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further fixes

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viessm_h
2025-12-16 11:21:18 +01:00
parent 5cbc746528
commit 1d21fc390f
12 changed files with 25 additions and 35 deletions
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2
docs/merlin6/99-support/known-problems.md
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@@ -157,7 +157,7 @@ fluent -driver x11
### Paraview ### Paraview
For running Paraview, one can run it with Mesa support or OpenGL support. Please refer to [OpenGL vs Mesa](/merlin6/known-problems.html#opengl-vs-mesa) for For running Paraview, one can run it with Mesa support or OpenGL support. Please refer to [OpenGL vs Mesa](#3d-acceleration-opengl-vs-mesa) for
further information about how to run it. further information about how to run it.
### Module command not found ### Module command not found

2
docs/merlin6/how-to-use-merlin/archive.md
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@@ -97,7 +97,7 @@ As of 2022-04-14 a secure token is required to interact with the data catalog. T
1. You should be redirected to your user settings and see a 'User Information' section. If not, click on1. your username in the top right and choose 'Settings' from the menu. 1. You should be redirected to your user settings and see a 'User Information' section. If not, click on1. your username in the top right and choose 'Settings' from the menu.
1. Look for the field 'Catamel Token'. This should be a 64-character string. Click the icon to copy the1. token. 1. Look for the field 'Catamel Token'. This should be a 64-character string. Click the icon to copy the1. token.
![SciCat website](/images/scicat_token.png) ![SciCat website](../../images/scicat_token.png)
You will need to save this token for later steps. To avoid including it in all the commands, I suggest saving it to an environmental variable (Linux): You will need to save this token for later steps. To avoid including it in all the commands, I suggest saving it to an environmental variable (Linux):

4
docs/merlin6/how-to-use-merlin/kerberos.md
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@@ -50,7 +50,7 @@ klist
krenew krenew
``` ```
* Keep in mind that the maximum lifetime for granting tickets is 7 days, therefore `krenew` can not be used beyond that limit, * Keep in mind that the maximum lifetime for granting tickets is 7 days, therefore `krenew` can not be used beyond that limit,
and then `kinit** should be used instead. and then `kinit` should be used instead.
## Obtanining granting tickets with keytab ## Obtanining granting tickets with keytab
@@ -101,7 +101,7 @@ aklog
## Slurm jobs accessing AFS ## Slurm jobs accessing AFS
Some jobs may require to access private areas in AFS. For that, having a valid [**keytab**](#generating-granting-tickets-with-keytab) file is required. Some jobs may require to access private areas in AFS. For that, having a valid [**keytab**](#obtaining-granting-tickets-with-username-and-password) file is required.
Then, from inside the batch script one can obtain granting tickets for Kerberos and AFS, which can be used for accessing AFS private areas. Then, from inside the batch script one can obtain granting tickets for Kerberos and AFS, which can be used for accessing AFS private areas.
The steps should be the following: The steps should be the following:

8
docs/merlin6/how-to-use-merlin/nomachine.md
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@@ -45,7 +45,7 @@ the following fields:
* **Protocol**: specify the protocol that will be used for the connection. *Recommended* protocol: **`NX`** * **Protocol**: specify the protocol that will be used for the connection. *Recommended* protocol: **`NX`**
* **Port**: Specify the listening port of the **front-end**. It must be **`4000`**. * **Port**: Specify the listening port of the **front-end**. It must be **`4000`**.
![Create New NoMachine Connection](/images/nomachine/screen_nx_connect.png) ![Create New NoMachine Connection](../../images/nomachine/screen_nx_connect.png)
#### Configuring NoMachine Authentication Method #### Configuring NoMachine Authentication Method
@@ -62,19 +62,19 @@ session if none exists.
If there are existing sessions, instead of opening a new desktop session, users can reconnect to an If there are existing sessions, instead of opening a new desktop session, users can reconnect to an
existing one by clicking to the proper icon (see image below). existing one by clicking to the proper icon (see image below).
![Open an existing Session](/images/nomachine/screen_nx_existingsession.png) ![Open an existing Session](../../images/nomachine/screen_nx_existingsession.png)
Users can also create a second desktop session by selecting the **`New Desktop`** button (*red* rectangle in the Users can also create a second desktop session by selecting the **`New Desktop`** button (*red* rectangle in the
below image). This will create a second session on the second login node, as long as this node is up and running. below image). This will create a second session on the second login node, as long as this node is up and running.
![Open a New Desktop](/images/nomachine/screen_nx_newsession.png) ![Open a New Desktop](../../images/nomachine/screen_nx_newsession.png)
### NoMachine LightDM Session Example ### NoMachine LightDM Session Example
An example of the NoMachine session, which is based on [LightDM](https://github.com/canonical/lightdm) An example of the NoMachine session, which is based on [LightDM](https://github.com/canonical/lightdm)
X Windows: X Windows:
![NoMachine Session: LightDM Desktop](/images/nomachine/screen_nx11.png) ![NoMachine Session: LightDM Desktop](../../images/nomachine/screen_nx11.png)
## Accessing Merlin6 NoMachine from outside PSI ## Accessing Merlin6 NoMachine from outside PSI

2
docs/merlin6/jupyterhub/jupyterhub.md
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@@ -52,7 +52,7 @@ When the `anaconda` module has been loaded, you can list the available environme
conda info -e conda info -e
``` ```
You can get more info on the use of the `conda` package management tool at its official [https://conda.io/projects/conda/en/latest/commands.html](documentation site). You can get more info on the use of the `conda` package management tool at its official [documentation site](https://conda.io/projects/conda/en/latest/commands.html).
## Using your own custom made environments with jupyterhub ## Using your own custom made environments with jupyterhub

4
docs/merlin6/quick-start-guide/requesting-accounts.md
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@@ -6,7 +6,7 @@ Access to Merlin6 is regulated by a PSI user's account being a member of the **`
Requesting **Merlin6** access *has to be done* with the corresponding **[Request Linux Group Membership](https://psi.service-now.com/psisp?id=psi_new_sc_cat_item&sys_id=84f2c0c81b04f110679febd9bb4bcbb1)** form, available in the [PSI Service Now Service Catalog](https://psi.service-now.com/psisp). Requesting **Merlin6** access *has to be done* with the corresponding **[Request Linux Group Membership](https://psi.service-now.com/psisp?id=psi_new_sc_cat_item&sys_id=84f2c0c81b04f110679febd9bb4bcbb1)** form, available in the [PSI Service Now Service Catalog](https://psi.service-now.com/psisp).
![Example: Requesting access to Merlin6](/images/Access/01-request-merlin6-membership.png) ![Example: Requesting access to Merlin6](../../images/Access/01-request-merlin6-membership.png)
Mandatory customizable fields are the following: Mandatory customizable fields are the following:
@@ -22,7 +22,7 @@ Access to Merlin5 is regulated by a PSI user's account being a member of the **`
Requesting **Merlin5** access *has to be done* with the corresponding **[Request Linux Group Membership](https://psi.service-now.com/psisp?id=psi_new_sc_cat_item&sys_id=84f2c0c81b04f110679febd9bb4bcbb1)** form, available in the [PSI Service Now Service Catalog](https://psi.service-now.com/psisp). Requesting **Merlin5** access *has to be done* with the corresponding **[Request Linux Group Membership](https://psi.service-now.com/psisp?id=psi_new_sc_cat_item&sys_id=84f2c0c81b04f110679febd9bb4bcbb1)** form, available in the [PSI Service Now Service Catalog](https://psi.service-now.com/psisp).
![Example: Requesting access to Merlin5](/images/Access/01-request-merlin5-membership.png) ![Example: Requesting access to Merlin5](../../images/Access/01-request-merlin5-membership.png)
Mandatory customizable fields are the following: Mandatory customizable fields are the following:

2
docs/merlin6/quick-start-guide/requesting-projects.md
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@@ -66,7 +66,7 @@ Supervisors should inform new users which extra groups are needed for their proj
Requesting membership for a specific Unix group *has to be done* with the corresponding **[Request Linux Group Membership](https://psi.service-now.com/psisp?id=psi_new_sc_cat_item&sys_id=84f2c0c81b04f110679febd9bb4bcbb1)** form, available in the [PSI Service Now Service Catalog](https://psi.service-now.com/psisp). Requesting membership for a specific Unix group *has to be done* with the corresponding **[Request Linux Group Membership](https://psi.service-now.com/psisp?id=psi_new_sc_cat_item&sys_id=84f2c0c81b04f110679febd9bb4bcbb1)** form, available in the [PSI Service Now Service Catalog](https://psi.service-now.com/psisp).
![Example: Requesting Unix Group membership](/images/Access/01-request-unx-group-membership.png) ![Example: Requesting Unix Group membership](../../images/Access/01-request-unx-group-membership.png)
Once submitted, the responsible of the Unix group has to approve the request. Once submitted, the responsible of the Unix group has to approve the request.

4
docs/merlin7/02-How-To-Use-Merlin/archive.md
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@@ -75,7 +75,7 @@ have been assigned a **``p-group``** (e.g. ``p12345``) for the experiment. Other
Groups are usually assigned to a PI, and then individual user accounts are added to the group. This must be done Groups are usually assigned to a PI, and then individual user accounts are added to the group. This must be done
under user request through PSI Service Now. For existing **a-groups** and **p-groups**, you can follow the standard under user request through PSI Service Now. For existing **a-groups** and **p-groups**, you can follow the standard
central procedures. Alternatively, if you do not know how to do that, follow the Merlin7 central procedures. Alternatively, if you do not know how to do that, follow the Merlin7
**[Requesting extra Unix groups](../01-Quick-Start-Guide/requesting-accounts.md#requesting-extra-unix-groups)** procedure, or open **[Requesting extra Unix groups](../01-Quick-Start-Guide/requesting-accounts.md)** procedure, or open
a **[PSI Service Now](https://psi.service-now.com/psisp)** ticket. a **[PSI Service Now](https://psi.service-now.com/psisp)** ticket.
### Documentation ### Documentation
@@ -102,7 +102,7 @@ As of 2022-04-14 a secure token is required to interact with the data catalog. T
1. You should be redirected to your user settings and see a 'User Information' section. If not, click on1. your username in the top right and choose 'Settings' from the menu. 1. You should be redirected to your user settings and see a 'User Information' section. If not, click on1. your username in the top right and choose 'Settings' from the menu.
1. Look for the field 'Catamel Token'. This should be a 64-character string. Click the icon to copy the1. token. 1. Look for the field 'Catamel Token'. This should be a 64-character string. Click the icon to copy the1. token.
![SciCat website](/images/scicat_token.png) ![SciCat website](../../images/scicat_token.png)
You will need to save this token for later steps. To avoid including it in all the commands, I suggest saving it to an environmental variable (Linux): You will need to save this token for later steps. To avoid including it in all the commands, I suggest saving it to an environmental variable (Linux):

2
docs/merlin7/02-How-To-Use-Merlin/connect-from-windows.md
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@@ -7,7 +7,7 @@ PuTTY is one of the most common tools for SSH.
Check, if the following software packages are installed on the Windows workstation by Check, if the following software packages are installed on the Windows workstation by
inspecting the *Start* menu (hint: use the *Search* box to save time): inspecting the *Start* menu (hint: use the *Search* box to save time):
* PuTTY (should be already installed) * PuTTY (should be already installed)
* *[Optional]* Xming (needed for [SSH with X11 Forwarding](connect-from-windows.md#ssh-with-x11-forwarding)) * *[Optional]* Xming (needed for [SSH with X11 Forwarding](#ssh-with-putty-with-x11-forwarding))
If they are missing, you can install them using the Software Kiosk icon on the Desktop. If they are missing, you can install them using the Software Kiosk icon on the Desktop.

18
docs/merlin7/02-How-To-Use-Merlin/merlin-rmount.md
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@@ -1,14 +1,4 @@
--- # Using merlin_rmount
title: Using merlin_rmount
#tags:
keywords: >-
transferring data, data transfer, rsync, dav, webdav, sftp, ftp, smb, cifs,
copy data, copying, mount, file, folder, sharing
last_updated: 24 August 2023
#summary: ""
sidebar: merlin7_sidebar
permalink: /merlin7/merlin-rmount.html
---
## Background ## Background
@@ -47,7 +37,7 @@ merlin_rmount --select-mount
Select the desired url using the arrow keys. Select the desired url using the arrow keys.
![merlin_rmount --select-mount](/images/rmount/select-mount.png) ![merlin_rmount --select-mount](../../images/rmount/select-mount.png)
From this list any of the standard supported endpoints can be mounted. From this list any of the standard supported endpoints can be mounted.
@@ -55,7 +45,7 @@ From this list any of the standard supported endpoints can be mounted.
Other endpoints can be mounted using the `merlin_rmount --mount <endpoint>` command. Other endpoints can be mounted using the `merlin_rmount --mount <endpoint>` command.
![merlin_rmount --mount](/images/rmount/mount.png) ![merlin_rmount --mount](../../images/rmount/mount.png)
### Accessing Files ### Accessing Files
@@ -95,7 +85,7 @@ Disconnecting will unmount all volumes.
Users that prefer a GUI file browser may prefer the `thunar` command, which opens the Gnome File Browser. This is also available in NoMachine sessions in the bottom bar (1). Thunar supports the same remote filesystems as `merlin_rmount`; just type the URL in the address bar (2). Users that prefer a GUI file browser may prefer the `thunar` command, which opens the Gnome File Browser. This is also available in NoMachine sessions in the bottom bar (1). Thunar supports the same remote filesystems as `merlin_rmount`; just type the URL in the address bar (2).
![Mounting with thunar](/images/rmount/thunar_mount.png) ![Mounting with thunar](../../images/rmount/thunar_mount.png)
When using thunar within a NoMachine session, file transfers continue after closing NoMachine (as long as the NoMachine session stays active). When using thunar within a NoMachine session, file transfers continue after closing NoMachine (as long as the NoMachine session stays active).

2
docs/merlin7/04-Jupyterhub/jupyterhub.md
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@@ -42,7 +42,7 @@ queue. Additional customization can be implemented using the *'Optional user
defined line to be added to the batch launcher script'* option. This line is defined line to be added to the batch launcher script'* option. This line is
added to the submission script at the end of other `#SBATCH` lines. Parameters can added to the submission script at the end of other `#SBATCH` lines. Parameters can
be passed to SLURM by starting the line with `#SBATCH`, like in [Running Slurm be passed to SLURM by starting the line with `#SBATCH`, like in [Running Slurm
Scripts](../slurm-general-docs/running-jobs.md). Some ideas: Scripts](../03-Slurm-General-Documentation/slurm-examples.md). Some ideas:
**Request additional memory** **Request additional memory**

8
docs/merlin7/99-support/migration-from-merlin6.md
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@@ -29,7 +29,7 @@ Contact the Merlin support team [merlin-admins@lists.psi.ch](mailto:merlin-admin
> ⚠️ In this phase, **it's important that you don't belong to any project**. > ⚠️ In this phase, **it's important that you don't belong to any project**.
> Once the migration is finished, **access to Merlin6 will be no longer possible.** > Once the migration is finished, **access to Merlin6 will be no longer possible.**
Please refer to the [Phase 1: Step-by-Step Migration Instructions](/merlin7/migrating.html#phase-1-step-by-step-migration-instructions) section Please refer to the [Phase 1: Step-by-Step Migration Instructions](#phase-1-step-by-step-migration-instructions) section
for detailed information about user data migration. for detailed information about user data migration.
### Phase 2: Project Members and Owners — **Start Before August 1** ### Phase 2: Project Members and Owners — **Start Before August 1**
@@ -42,7 +42,7 @@ For users in active projects:
> ⚠️ In this phase, **data and home directories of group owners and members will be also requested to be migrated in parallel.** > ⚠️ In this phase, **data and home directories of group owners and members will be also requested to be migrated in parallel.**
Please refer to the [Phase 2: Migration Instructions](/merlin7/migrating.html#phase-2-migration-instructions) section Please refer to the [Phase 2: Migration Instructions](#phase-2-migration-instructions) section
for further information. for further information.
--- ---
@@ -162,7 +162,7 @@ If a problem occurs during the migration process:
* Files with incorrect permissions * Files with incorrect permissions
* Ownership mismatches * Ownership mismatches
* Disk quota exceeded on Merlin7 * Disk quota exceeded on Merlin7
* 📚 Refer to the [⚠️ Common rsync/fpsync Migration Issues](/merlin7/migrating.html#%EF%B8%8F--common-rsyncfpsync-migration-issues) section below for detailed explanations and solutions. * 📚 Refer to the [⚠️ Common rsync/fpsync Migration Issues](#common-rsyncfpsync-migration-issues) section below for detailed explanations and solutions.
> ℹ️ **Important:** If `migrate_merlin6data.batch` fails, the migration process will automatically cancel `migrate_merlin6home.batch` to avoid ending in an inconsistent state. > ℹ️ **Important:** If `migrate_merlin6data.batch` fails, the migration process will automatically cancel `migrate_merlin6home.batch` to avoid ending in an inconsistent state.
@@ -266,7 +266,7 @@ CLUSTER: merlin6
## Phase 2: Migration Instructions ## Phase 2: Migration Instructions
Please refer to the [Prerequisites and Preparation](/merlin7/migrating.html#-prerequisites-and-preparation) section for initial setup steps. Please refer to the [Prerequisites and Preparation](#prerequisites-and-preparation) section for initial setup steps.
Further instructions will be sent via email once the owning team is contacted by the Merlin administrators. Further instructions will be sent via email once the owning team is contacted by the Merlin administrators.
--- ---