPU), and has the highest priority. In general, access to this
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partition should be quick, and can be used as an extension of the login nodes.
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Other interactive partitions are available on the `gmerlin7` cluster, however, the main user is for CPU access only.
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Since the GPU resources are very expensive and we don't have many, please do not submit interactive allocations on GPU
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nodes using GPUs unless strongly 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](/merlin7/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}](/merlin7/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}](/merlin7/connect-from-linux.html)
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* For Windows clients, please follow [{How To Use Merlin -> Accessing from Windows Clients}](/merlin7/connect-from-windows.html)
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* For MacOS clients, please follow [{How To Use Merlin -> Accessing from MacOS Clients}](/merlin7/connect-from-macos.html)
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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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