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10
docs/merlin7/01-Quick-Start-Guide/accessing-interactive-nodes.md
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@@ -1,12 +1,4 @@
---
title: Accessing Interactive Nodes
#tags:
keywords: How to, HowTo, access, accessing, nomachine, ssh
last_updated: 07 September 2022
#summary: ""
sidebar: merlin7_sidebar
permalink: /merlin7/interactive.html
---
# Accessing Interactive Nodes
## SSH Access

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docs/merlin7/01-Quick-Start-Guide/accessing-slurm.md
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@@ -18,7 +18,7 @@ It basically contains the following clusters:
## Accessing the Slurm clusters
Any job submission must be performed from a **Merlin login node**. Please refer to the [**Accessing the Interactive Nodes documentation**](/merlin7/interactive.html)
Any job submission must be performed from a **Merlin login node**. Please refer to the [**Accessing the Interactive Nodes documentation**](accessing-interactive-nodes.md)
for further information about how to access the cluster.
In addition, any job *must be submitted from a high performance storage area visible by the login nodes and by the computing nodes*. For this, the possible storage areas are the following:

2
docs/merlin7/01-Quick-Start-Guide/introduction.md
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@@ -16,7 +16,7 @@ The Merlin7 cluster is moving toward **production** state since August 2024, thi
but due to some remaining issues with the platform, the schedule of the migration of users and communities has been delayed. You will be notified well in advance
regarding the migration of data.
All PSI users can request access to Merlin7, please go to the [Requesting Merlin Accounts](/merlin7/request-account.html) page and complete the steps given there.
All PSI users can request access to Merlin7, please go to the [Requesting Merlin Accounts](requesting-accounts.md) page and complete the steps given there.
In case you identify errors or missing information, please provide feedback through [merlin-admins mailing list](mailto:merlin-admins@lists.psi.ch) mailing list or [submit a ticket using the PSI service portal](https://psi.service-now.com/psisp).

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.

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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 %}

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docs/merlin7/03-Slurm-General-Documentation/interactive-jobs.md
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@@ -1,12 +1,4 @@
---
title: Running Interactive Jobs
#tags:
keywords: interactive, X11, X, srun, salloc, job, jobs, slurm, nomachine, nx
last_updated: 07 August 2024
summary: "This document describes how to run interactive jobs as well as X based software."
sidebar: merlin7_sidebar
permalink: /merlin7/interactive-jobs.html
---
# Running Interactive Jobs
### The Merlin7 'interactive' partition
@@ -120,16 +112,16 @@ salloc: Relinquishing job allocation 165
#### Graphical access
[NoMachine](/merlin7/nomachine.html) is the official supported service for graphical
[NoMachine](../02-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}](/merlin7/nomachine.html) for details about
document [{Accessing Merlin -> NoMachine}](../02-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}](/merlin7/connect-from-linux.html)
* For Windows clients, please follow [{How To Use Merlin -> Accessing from Windows Clients}](/merlin7/connect-from-windows.html)
* For MacOS clients, please follow [{How To Use Merlin -> Accessing from MacOS Clients}](/merlin7/connect-from-macos.html)
* For Linux clients, please follow [{How To Use Merlin -> Accessing from Linux Clients}](../02-How-To-Use-Merlin/connect-from-linux.md)
* For Windows clients, please follow [{How To Use Merlin -> Accessing from Windows Clients}](../02-How-To-Use-Merlin/connect-from-windows.md)
* For MacOS clients, please follow [{How To Use Merlin -> Accessing from MacOS Clients}](../02-How-To-Use-Merlin/connect-from-macos.md)
### 'srun' with x11 support

4
docs/merlin7/03-Slurm-General-Documentation/slurm-configuration.md
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@@ -132,7 +132,7 @@ Where:
* **`cpu_interactive` QoS:** Is restricted to one node and a few CPUs only, and is intended to be used when interactive
allocations are necessary (`salloc`, `srun`).
For additional details, refer to the [CPU partitions](/merlin7/slurm-configuration.html#CPU-partitions) section.
For additional details, refer to the [CPU partitions](slurm-configuration.md#CPU-partitions) section.
{{site.data.alerts.tip}}
Always verify QoS definitions for potential changes using the <b>'sacctmgr show qos format="Name%22,MaxTRESPU%35,MaxTRES%35"'</b> command.
@@ -308,7 +308,7 @@ Where:
* **`gpu_a100_interactive` & `gpu_gh_interactive` QoS:** Guarantee interactive access to GPU nodes for software compilation and
small testing.
For additional details, refer to the [GPU partitions](/merlin7/slurm-configuration.html#GPU-partitions) section.
For additional details, refer to the [GPU partitions](slurm-configuration.md#GPU-partitions) section.
{{site.data.alerts.tip}}
Always verify QoS definitions for potential changes using the <b>'sacctmgr show qos format="Name%22,MaxTRESPU%35,MaxTRES%35"'</b> command.

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docs/merlin7/05-Software-Support/ansys.md
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@@ -12,7 +12,7 @@ This document describes generic information of how to load and run ANSYS softwar
## ANSYS software in Pmodules
The ANSYS software can be loaded through **[PModules](/merlin7/pmodules.html)**.
The ANSYS software can be loaded through **[PModules](pmodules.md)**.
The default ANSYS versions are loaded from the central PModules repository.
@@ -80,16 +80,16 @@ ANSYS/2025R2:
**ANSYS Remote Solve Manager (RSM)** is used by ANSYS Workbench to submit computational jobs to HPC clusters directly from Workbench on your desktop.
Therefore, PSI workstations with direct access to Merlin can submit jobs by using RSM.
For further information, please visit the **[ANSYS RSM](/merlin7/ansys-rsm.html)** section.
For further information, please visit the **[ANSYS RSM](ansys-rsm.md)** section.
### ANSYS Fluent
For further information, please visit the **[ANSYS RSM](/merlin7/ansys-fluent.html)** section.
For further information, please visit the **[ANSYS RSM](ansys-fluent.md)** section.
### ANSYS CFX
For further information, please visit the **[ANSYS RSM](/merlin7/ansys-cfx.html)** section.
For further information, please visit the **[ANSYS RSM](ansys-cfx.md)** section.
### ANSYS MAPDL
For further information, please visit the **[ANSYS RSM](/merlin7/ansys-mapdl.html)** section.
For further information, please visit the **[ANSYS RSM](ansys-mapdl.md)** section.

4
docs/merlin7/05-Software-Support/openmpi.md
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@@ -19,7 +19,7 @@ The Merlin cluster supports OpenMPI versions across three distinct stages: stabl
#### Stable
Versions in the `stable` stage are fully functional, thoroughly tested, and officially supported by the Merlin administrators.
These versions are available via [Pmodules](/merlin7/pmodules.html) and [Spack](/merlin7/spack.html), ensuring compatibility and reliability for production use.
These versions are available via [PModules](pmodules.md) and [Spack](spack.md), ensuring compatibility and reliability for production use.
#### Unstable
@@ -71,7 +71,7 @@ specific pmix plugin versions available: pmix_v5,pmix_v4,pmix_v3,pmix_v2
```
Important Notes:
* For OpenMPI, always use `pmix` by specifying the appropriate version (`pmix_$version`).
When loading an OpenMPI module (via [Pmodules](/merlin7/pmodules.html) or [Spack](/merlin7/spack.html)), the corresponding PMIx version will be automatically loaded.
When loading an OpenMPI module (via [PModules](pmodules.md) or [Spack](spack.md)), the corresponding PMIx version will be automatically loaded.
* Users do not need to manually manage PMIx compatibility.
{{site.data.alerts.warning}}

2
docs/merlin7/05-Software-Support/pmodules.md
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@@ -136,7 +136,7 @@ The PModules system is designed to accommodate the diverse software needs of Mer
### Requesting Missing Software
If a specific software package is not available in PModules and there is interest from multiple users:
* **[Contact Support](/merlin7/contact.html):** Let us know about the software, and we will assess its feasibility for deployment.
* **[Contact Support](../99-support/contact.md):** Let us know about the software, and we will assess its feasibility for deployment.
* **Deployment Timeline:** Adding new software to PModules typically takes a few days, depending on complexity and compatibility.
* **User Involvement:** If you are interested in maintaining the software package, please inform us. Collaborative maintenance helps
ensure timely updates and support.