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2025-12-11 10:32:15 +01:00
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6
docs/merlin7/02-How-To-Use-Merlin/connect-from-linux.md
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@@ -10,7 +10,7 @@ permalink: /merlin7/connect-from-linux.html
## SSH without X11 Forwarding
This is the standard method. Official X11 support is provided through [NoMachine](/merlin7/nomachine.html).
This is the standard method. Official X11 support is provided through [NoMachine](nomachine.md).
For normal SSH sessions, use your SSH client as follows:
```bash
@@ -21,8 +21,8 @@ ssh $username@login002.merlin7.psi.ch
## SSH with X11 Forwarding
Official X11 Forwarding support is through NoMachine. Please follow the document
[{Job Submission -> Interactive Jobs}](/merlin7/interactive-jobs.html#Requirements) and
[{Accessing Merlin -> NoMachine}](/merlin7/nomachine.html) for more details. However,
[{Job Submission -> Interactive Jobs}](../03-Slurm-General-Documentation/interactive-jobs.md#requirements) and
[{Accessing Merlin -> NoMachine}](nomachine.md) for more details. However,
we provide a small recipe for enabling X11 Forwarding in Linux.
* For enabling client X11 forwarding, add the following to the start of ``~/.ssh/config``

6
docs/merlin7/02-How-To-Use-Merlin/connect-from-macos.md
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@@ -10,7 +10,7 @@ permalink: /merlin7/connect-from-macos.html
## SSH without X11 Forwarding
This is the standard method. Official X11 support is provided through [NoMachine](/merlin7/nomachine.html).
This is the standard method. Official X11 support is provided through [NoMachine](nomachine.md).
For normal SSH sessions, use your SSH client as follows:
```bash
@@ -29,8 +29,8 @@ you have it running before starting a SSH connection with X11 forwarding.
### SSH with X11 Forwarding in MacOS
Official X11 support is through NoMachine. Please follow the document
[{Job Submission -> Interactive Jobs}](/merlin7/interactive-jobs.html#Requirements) and
[{Accessing Merlin -> NoMachine}](/merlin7/nomachine.html) for more details. However,
[{Job Submission -> Interactive Jobs}](../03-Slurm-General-Documentation/interactive-jobs.md#requirements) and
[{Accessing Merlin -> NoMachine}](nomachine.md) for more details. However,
we provide a small recipe for enabling X11 Forwarding in MacOS.
* Ensure that **[XQuartz](https://www.xquartz.org/)** is installed and running in your MacOS.

13
docs/merlin7/02-How-To-Use-Merlin/connect-from-windows.md
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@@ -1,11 +1,4 @@
---
title: Connecting from a Windows Client
keywords: microsoft, mocosoft, windows, putty, xming, connecting, client, configuration, SSH, X11
last_updated: 07 September 2022
summary: "This document describes a recommended setup for a Windows client."
sidebar: merlin7_sidebar
permalink: /merlin7/connect-from-windows.html
---
# Connecting from a Windows Client
## SSH with PuTTY without X11 Forwarding
@@ -14,7 +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
inspecting the *Start* menu (hint: use the *Search* box to save time):
* PuTTY (should be already installed)
* *[Optional]* Xming (needed for [SSH with X11 Forwarding](/merlin7/connect-from-windows.html#ssh-with-x11-forwarding))
* *[Optional]* Xming (needed for [SSH with X11 Forwarding](connect-from-windows.md#ssh-with-x11-forwarding))
If they are missing, you can install them using the Software Kiosk icon on the Desktop.
@@ -32,7 +25,7 @@ If they are missing, you can install them using the Software Kiosk icon on the D
## SSH with PuTTY with X11 Forwarding
Official X11 Forwarding support is through NoMachine. Please follow the document
[{Job Submission -> Interactive Jobs}](/merlin7/interactive-jobs.html#Requirements) and
[{Job Submission -> Interactive Jobs}](../03-Slurm-General-Documentation/interactive-jobs.md#requirements) and
[{Accessing Merlin -> NoMachine}](/merlin7/nomachine.html) for more details. However,
we provide a small recipe for enabling X11 Forwarding in Windows.

2
docs/merlin7/02-How-To-Use-Merlin/kerberos.md
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@@ -134,7 +134,7 @@ aklog
## Slurm jobs accessing AFS
Some jobs may require to access private areas in AFS. For that, having a valid [**keytab**](/merlin7/kerberos.html#generating-granting-tickets-with-keytab) file is required.
Some jobs may require to access private areas in AFS. For that, having a valid [**keytab**](kerberos.md#creating-a-keytab-file) 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.
The steps should be the following:

2
docs/merlin7/02-How-To-Use-Merlin/merlin_tools.md
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@@ -20,7 +20,7 @@ described here are organised by use case and include usage examples.
This tool is available on all of the login nodes and provides a brief overview of
a user's filesystem quotas. These are limits which restrict how much storage (or
number of files) a user can create. A generic table of filesystem quotas can be
found on the [Storage page](/merlin7/storage.html#dir_classes).
found on the [Storage page](storage.md#dir_classes).
#### Example #1: Viewing quotas

6
docs/merlin7/02-How-To-Use-Merlin/software-repositories.md
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@@ -23,7 +23,7 @@ Key Features:
* **Custom Requests:** If a package, version, or feature is missing, users can contact the support team to explore feasibility for installation.
{{site.data.alerts.tip}}
For further information about <b>Pmodules</b> on Merlin7 please refer to the <b><a href="/merlin7/pmodules.html">PSI Modules</a></b> chapter.
For further information about **PModules** on Merlin7 please refer to the [PSI Modules](../05-Software-Support/pmodules.md) chapter.
{{site.data.alerts.end}}
### Spack Modules
@@ -31,7 +31,7 @@ For further information about <b>Pmodules</b> on Merlin7 please refer to the <b>
Merlin7 also provides Spack modules, offering a modern and flexible package management system. Spack supports a wide variety of software packages and versions. For more information, refer to the **external [PSI Spack](https://gitea.psi.ch/HPCE/spack-psi) documentation**.
{{site.data.alerts.tip}}
For further information about <b>Spack</b> on Merlin7 please refer to the <b><a href="/merlin7/spack.html">Spack</a></b> chapter.
For further information about **Spack** on Merlin7 please refer to the [Spack](../05-Software-Support/spack.md) chapter.
{{site.data.alerts.end}}
### Cray Environment Modules
@@ -45,6 +45,6 @@ Recommendations:
* **General Use:** For most applications, prefer PModules, which ensure stability, backward compatibility, and long-term support.
{{site.data.alerts.tip}}
For further information about <b>CPE</b> on Merlin7 please refer to the <b><a href="/merlin7/cray-module-env.html">Cray Modules</a></b> chapter.
For further information about **CPE** on Merlin7 please refer to the [Cray Modules](../05-Software-Support/cray-module.env.md) chapter.
{{site.data.alerts.end}}

10
docs/merlin7/02-How-To-Use-Merlin/storage.md
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@@ -104,12 +104,12 @@ The home directories are mounted in the login and computing nodes under the dire
Directory policies:
* Read **[Important: Code of Conduct](/merlin7/code-of-conduct.html)** for more information about Merlin7 policies.
* Is **forbidden** to use the home directories for IO-intensive tasks, instead use one of the **[scratch](/merlin7/storage.html#scratch-directories)** areas instead!
* Read **[Important: Code of Conduct](../01-Quick-Start-Guide/code-of-conduct.md)** for more information about Merlin7 policies.
* Is **forbidden** to use the home directories for IO-intensive tasks, instead use one of the **[scratch](storage.md#scratch-directories)** areas instead!
* No backup policy is applied for the user home directories: **users are responsible for backing up their data**.
Home directory quotas are defined in a per Lustre project basis. The quota can be checked using the `merlin_quotas` command described
[above](/merlin7/storage.html#how-to-check-quotas).
[above](storage.md#how-to-check-quotas).
### Project data directory
@@ -118,7 +118,7 @@ shared by all members of the project (the project's corresponding UNIX group). W
project related storage spaces, since it allows users to coordinate. Also, project spaces have more flexible policies
regarding extending the available storage space.
Scientists can request a Merlin project space as described in **[[Accessing Merlin -> Requesting a Project]](/merlin7/request-project.html)**.
Scientists can request a Merlin project space as described in **[[Accessing Merlin -> Requesting a Project]](../01-Quick-Start-Guide/requesting-projects.md)**.
By default, Merlin can offer **general** project space, centrally covered, as long as it does not exceed 10TB (otherwise, it has to be justified).
General Merlin projects might need to be reviewed after one year of their creation.
@@ -140,7 +140,7 @@ In the future, a list of `projectid` will be provided, so users can check their
Directory policies:
* Read **[Important: Code of Conduct](/merlin7/code-of-conduct.html)** for more information about Merlin7 policies.
* Read **[Important: Code of Conduct](../01-Quick-Start-Guide/code-of-conduct.md)** for more information about Merlin7 policies.
* It is **forbidden** to use the data directories as `/scratch` area during a job's runtime, i.e. for high throughput I/O for a job's temporary files.
* Please Use `/scratch`, `/data/scratch/shared` for this purpose.
* No backups: users are responsible for managing the backups of their data directories.

6
docs/merlin7/02-How-To-Use-Merlin/transfer-data.md
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@@ -41,7 +41,7 @@ The next chapters contain detailed information about the different transfer meth
## Direct Transfer via Merlin7 Login Nodes
The following methods transfer data directly via the [login nodes](/merlin7/interactive.html#login-nodes-hardware-description). They are suitable for use from **within the PSI network**.
The following methods transfer data directly via the [login nodes](../01-Quick-Start-Guide/accessing-interactive-nodes.md#login-nodes-hardware-description). They are suitable for use from **within the PSI network**.
### Rsync (Recommended for Linux/macOS)
@@ -133,7 +133,7 @@ SWITCHfilesender <b>is not</b> a long-term storage or archiving solution.
From August 2024, Merlin is connected to the **[PSI Data Transfer](https://www.psi.ch/en/photon-science-data-services/data-transfer)** service,
`datatransfer.psi.ch`. This is a central service managed by the **[Linux team](https://linux.psi.ch/index.html)**. However, any problems or questions related to it can be directly
[reported](/merlin7/contact.html) to the Merlin administrators, which will forward the request if necessary.
[reported](../99-support/contact.md) to the Merlin administrators, which will forward the request if necessary.
The PSI Data Transfer servers supports the following protocols:
* Data Transfer - SSH (scp / rsync)
@@ -172,6 +172,6 @@ provides a helpful wrapper over the Gnome storage utilities, and provides suppor
- [others](https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/8/html/using_the_desktop_environment_in_rhel_8/managing-storage-volumes-in-gnome_using-the-desktop-environment-in-rhel-8#gvfs-back-ends_managing-storage-volumes-in-gnome)
[More instruction on using `merlin_rmount`](/merlin7/merlin-rmount.html)
[More instruction on using `merlin_rmount`](merlin-rmount.md)
{% endcomment %}