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Author SHA1 Message Date
b7107b9210 final changes 2026-01-12 17:47:15 +01:00
8100c03090 add/rm final files 2026-01-12 17:45:03 +01:00
f89fe6a3e5 minor improvements 2026-01-12 17:45:03 +01:00
a1c009de6e add latest new section to frontpage
We use a custom override template (jinja) to generate a suitable list of
new items.

Also added first text for announcing our new user docs
2026-01-12 17:45:03 +01:00
865ce6dd34 merge and move support pages
this are now under the /support path, meaning that this is unified for
all clusters.
2026-01-12 17:45:03 +01:00
58b44f51b9 fix issue with the news page 2026-01-12 17:45:02 +01:00
280d4a76a0 minor fixes
* added back the HPCE logo to landing page
* activated the sticky tabs navigation feature (so navigation bar stays
  visible)
* added edit buttons to content (so users can _maybe_ help us in keeping
  our docs up to date)
2026-01-12 17:45:02 +01:00
884be481a4 update main Merlin7 page with production status, remove dead links 2026-01-12 17:45:02 +01:00
c0c1c681fd initial formatting changes complete 2026-01-12 17:44:58 +01:00
a83a18d9fc fixed all links now 2026-01-12 17:43:31 +01:00
8d5f487638 ensure headers have permalinks usable 2026-01-12 17:43:31 +01:00
1d21fc390f further fixes 2026-01-12 17:43:30 +01:00
5cbc746528 vibe #3 2026-01-12 17:43:30 +01:00
25c81a6b4d further vibing #2 2026-01-12 17:43:30 +01:00
42a937f71e add missing pages 2026-01-12 17:43:30 +01:00
2664690d34 vibed changes #1 2026-01-12 17:43:30 +01:00
8c9e8c7593 add all files to nav 2026-01-12 17:43:30 +01:00
f51cc6060b add software support m6 docs 2026-01-12 17:43:29 +01:00
5485cc53dc add merlin6 JB docs 2026-01-12 17:43:29 +01:00
2ad471685d refactored slurm general docs merlin6 2026-01-12 17:43:29 +01:00
192578fe18 give the userdoc its own color scheme
we use the Materials default one
2026-01-12 17:43:29 +01:00
0a4ab096e3 update merlin6 nomachine docs 2026-01-12 17:43:29 +01:00
f26d7c4352 add merlin6 quick start 2026-01-12 17:43:29 +01:00
dbfb393a71 refactor CSCS and Meg content 2026-01-12 17:43:29 +01:00
1d9c01572d first stab at mkdocs migration 2026-01-12 17:43:28 +01:00
149de6fb18 FIX: old gitlab links
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2025-12-18 10:39:01 +01:00
c332469434 added average allocation number for GPU projects
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2025-12-09 13:09:22 +01:00
f95af6babe FIX: old IPPL modules
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2025-12-03 13:10:47 +01:00
643d0873be ADD: q-e@7.5
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2025-11-28 18:01:36 +01:00
921a62b702 ADD: gromacs@2025.3 all systems
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2025-11-27 16:41:09 +01:00
8 changed files with 51 additions and 14 deletions

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@@ -3,7 +3,7 @@ name: Build and deploy documentation
on: on:
push: push:
branches: branches:
- main - master
workflow_dispatch: workflow_dispatch:
jobs: jobs:
build-and-deploy-docs: build-and-deploy-docs:

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@@ -32,7 +32,9 @@ oversubscription, will be arbitrated by a panel within CSD.
### Instructions for filling out the 2026 survey ### Instructions for filling out the 2026 survey
* We have a budget of 100 kCHF for 2026, which translates to 435'000 multicore node hours or 35'600 node hours on the GPU Grace Hopper nodes. The minimum allocation is 10'000 node hours for multicore projects, an average project allocation would amount to 30'000 node hours * We have a budget of 100 kCHF for 2026, which translates to 435'000 multicore node hours or 35'600 node hours on the GPU Grace Hopper nodes.
* multicore projects: The minimum allocation is 10'000 node hours, an average project allocation amounts to 30'000 node hours
* GPU projects: The minimum allocation is 800 node hours, an average project allocation is 2000 node hours.
* You need to specify the total resource request for your project in node hours, and how you would like to split the resources over the 4 quarters. For the allocations per quarter year, please enter the number in percent (e.g. 25%, 25%, 25%, 25%). If you indicate nothing, a 25% per quarter will be assumed. * You need to specify the total resource request for your project in node hours, and how you would like to split the resources over the 4 quarters. For the allocations per quarter year, please enter the number in percent (e.g. 25%, 25%, 25%, 25%). If you indicate nothing, a 25% per quarter will be assumed.
* We currently have a total of 65 TB of storage for all projects. Additional storage * We currently have a total of 65 TB of storage for all projects. Additional storage
can be obtained, but large storage assignments are not in scope for these projects. can be obtained, but large storage assignments are not in scope for these projects.

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@@ -11,6 +11,7 @@ It is primarily designed for biochemical molecules like proteins, lipids and nuc
GROMACS is a joint effort, with contributions from developers around the world: users agree to acknowledge use of GROMACS in any reports or publications of results obtained with the Software (see GROMACS Homepage for details). GROMACS is a joint effort, with contributions from developers around the world: users agree to acknowledge use of GROMACS in any reports or publications of results obtained with the Software (see GROMACS Homepage for details).
## How to run on Merlin7 ## How to run on Merlin7
## 2025.2
### CPU nodes ### CPU nodes
```bash ```bash
module use Spack unstable module use Spack unstable
@@ -26,6 +27,22 @@ module load gcc/12.3 openmpi/5.0.7-3vzj-A100-gpu gromacs/2025.2-vbj4-A100-gpu-om
module use Spack unstable module use Spack unstable
module load gcc/12.3 openmpi/5.0.7-blxc-GH200-gpu gromacs/2025.2-cjnq-GH200-gpu-omp module load gcc/12.3 openmpi/5.0.7-blxc-GH200-gpu gromacs/2025.2-cjnq-GH200-gpu-omp
``` ```
## 2025.3
### CPU nodes
```bash
module use Spack unstable
module load gcc/12.3 openmpi/5.0.9-n4yf-A100-gpu gromacs/2025.3-6ken-omp
```
### A100 nodes
```bash
module use Spack unstable
module load gcc/12.3 openmpi/5.0.9-xqhy-A100-gpu gromacs/2025.3-ohlj-A100-gpu-omp
```
### GH nodes
```bash
module use Spack unstable
module load gcc/12.3 openmpi/5.0.9-inxi-GH200-gpu gromacs/2025.3-yqlu-GH200-gpu-omp
```
### SBATCH CPU, 4 MPI ranks, 16 OMP threads ### SBATCH CPU, 4 MPI ranks, 16 OMP threads
```bash ```bash

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@@ -13,8 +13,7 @@ GNU GPLv3
[![Pipeline](https://gitea.psi.ch/HPCE/spack-psi/actions/workflows/ippl_gpu_merlin7.yml/badge.svg?branch=main)](https://gitea.psi.ch/HPCE/spack-psi) [![Pipeline](https://gitea.psi.ch/HPCE/spack-psi/actions/workflows/ippl_gpu_merlin7.yml/badge.svg?branch=main)](https://gitea.psi.ch/HPCE/spack-psi)
```bash ```bash
module use Spack unstable module use Spack unstable
module load gcc/13.2.0 openmpi/4.1.6-57rc-A100-gpu module load gcc/13.2.0 openmpi/5.0.7-dnpr-A100-gpu boost/1.82.0-lgrt fftw/3.3.10.6-zv2b-omp googletest/1.14.0-msmu h5hut/2.0.0rc7-zy7s openblas/0.3.29-zkwb cmake/3.31.6-ufy7
module load boost/1.82.0-e7gp fftw/3.3.10 gnutls/3.8.3 googletest/1.14.0 gsl/2.8 h5hut/2.0.0rc7 openblas/0.3.26-omp cmake/3.31.6-oe7u
cd <path to IPPL source directory> cd <path to IPPL source directory>
mkdir build_gpu mkdir build_gpu

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@@ -33,7 +33,7 @@ module purge
module use Spack unstable module use Spack unstable
module load gcc/13.2.0 openmpi/5.0.7-dnpr-A100-gpu module load gcc/13.2.0 openmpi/5.0.7-dnpr-A100-gpu
module load boost/1.82.0-lgrt fftw/3.3.10.6-zv2b-omp gnutls/3.8.9-mcdr googletest/1.14.0-msmu gsl/2.7.1-hxwy h5hut/2.0.0rc7-zy7s openblas/0.3.29-zkwb cmake/3.31.6-oe7u module load boost/1.82.0-lgrt fftw/3.3.10.6-zv2b-omp gnutls/3.8.9-mcdr googletest/1.14.0-msmu gsl/2.7.1-hxwy h5hut/2.0.0rc7-zy7s openblas/0.3.29-zkwb cmake/3.31.6-oe7u
git clone https://gitlab.psi.ch/OPAL/opal-x/src.git opal-x git clone https://github.com/OPALX-project/OPALX.git opal-x
cd opal-x cd opal-x
./gen_OPALrevision ./gen_OPALrevision
@@ -56,7 +56,7 @@ module use Spack unstable
module load gcc/13.2.0 openmpi/5.0.7-z3y6-GH200-gpu module load gcc/13.2.0 openmpi/5.0.7-z3y6-GH200-gpu
module load boost/1.82.0-znbt fftw/3.3.10-jctz gnutls/3.8.9-rtrg googletest/1.15.2-odox gsl/2.7.1-j2dk h5hut/2.0.0rc7-k63k openblas/0.3.29-d3m2 cmake/3.31.4-u2nm module load boost/1.82.0-znbt fftw/3.3.10-jctz gnutls/3.8.9-rtrg googletest/1.15.2-odox gsl/2.7.1-j2dk h5hut/2.0.0rc7-k63k openblas/0.3.29-d3m2 cmake/3.31.4-u2nm
git clone https://gitlab.psi.ch/OPAL/opal-x/src.git opal-x git clone https://github.com/OPALX-project/OPALX.git opal-x
cd opal-x cd opal-x
./gen_OPALrevision ./gen_OPALrevision
mkdir build_gh mkdir build_gh

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@@ -13,6 +13,20 @@ Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electr
Quantum ESPRESSO is an open initiative, in collaboration with many groups world-wide, coordinated by the Quantum ESPRESSO Foundation. Scientific work done using Quantum ESPRESSO should contain an explicit acknowledgment and reference to the main papers (see Quantum Espresso Homepage for the details). Quantum ESPRESSO is an open initiative, in collaboration with many groups world-wide, coordinated by the Quantum ESPRESSO Foundation. Scientific work done using Quantum ESPRESSO should contain an explicit acknowledgment and reference to the main papers (see Quantum Espresso Homepage for the details).
## How to run on Merlin7 ## How to run on Merlin7
### 7.5
### CPU nodes
```bash
module purge
module use Spack unstable
module load gcc/12.3 openmpi/5.0.9-xqhy-A100-gpu quantum-espresso/7.5-zfwh-omp
```
### GH nodes
```bash
module purge
module use Spack unstable
module load nvhpc/25.7 openmpi/4.1.8-l3jj-GH200-gpu quantum-espresso/7.5-2ysd-gpu-omp
```
### 7.4.1
### A100 nodes ### A100 nodes
```bash ```bash
module purge module purge

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@@ -3,20 +3,25 @@ date:
created: 2026-01-12 created: 2026-01-12
tags: tags:
- getting_started - getting_started
- draft
--- ---
# New User Documentation Site # New User Documentation Site
Starting in 2026, we are changing the design of the user documentation website. Starting in 2026, we are changing the design of the user documentation website.
Previously we had used the [documentation Previously we had used the theme [Documentation for
theme](https://github.com/tomjoht/documentation-theme-jekyll) together with the Jekyll](https://github.com/tomjoht/documentation-theme-jekyll) together with
[Jykell SSG](https://jekyllrb.com/), but have now switch to the more modern the [Jykell SSG](https://jekyllrb.com/), but have now switch to the more modern
[Material for MkDocs](https://squidfunk.github.io/mkdocs-material/) theme and [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/) theme and
SSG engine. This comes with a few improvements: SSG engine. This comes with a few improvements:
* searching is more complete and provides better results * searching is more complete and provides better results
* theme related improvements (day-night coloring, page layout, content formatting) * theme related improvements (day-night coloring, page layout, content formatting)
* edits for pages can be submitted via the *Edit* (this will direct you to the Gitea repository which hosts the documentation) * edits for pages can be submitted via the *Edit* button (taking you to the
Gitea editor and letting you submit a pull request)
TBD With the latter new feature, we encourage our users to point out any issues they
find with the documentation. Contributation are very welcome and will help in
ensuring that the documentation is kept up-to-date.
Notice also that we now have a dedicated [Support](../../support/index.md) page,
making it easier to find and use our different contact options.

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@@ -9,10 +9,10 @@
There are several channels you can use to get support: There are several channels you can use to get support:
* the **preferred** choice is to submit a ticket with [PSI Service Now](https://psi.service-now.com/psisp), alternatively * the **preferred** choice is to submit a ticket with [PSI Service Now](https://psi.service-now.com/psisp), alternatively
* you can also us our [user mailing list](#merlin-user-mailing-list), or lastly * you can also us our [user mailing list](#merlin-user-mailing-list), or
* you can email the Admins directly <merlin-admins@lists.psi.ch> * you can email the Admins directly <merlin-admins@lists.psi.ch>
!!! info ??? info
Basic contact information is also displayed on every shell login to the Basic contact information is also displayed on every shell login to the
system using the *Message of the Day* mechanism. system using the *Message of the Day* mechanism.