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vibed changes #1

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viessm_h
2025-12-11 10:32:15 +01:00
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10
docs/merlin6/slurm-general-docs/interactive-jobs.md
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@@ -119,16 +119,16 @@ salloc --clusters=merlin6 -N 2 -n 2 $SHELL
#### Graphical access
[NoMachine](/merlin6/nomachine.html) is the official supported service for graphical
[NoMachine](../../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}](/merlin6/nomachine.html) for details about
document [{Accessing Merlin -> NoMachine}](../../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}](/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)
* For Linux clients, please follow [{How To Use Merlin -> Accessing from Linux Clients}](../../how-to-use-merlin/connect-from-linux.md)
* For Windows clients, please follow [{How To Use Merlin -> Accessing from Windows Clients}](../../how-to-use-merlin/connect-from-windows.md)
* For MacOS clients, please follow [{How To Use Merlin -> Accessing from MacOS Clients}](../../how-to-use-merlin/connect-from-macos.md)
### 'srun' with x11 support

16
docs/merlin6/slurm-general-docs/running-jobs.md
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@@ -6,18 +6,18 @@ Before starting using the cluster, please read the following rules:
1. To ease and improve *scheduling* and *backfilling*, always try to **estimate and** to **define a proper run time** of your jobs:
* Use `--time=<D-HH:MM:SS>` for that.
* For very long runs, please consider using ***[Job Arrays with Checkpointing](/merlin6/running-jobs.html#array-jobs-running-very-long-tasks-with-checkpoint-files)***
* For very long runs, please consider using ***[Job Arrays with Checkpointing](#array-jobs-running-very-long-tasks-with-checkpoint-files)***
2. Try to optimize your jobs for running at most within **one day**. Please, consider the following:
* Some software can simply scale up by using more nodes while drastically reducing the run time.
* Some software allow to save a specific state, and a second job can start from that state: ***[Job Arrays with Checkpointing](/merlin6/running-jobs.html#array-jobs-running-very-long-tasks-with-checkpoint-files)*** can help you with that.
* Some software allow to save a specific state, and a second job can start from that state: ***[Job Arrays with Checkpointing](#array-jobs-running-very-long-tasks-with-checkpoint-files)*** can help you with that.
* Jobs submitted to **`hourly`** get more priority than jobs submitted to **`daily`**: always use **`hourly`** for jobs shorter than 1 hour.
* Jobs submitted to **`daily`** get more priority than jobs submitted to **`general`**: always use **`daily`** for jobs shorter than 1 day.
3. Is **forbidden** to run **very short jobs** as they cause a lot of overhead but also can cause severe problems to the main scheduler.
* ***Question:*** Is my job a very short job? ***Answer:*** If it lasts in few seconds or very few minutes, yes.
* ***Question:*** How long should my job run? ***Answer:*** as the *Rule of Thumb*, from 5' would start being ok, from 15' would preferred.
* Use ***[Packed Jobs](/merlin6/running-jobs.html#packed-jobs-running-a-large-number-of-short-tasks)*** for running a large number of short tasks.
* Use ***[Packed Jobs](#packed-jobs-running-a-large-number-of-short-tasks)*** for running a large number of short tasks.
4. Do not submit hundreds of similar jobs!
* Use ***[Array Jobs](/merlin6/running-jobs.html#array-jobs-launching-a-large-number-of-related-jobs)*** for gathering jobs instead.
* Use ***[Array Jobs](#array-jobs-launching-a-large-number-of-related-jobs)*** for gathering jobs instead.
!!! tip
Having a good estimation of the *time* needed by your jobs, a proper way for
@@ -51,7 +51,7 @@ The following settings are the minimum required for running a job in the Merlin
#SBATCH --clusters=<cluster_name> # Possible values: merlin5, merlin6, gmerlin6
```
Refer to the documentation of each cluster ([**`merlin6`**](/merlin6/slurm-configuration.html),[**`gmerlin6`**](/gmerlin6/slurm-configuration.html),[**`merlin5`**](/merlin5/slurm-configuration.html) for further information.
Refer to the documentation of each cluster ([**`merlin6`**](../slurm-configuration.md),[**`gmerlin6`**](../../gmerlin6/slurm-configuration.md),[**`merlin5`**](../../merlin5/slurm-configuration.md) for further information.
* **Partitions:** except when using the *default* partition for each cluster, one needs to specify the partition:
@@ -59,7 +59,7 @@ The following settings are the minimum required for running a job in the Merlin
#SBATCH --partition=<partition_name> # Check each cluster documentation for possible values
```
Refer to the documentation of each cluster ([**`merlin6`**](/merlin6/slurm-configuration.html),[**`gmerlin6`**](/gmerlin6/slurm-configuration.html),[**`merlin5`**](/merlin5/slurm-configuration.html) for further information.
Refer to the documentation of each cluster ([**`merlin6`**](../slurm-configuration.md),[**`gmerlin6`**](../../gmerlin6/slurm-configuration.md),[**`merlin5`**](../../merlin5/slurm-configuration.md) for further information.
* **[Optional] Disabling shared nodes**: by default, nodes are not exclusive. Hence, multiple users can run in the same node. One can request exclusive node usage with the following option:
@@ -73,7 +73,7 @@ The following settings are the minimum required for running a job in the Merlin
#SBATCH --time=<D-HH:MM:SS> # Can not exceed the partition `MaxTime`
```
Refer to the documentation of each cluster ([**`merlin6`**](/merlin6/slurm-configuration.html),[**`gmerlin6`**](/gmerlin6/slurm-configuration.html),[**`merlin5`**](/merlin5/slurm-configuration.html) for further information about partition `MaxTime` values.
Refer to the documentation of each cluster ([**`merlin6`**](../slurm-configuration.md),[**`gmerlin6`**](../../gmerlin6/slurm-configuration.md),[**`merlin5`**](../../merlin5/slurm-configuration.md) for further information about partition `MaxTime` values.
* **Output and error files**: by default, Slurm script will generate standard output (`slurm-%j.out`, where `%j` is the job_id) and error (`slurm-%j.err`, where `%j` is the job_id) files in the directory from where the job was submitted. Users can change default name with the following options:
@@ -91,7 +91,7 @@ The following settings are the minimum required for running a job in the Merlin
#SBATCH --hint=nomultithread # Don't use extra threads with in-core multi-threading.
```
Refer to the documentation of each cluster ([**`merlin6`**](/merlin6/slurm-configuration.html),[**`gmerlin6`**](/gmerlin6/slurm-configuration.html),[**`merlin5`**](/merlin5/slurm-configuration.html) for further information about node configuration and Hyper-Threading.
Refer to the documentation of each cluster ([**`merlin6`**](../slurm-configuration.md),[**`gmerlin6`**](../../gmerlin6/slurm-configuration.md),[**`merlin5`**](../../merlin5/slurm-configuration.md) for further information about node configuration and Hyper-Threading.
Consider that, sometimes, depending on your job requirements, you might need also to setup how many `--ntasks-per-core` or `--cpus-per-task` (even other options) in addition to the `--hint` command. Please, contact us in case of doubts.
!!! tip