[Show Example]: Sample ingestion output (datasetIngestor 1.1.11)
diff --git a/docs/merlin7/02-How-To-Use-Merlin/kerberos.md b/docs/merlin7/03-how-to-use-merlin/kerberos.md
similarity index 100%
rename from docs/merlin7/02-How-To-Use-Merlin/kerberos.md
rename to docs/merlin7/03-how-to-use-merlin/kerberos.md
diff --git a/docs/merlin7/02-How-To-Use-Merlin/merlin-rmount.md b/docs/merlin7/03-how-to-use-merlin/merlin-rmount.md
similarity index 100%
rename from docs/merlin7/02-How-To-Use-Merlin/merlin-rmount.md
rename to docs/merlin7/03-how-to-use-merlin/merlin-rmount.md
diff --git a/docs/merlin7/02-How-To-Use-Merlin/merlin_tools.md b/docs/merlin7/03-how-to-use-merlin/merlin_tools.md
similarity index 100%
rename from docs/merlin7/02-How-To-Use-Merlin/merlin_tools.md
rename to docs/merlin7/03-how-to-use-merlin/merlin_tools.md
diff --git a/docs/merlin7/02-How-To-Use-Merlin/software-repositories.md b/docs/merlin7/03-how-to-use-merlin/software-repositories.md
similarity index 91%
rename from docs/merlin7/02-How-To-Use-Merlin/software-repositories.md
rename to docs/merlin7/03-how-to-use-merlin/software-repositories.md
index adacde2..b95ad62 100644
--- a/docs/merlin7/02-How-To-Use-Merlin/software-repositories.md
+++ b/docs/merlin7/03-how-to-use-merlin/software-repositories.md
@@ -16,14 +16,14 @@ Key Features:
* **Custom Requests:** If a package, version, or feature is missing, users can contact the support team to explore feasibility for installation.
!!! tip
- For further information about **PModules** on Merlin7 please refer to the [PSI Modules](../06-Software-Support/pmodules.md) chapter.
+ For further information about **PModules** on Merlin7 please refer to the [PSI Modules](../07-software-support/pmodules.md) chapter.
### Spack Modules
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**.
!!! tip
- For further information about **Spack** on Merlin7 please refer to the [Spack](../06-Software-Support/spack.md) chapter.
+ For further information about **Spack** on Merlin7 please refer to the [Spack](../07-software-support/spack.md) chapter.
### Cray Environment Modules
@@ -37,5 +37,5 @@ Recommendations:
* **General Use:** For most applications, prefer PModules, which ensure stability, backward compatibility, and long-term support.
!!! tip
- For further information about **CPE** on Merlin7 please refer to the [Cray Modules](../06-Software-Support/cray-module.env.md) chapter.
+ For further information about **CPE** on Merlin7 please refer to the [Cray Modules](../07-software-support/cray-module.env.md) chapter.
diff --git a/docs/merlin7/02-How-To-Use-Merlin/storage.md b/docs/merlin7/03-how-to-use-merlin/storage.md
similarity index 96%
rename from docs/merlin7/02-How-To-Use-Merlin/storage.md
rename to docs/merlin7/03-how-to-use-merlin/storage.md
index 8602830..19916a7 100644
--- a/docs/merlin7/02-How-To-Use-Merlin/storage.md
+++ b/docs/merlin7/03-how-to-use-merlin/storage.md
@@ -103,12 +103,12 @@ The home directories are mounted in the login and computing nodes under the dire
Directory policies:
-* 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!
+* 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](#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](storage.md#how-to-check-quotas).
+[above](#how-to-check-quotas).
### Project data directory
@@ -117,7 +117,7 @@ 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]](../01-Quick-Start-Guide/requesting-projects.md)**.
+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 @@ lfs quota -h -p $projectid /data
Directory policies:
-* Read **[Important: Code of Conduct](../01-Quick-Start-Guide/code-of-conduct.md)** 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.
@@ -178,7 +178,7 @@ and all tasks need to do I/O on the same temporary files.
Scratch directories policies:
-* Read **[Important: Code of Conduct](../01-Quick-Start-Guide/code-of-conduct.md)** 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.
* By default, *always* use **local** first and only use **shared** if your specific use case requires it.
* Temporary files *must be deleted at the end of the job by the user*.
* Remaining files will be deleted by the system if detected.
diff --git a/docs/merlin7/02-How-To-Use-Merlin/transfer-data.md b/docs/merlin7/03-how-to-use-merlin/transfer-data.md
similarity index 99%
rename from docs/merlin7/02-How-To-Use-Merlin/transfer-data.md
rename to docs/merlin7/03-how-to-use-merlin/transfer-data.md
index 17f4899..228b5d3 100644
--- a/docs/merlin7/02-How-To-Use-Merlin/transfer-data.md
+++ b/docs/merlin7/03-how-to-use-merlin/transfer-data.md
@@ -34,7 +34,7 @@ The next chapters contain detailed information about the different transfer meth
## Transferring from within PSI
-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**.
+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**.
### Secure FTP
@@ -121,7 +121,7 @@ Merlin7 is fully accessible from within the PSI network. To connect from outside
* [VPN](https://www.psi.ch/en/computing/vpn) ([alternate instructions](https://intranet.psi.ch/BIO/ComputingVPN))
* [SSH hopx](https://www.psi.ch/en/computing/ssh-hop)
* Please avoid transferring big amount data through **hop**
-* [No Machine](nomachine.md)
+* [No Machine](../02-connecting-to-merlin/nomachine.md)
* Remote Interactive Access through [**'nx.psi.ch'**](https://www.psi.ch/en/photon-science-data-services/remote-interactive-access)
* Please avoid transferring big amount of data through **NoMachine**
diff --git a/docs/merlin7/03-Slurm-General-Documentation/interactive-jobs.md b/docs/merlin7/04-slurm-general-documentation/interactive-jobs.md
similarity index 94%
rename from docs/merlin7/03-Slurm-General-Documentation/interactive-jobs.md
rename to docs/merlin7/04-slurm-general-documentation/interactive-jobs.md
index 698ae75..8b4a168 100644
--- a/docs/merlin7/03-Slurm-General-Documentation/interactive-jobs.md
+++ b/docs/merlin7/04-slurm-general-documentation/interactive-jobs.md
@@ -111,16 +111,16 @@ salloc: Relinquishing job allocation 165
#### Graphical access
-[NoMachine](../02-How-To-Use-Merlin/nomachine.md) is the official supported service for graphical
+[NoMachine](../02-connecting-to-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}](../02-How-To-Use-Merlin/nomachine.md) for details about
+document [{Accessing Merlin -> NoMachine}](../02-connecting-to-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}](../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)
+* For Linux clients, please follow [{How To Use Merlin -> Accessing from Linux Clients}](../02-connecting-to-merlin/connect-from-linux.md)
+* For Windows clients, please follow [{How To Use Merlin -> Accessing from Windows Clients}](../02-connecting-to-merlin/connect-from-windows.md)
+* For MacOS clients, please follow [{How To Use Merlin -> Accessing from MacOS Clients}](../02-connecting-to-merlin/connect-from-macos.md)
### 'srun' with x11 support
diff --git a/docs/merlin7/03-Slurm-General-Documentation/interactive-sessions.md b/docs/merlin7/04-slurm-general-documentation/interactive-sessions.md
similarity index 100%
rename from docs/merlin7/03-Slurm-General-Documentation/interactive-sessions.md
rename to docs/merlin7/04-slurm-general-documentation/interactive-sessions.md
diff --git a/docs/merlin7/03-Slurm-General-Documentation/merlin7-configuration.md b/docs/merlin7/04-slurm-general-documentation/merlin7-configuration.md
similarity index 100%
rename from docs/merlin7/03-Slurm-General-Documentation/merlin7-configuration.md
rename to docs/merlin7/04-slurm-general-documentation/merlin7-configuration.md
diff --git a/docs/merlin7/03-Slurm-General-Documentation/slurm-configuration.md b/docs/merlin7/04-slurm-general-documentation/slurm-configuration.md
similarity index 100%
rename from docs/merlin7/03-Slurm-General-Documentation/slurm-configuration.md
rename to docs/merlin7/04-slurm-general-documentation/slurm-configuration.md
diff --git a/docs/merlin7/03-Slurm-General-Documentation/slurm-examples.md b/docs/merlin7/04-slurm-general-documentation/slurm-examples.md
similarity index 100%
rename from docs/merlin7/03-Slurm-General-Documentation/slurm-examples.md
rename to docs/merlin7/04-slurm-general-documentation/slurm-examples.md
diff --git a/docs/merlin7/03-Slurm-General-Documentation/slurm-mail.md b/docs/merlin7/04-slurm-general-documentation/slurm-mail.md
similarity index 100%
rename from docs/merlin7/03-Slurm-General-Documentation/slurm-mail.md
rename to docs/merlin7/04-slurm-general-documentation/slurm-mail.md
diff --git a/docs/merlin7/04-Jupyterhub/jupyterhub.md b/docs/merlin7/05-jupyterhub/jupyterhub.md
similarity index 97%
rename from docs/merlin7/04-Jupyterhub/jupyterhub.md
rename to docs/merlin7/05-jupyterhub/jupyterhub.md
index 301fd0f..1a19a0c 100644
--- a/docs/merlin7/04-Jupyterhub/jupyterhub.md
+++ b/docs/merlin7/05-jupyterhub/jupyterhub.md
@@ -34,7 +34,7 @@ queue. Additional customization can be implemented using the *'Optional user
defined line to be added to the batch launcher script'* option. This line is
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
-Scripts](../03-Slurm-General-Documentation/slurm-examples.md). Some ideas:
+Scripts](../04-slurm-general-documentation/slurm-examples.md). Some ideas:
**Request additional memory**
diff --git a/docs/merlin7/05-Open-OnDemand/open-ondemand.md b/docs/merlin7/06-open-ondemand/open-ondemand.md
similarity index 99%
rename from docs/merlin7/05-Open-OnDemand/open-ondemand.md
rename to docs/merlin7/06-open-ondemand/open-ondemand.md
index 4629e99..cdd9e25 100644
--- a/docs/merlin7/05-Open-OnDemand/open-ondemand.md
+++ b/docs/merlin7/06-open-ondemand/open-ondemand.md
@@ -1,4 +1,5 @@
-# ondemand.psi.ch
+# Open OnDemand @ PSI
+
[Open OnDemand](https://www.openondemand.org/) is an open-source, web-based portal that allows researchers, students, and engineers to access High-Performance Computing (HPC) resources from any device using a web browser.
!!! warning "Open OnDemand is currently in preview"
@@ -17,6 +18,7 @@
see the [official Open OnDemand documentation](https://osc.github.io/ood-documentation/latest/install-ihpc-apps.html)
## Accessing Open OnDemand
+
**Open Ondemand** can be accessed from your browser at .
!!! tip "Recommended browser"
diff --git a/docs/merlin7/07-software-support/ansys-cfx.md b/docs/merlin7/07-software-support/ansys-cfx.md
new file mode 100644
index 0000000..64a67a8
--- /dev/null
+++ b/docs/merlin7/07-software-support/ansys-cfx.md
@@ -0,0 +1,144 @@
+# ANSYS - CFX
+
+!!! tip
+ It is recommended to check which parameters are available in CFX and adapt
+ the below examples according to your needs. For that, run `cfx5solve
+ -help` to get a list of options.
+
+## Running CFX jobs
+
+### PModules
+
+We strongly recommend that you use the latest version of ANSYS software available in PModules.
+
+```bash
+module use unstable
+module load Pmodules/2.0.4
+module use merlin
+module load ANSYS/2022R1
+```
+
+### Interactive: RSM from remote PSI Workstations
+
+It is possible to run CFX through RSM from remote PSI (Linux or Windows)
+Workstation having a local installation of ANSYS CFX and RSM client. For that,
+please refer to the **[ANSYS RSM](ansys-rsm.md)** documentation
+for further information of how to setup a RSM client for submitting jobs to
+Merlin.
+
+### Non-interactive: sbatch
+
+Running jobs with `sbatch` is always the recommended method. This makes the use
+of the resources more efficient. Notice that for running non interactive
+Mechanical APDL jobs one must specify the `-batch` option.
+
+#### Serial example
+
+This example shows a very basic serial job.
+
+```bash
+#!/bin/bash
+#SBATCH --job-name=CFX # Job Name
+#SBATCH --partition=hourly # Using 'daily' will grant higher priority than 'general'
+#SBATCH --time=0-01:00:00 # Time needed for running the job. Must match with 'partition' limits.
+#SBATCH --cpus-per-task=1 # Double if hyperthreading enabled
+#SBATCH --ntasks-per-core=1 # Double if hyperthreading enabled
+#SBATCH --hint=nomultithread # Disable Hyperthreading
+#SBATCH --error=slurm-%j.err # Define your error file
+
+module use unstable
+module load ANSYS/2020R1-1
+
+# [Optional:BEGIN] Specify your license server if this is not 'lic-ansys.psi.ch'
+LICENSE_SERVER=
+export ANSYSLMD_LICENSE_FILE=1055@$LICENSE_SERVER
+export ANSYSLI_SERVERS=2325@$LICENSE_SERVER
+# [Optional:END]
+
+SOLVER_FILE=/data/user/caubet_m/CFX5/mysolver.in
+cfx5solve -batch -def "$JOURNAL_FILE"
+```
+
+One can enable hypertheading by defining `--hint=multithread`,
+`--cpus-per-task=2` and `--ntasks-per-core=2`. However, this is in general not
+recommended, unless one can ensure that can be beneficial.
+
+#### MPI-based example
+
+An example for running CFX using a Slurm batch script is the following:
+
+```bash
+#!/bin/bash
+#SBATCH --job-name=CFX # Job Name
+#SBATCH --partition=hourly # Using 'daily' will grant higher priority than 'general'
+#SBATCH --time=0-01:00:00 # Time needed for running the job. Must match with 'partition' limits.
+#SBATCH --nodes=1 # Number of nodes
+#SBATCH --ntasks=44 # Number of tasks
+#SBATCH --cpus-per-task=1 # Double if hyperthreading enabled
+#SBATCH --ntasks-per-core=1 # Double if hyperthreading enabled
+#SBATCH --hint=nomultithread # Disable Hyperthreading
+#SBATCH --error=slurm-%j.err # Define a file for standard error messages
+##SBATCH --exclusive # Uncomment if you want exclusive usage of the nodes
+
+module use unstable
+module load ANSYS/2020R1-1
+
+# [Optional:BEGIN] Specify your license server if this is not 'lic-ansys.psi.ch'
+LICENSE_SERVER=
+export ANSYSLMD_LICENSE_FILE=1055@$LICENSE_SERVER
+export ANSYSLI_SERVERS=2325@$LICENSE_SERVER
+# [Optional:END]
+
+export HOSTLIST=$(scontrol show hostname | tr '\n' ',' | sed 's/,$//g')
+
+JOURNAL_FILE=myjournal.in
+
+# INTELMPI=no for IBM MPI
+# INTELMPI=yes for INTEL MPI
+INTELMPI=no
+
+if [ "$INTELMPI" == "yes" ]
+then
+ export I_MPI_DEBUG=4
+ export I_MPI_PIN_CELL=core
+
+ # Simple example: cfx5solve -batch -def "$JOURNAL_FILE" -par-dist "$HOSTLIST" \
+ # -part $SLURM_NTASKS \
+ # -start-method 'Intel MPI Distributed Parallel'
+ cfx5solve -batch -part-large -double -verbose -def "$JOURNAL_FILE" -par-dist "$HOSTLIST" \
+ -part $SLURM_NTASKS -par-local -start-method 'Intel MPI Distributed Parallel'
+else
+ # Simple example: cfx5solve -batch -def "$JOURNAL_FILE" -par-dist "$HOSTLIST" \
+ # -part $SLURM_NTASKS \
+ # -start-method 'IBM MPI Distributed Parallel'
+ cfx5solve -batch -part-large -double -verbose -def "$JOURNAL_FILE" -par-dist "$HOSTLIST" \
+ -part $SLURM_NTASKS -par-local -start-method 'IBM MPI Distributed Parallel'
+fi
+```
+
+In the above example, one can increase the number of *nodes* and/or *ntasks* if needed and combine it
+with `--exclusive` whenever needed. In general, **no hypertheading** is recommended for MPI based jobs.
+
+Also, one can combine it with `--exclusive` when necessary. Finally, one can change the MPI technology in `-start-method`
+(check CFX documentation for possible values).
+
+## CFX5 Launcher: CFD-Pre/Post, Solve Manager, TurboGrid
+
+Some users might need to visualize or change some parameters when running calculations with the CFX Solver. For running
+**TurboGrid**, **CFX-Pre**, **CFX-Solver Manager** or **CFD-Post** one should run it with the **`cfx5` launcher** binary:
+
+```bash
+cfx5
+```
+
+
+/// caption
+///
+
+Then, from the launcher, one can open the proper application (i.e. **CFX-Solver
+Manager** for visualizing and modifying an existing job run)
+
+For running CFX5 Launcher, is required a proper SSH + X11 Forwarding access
+(`ssh -XY`) or *preferrible* **NoMachine**. If **ssh** does not work for you,
+please use **NoMachine** instead (which is the supported X based access, and
+simpler).
diff --git a/docs/merlin7/07-software-support/ansys-fluent.md b/docs/merlin7/07-software-support/ansys-fluent.md
new file mode 100644
index 0000000..c72e62b
--- /dev/null
+++ b/docs/merlin7/07-software-support/ansys-fluent.md
@@ -0,0 +1,167 @@
+# ANSYS - Fluent
+
+Is always recommended to check which parameters are available in Fluent and adapt the below example according to your needs.
+For that, run `fluent -help` for getting a list of options. However, as when running Fluent one must specify one of the
+following flags:
+
+* **2d**: This is a 2D solver with single point precision.
+* **3d**: This is a 3D solver with single point precision.
+* **2dpp**: This is a 2D solver with double point precision.
+* **3dpp**: This is a 3D solver with double point precision.
+
+## Running Fluent jobs
+
+### PModules
+
+Is strongly recommended the use of the latest ANSYS software available in PModules.
+
+```bash
+module use unstable
+module load Pmodules/2.0.4
+module use merlin
+module load ANSYS/2024R2
+```
+
+### Interactive: RSM from remote PSI Workstations
+
+Is possible to run Fluent through RSM from remote PSI (Linux or Windows)
+Workstation having a local installation of ANSYS Fluent and RSM client. For
+that, please refer to the [ANSYS RSM](ansys-rsm.md) in the Merlin
+documentation for further information of how to setup a RSM client for
+submitting jobs to Merlin.
+
+### Non-interactive: sbatch
+
+Running jobs with `sbatch` is always the recommended method. This makes the use
+of the resources more efficient. For running it as a job, one needs to run in
+no graphical mode (`-g` option).
+
+#### Serial example
+
+This example shows a very basic serial job.
+
+```bash
+#!/bin/bash
+#SBATCH --job-name=Fluent # Job Name
+#SBATCH --partition=hourly # Using 'daily' will grant higher priority than 'general'
+#SBATCH --time=0-01:00:00 # Time needed for running the job. Must match with 'partition' limits.
+#SBATCH --cpus-per-task=1 # Double if hyperthreading enabled
+#SBATCH --hint=nomultithread # Disable Hyperthreading
+#SBATCH --error=slurm-%j.err # Define your error file
+
+module use unstable
+module load Pmodules/2.0.4
+module use merlin
+module load ANSYS/2024R2
+
+# [Optional:BEGIN] Specify your license server if this is not 'lic-ansys.psi.ch'
+LICENSE_SERVER=
+export ANSYSLMD_LICENSE_FILE=1055@$LICENSE_SERVER
+export ANSYSLI_SERVERS=2325@$LICENSE_SERVER
+# [Optional:END]
+
+JOURNAL_FILE=/data/user/caubet_m/Fluent/myjournal.in
+fluent 3ddp -g -i ${JOURNAL_FILE}
+```
+
+One can enable hypertheading by defining `--hint=multithread`, `--cpus-per-task=2` and `--ntasks-per-core=2`.
+However, this is in general not recommended, unless one can ensure that can be beneficial.
+
+#### MPI-based example
+
+An example for running Fluent using a Slurm batch script is the following:
+
+```bash
+#!/bin/bash
+#SBATCH --job-name=Fluent # Job Name
+#SBATCH --partition=hourly # Using 'daily' will grant higher priority than 'general'
+#SBATCH --time=0-01:00:00 # Time needed for running the job. Must match with 'partition' limits.
+#SBATCH --nodes=1 # Number of nodes
+#SBATCH --ntasks=44 # Number of tasks
+#SBATCH --cpus-per-task=1 # Double if hyperthreading enabled
+#SBATCH --ntasks-per-core=1 # Run one task per core
+#SBATCH --hint=nomultithread # Disable Hyperthreading
+#SBATCH --error=slurm-%j.err # Define a file for standard error messages
+##SBATCH --exclusive # Uncomment if you want exclusive usage of the nodes
+
+module use unstable
+module load Pmodules/2.0.4
+module use merlin
+module load ANSYS/2024R2
+
+# [Optional:BEGIN] Specify your license server if this is not 'lic-ansys.psi.ch'
+LICENSE_SERVER=
+export ANSYSLMD_LICENSE_FILE=1055@$LICENSE_SERVER
+export ANSYSLI_SERVERS=2325@$LICENSE_SERVER
+# [Optional:END]
+
+JOURNAL_FILE=/data/user/caubet_m/Fluent/myjournal.in
+fluent 3ddp -g -t ${SLURM_NTASKS} -i ${JOURNAL_FILE}
+```
+
+In the above example, one can increase the number of *nodes* and/or *ntasks* if needed. One can remove
+`--nodes` for running on multiple nodes, but may lead to communication overhead. In general, **no
+hyperthreading** is recommended for MPI based jobs. Also, one can combine it with `--exclusive` when necessary.
+
+## Interactive: salloc
+
+Running Fluent interactively is strongly not recommended and one should
+whenever possible use `sbatch`. However, sometimes interactive runs are
+needed. For jobs requiring only few CPUs (in example, 2 CPUs) **and** for a
+short period of time, one can use the login nodes. Otherwise, one must use the
+Slurm batch system using allocations:
+
+* For short jobs requiring more CPUs, one can use the Merlin shortest partitions (`hourly`).
+* For longer jobs, one can use longer partitions, however, interactive access
+ is not always possible (depending on the usage of the cluster).
+
+Please refer to the documentation **[Running Interactive
+Jobs](../04-slurm-general-documentation/interactive-jobs.md)** for firther information about different
+ways for running interactive jobs in the Merlin6 cluster.
+
+### Requirements
+
+#### SSH Keys
+
+Running Fluent interactively requires the use of SSH Keys. This is the way of
+communication between the GUI and the different nodes. For doing that, one must
+have a **passphrase protected** SSH Key. If the user does not have SSH Keys yet
+(simply run **`ls $HOME/.ssh/`** to check whether **`id_rsa`** files exist or
+not). For deploying SSH Keys for running Fluent interactively, one should
+follow this documentation: **[Configuring SSH Keys](../02-connecting-to-merlin/ssh-keys.md)**
+
+#### List of hosts
+
+For running Fluent using Slurm computing nodes, one needs to get the list of
+the reserved nodes. For getting that list, once you have the allocation, one
+can run the following command:
+
+```bash
+scontrol show hostname
+```
+
+This list must be included in the settings as the list of hosts where to run
+Fluent. Alternatively, one can give that list as parameter (`-cnf` option) when
+running `fluent`, as follows:
+
+??? example "Running Fluent with 'salloc'"
+ ```console
+ $ salloc --nodes=2 --ntasks=88 --hint=nomultithread --time=0-01:00:00 --partition=test $SHELL
+ salloc: Pending job allocation 135030174
+ salloc: job 135030174 queued and waiting for resources
+ salloc: job 135030174 has been allocated resources
+ salloc: Granted job allocation 135030174
+
+ $ module use unstable
+ $ module load Pmodules/2.0.4
+ $ module use merlin
+ $ module load ANSYS/2024R2
+ module load: unstable module has been loaded -- ANSYS/2024R2
+
+ $ fluent 3ddp -t$SLURM_NPROCS -cnf=$(scontrol show hostname | tr '\n' ',')
+
+ $ exit
+ exit
+ salloc: Relinquishing job allocation 135030174
+ salloc: Job allocation 135030174 has been revoked.
+ ```
diff --git a/docs/merlin7/07-software-support/ansys-hfss.md b/docs/merlin7/07-software-support/ansys-hfss.md
new file mode 100644
index 0000000..3e637a4
--- /dev/null
+++ b/docs/merlin7/07-software-support/ansys-hfss.md
@@ -0,0 +1,133 @@
+# ANSYS HFSS (ElectroMagnetics)
+
+This recipe is intended to show how to run ANSYS HFSS (ElectroMagnetics) in Slurm.
+Having in mind that in general, running ANSYS HFSS means running **ANSYS Electronics Desktop**.
+
+## Running HFSS / Electromagnetics jobs
+
+### PModules
+
+Is necessary to run at least ANSYS software **ANSYS/2022R1**, which is available in PModules:
+
+```bash
+module use unstable
+module load Pmodules/2.0.4
+module use merlin
+module load ANSYS/2024R2
+```
+
+## Remote job submission: HFSS RSM and SLURM
+
+Running jobs through Remote RSM or Slurm is the recommended way for running ANSYS HFSS.
+
+* **HFSS RSM** can be used from ANSYS HFSS installations running on Windows workstations at PSI (as long as are in the internal PSI network).
+* **Slurm** can be used when submitting directly from a Merlin login node (i.e. `sbatch` command or interactively from **ANSYS Electronics Desktop**)
+
+### HFSS RSM (from remote workstations)
+
+Running jobs through Remote RSM is the way for running ANSYS HFSS when submitting from an ANSYS HFSS installation on a PSI Windows workstation.
+A HFSS RSM service is running on each **Merlin login node**, and the listening port depends on the ANSYS EM version. Current support ANSYS EM RSM
+release and associated listening ports are the following:
+
+
+
+
+ | ANSYS version |
+ Login nodes |
+ Listening port |
+
+
+
+
+ | 2022R1 |
+ merlin-l-001 merlin-l-001 merlin-l-001 |
+ 32958 |
+
+
+ | 2022R2 |
+ merlin-l-001 merlin-l-001 merlin-l-001 |
+ 32959 |
+
+
+ | 2023R2 |
+ merlin-l-001 merlin-l-001 merlin-l-001 |
+ 32960 |
+
+
+
+
+Notice that by default ANSYS EM is listening on port **`32958`**, this is the default for **ANSYS/2022R1** only.
+
+* Workstations connecting to the Merlin ANSYS EM service must ensure that **Electronics Desktop** is connecting to the proper port.
+* In the same way, the ANSYS Workstation version must be the same as the version running on Merlin.
+
+Notice that *HFSS RSM is not the same RSM provided for other ANSYS products*.
+Therefore, the configuration is different from [ANSYS
+RSM](ansys-rsm.md).
+
+To setup HFSS RSM for using it with the Merlin cluster, it must be done from the following **ANSYS Electronics Desktop** menu:
+
+1. **[Tools]->[Job Management]->[Select Scheduler]**:
+
+ 
+
+2. In the new **[Select scheduler]** window, setup the following settings and **Refresh**:
+
+ 
+
+ * **Select Scheduler**: `Remote RSM`.
+ * **Server**: Add a Merlin login node.
+ * **User name**: Add your Merlin username.
+ * **Password**: Add you Merlin username password.
+
+ Once *refreshed*, the **Scheduler info** box must provide **Slurm**
+ information of the server (see above picture). If the box contains that
+ information, then you can save changes (`OK` button).
+
+3. **[Tools]->[Job Management]->[Submit Job...]**:
+
+ 
+
+4. In the new **[Submite Job]** window, you must specify the location of the **ANSYS Electronics Desktop** binary:
+
+ 
+
+ * In example, for **ANSYS/2022R1**, the location is `/data/software/pmodules/Tools/ANSYS/2021R1/v211/AnsysEM21.1/Linux64/ansysedt.exe`.
+
+### HFSS Slurm (from login node only)
+
+Running jobs through Slurm from **ANSYS Electronics Desktop** is the way for
+running ANSYS HFSS when submitting from an ANSYS HFSS installation in a Merlin
+login node. **ANSYS Electronics Desktop** usually needs to be run from the
+**[Merlin NoMachine](../02-connecting-to-merlin/nomachine.md)** service, which currently runs
+on:
+
+* `merlin-l-001.psi.ch`
+* `merlin-l-002.psi.ch`
+
+Since the Slurm client is present in the login node (where **ANSYS Electronics
+Desktop** is running), the application will be able to detect and to submit
+directly to Slurm. Therefore, we only have to configure **ANSYS Electronics
+Desktop** to submit to Slurm. This can set as follows:
+
+1. **[Tools]->[Job Management]->[Select Scheduler]**:
+
+ 
+
+2. In the new **[Select scheduler]** window, setup the following settings and **Refresh**:
+
+ 
+
+ * **Select Scheduler**: `Slurm`.
+ * **Server**: must point to `localhost`.
+ * **User name**: must be empty.
+ * **Password**: must be empty.
+
+ The **Server, User name** and **Password** boxes can't be modified, but if
+ value do not match with the above settings, they should be changed by
+ selecting another Scheduler which allows editig these boxes (i.e. **RSM
+ Remote**).
+
+ Once *refreshed*, the **Scheduler info** box must provide **Slurm**
+ information of the server (see above picture). If the box contains that
+ information, then you can save changes (`OK` button).
diff --git a/docs/merlin7/07-software-support/ansys-mapdl.md b/docs/merlin7/07-software-support/ansys-mapdl.md
new file mode 100644
index 0000000..93f00c8
--- /dev/null
+++ b/docs/merlin7/07-software-support/ansys-mapdl.md
@@ -0,0 +1,164 @@
+# ANSYS - MAPDL
+
+# ANSYS - Mechanical APDL
+
+Is always recommended to check which parameters are available in Mechanical APDL and adapt the below examples according to your needs.
+For that, please refer to the official Mechanical APDL documentation.
+
+## Running Mechanical APDL jobs
+
+### PModules
+
+Is strongly recommended the use of the latest ANSYS software available in PModules.
+
+```bash
+module use unstable
+module load Pmodules/2.0.4
+module use merlin
+module load ANSYS/2024R2
+```
+
+### Interactive: RSM from remote PSI Workstations
+
+Is possible to run Mechanical through RSM from remote PSI (Linux or Windows)
+Workstation having a local installation of ANSYS Mechanical and RSM client.
+For that, please refer to the ***[ANSYS RSM](ansys-rsm.md)*** in the Merlin
+documentation for further information of how to setup a RSM client for
+submitting jobs to Merlin.
+
+### Non-interactive: sbatch
+
+Running jobs with `sbatch` is always the recommended method. This makes the use
+of the resources more efficient. Notice that for running non interactive
+Mechanical APDL jobs one must specify the `-b` option.
+
+#### Serial example
+
+This example shows a very basic serial job.
+
+```bash
+#!/bin/bash
+#SBATCH --job-name=MAPDL # Job Name
+#SBATCH --partition=hourly # Using 'daily' will grant higher priority than 'general'
+#SBATCH --time=0-01:00:00 # Time needed for running the job. Must match with 'partition' limits.
+#SBATCH --cpus-per-task=1 # Double if hyperthreading enabled
+#SBATCH --ntasks-per-core=1 # Double if hyperthreading enabled
+#SBATCH --hint=nomultithread # Disable Hyperthreading
+#SBATCH --error=slurm-%j.err # Define your error file
+
+module use unstable
+module load Pmodules/2.0.4
+module use merlin
+module load ANSYS/2024R2
+
+# [Optional:BEGIN] Specify your license server if this is not 'lic-ansys.psi.ch'
+LICENSE_SERVER=
+export ANSYSLMD_LICENSE_FILE=1055@$LICENSE_SERVER
+export ANSYSLI_SERVERS=2325@$LICENSE_SERVER
+# [Optional:END]
+
+SOLVER_FILE=/data/user/caubet_m/MAPDL/mysolver.in
+mapdl -b -i "$SOLVER_FILE"
+```
+
+One can enable hypertheading by defining `--hint=multithread`,
+`--cpus-per-task=2` and `--ntasks-per-core=2`. However, this is in general not
+recommended, unless one can ensure that can be beneficial.
+
+#### SMP-based example
+
+This example shows how to running Mechanical APDL in Shared-Memory Parallelism
+mode. It limits the use to 1 single node, but by using many cores. In the
+example below, we use a node by using all his cores and the whole memory.
+
+```bash
+#!/bin/bash
+#SBATCH --job-name=MAPDL # Job Name
+#SBATCH --partition=hourly # Using 'daily' will grant higher priority than 'general'
+#SBATCH --time=0-01:00:00 # Time needed for running the job. Must match with 'partition' limits.
+#SBATCH --nodes=1 # Number of nodes
+#SBATCH --ntasks=1 # Number of tasks
+#SBATCH --cpus-per-task=44 # Double if hyperthreading enabled
+#SBATCH --hint=nomultithread # Disable Hyperthreading
+#SBATCH --error=slurm-%j.err # Define a file for standard error messages
+#SBATCH --exclusive # Uncomment if you want exclusive usage of the nodes
+
+module use unstable
+module load Pmodules/2.0.4
+module use merlin
+module load ANSYS/2024R2
+
+# [Optional:BEGIN] Specify your license server if this is not 'lic-ansys.psi.ch'
+LICENSE_SERVER=
+export ANSYSLMD_LICENSE_FILE=1055@$LICENSE_SERVER
+export ANSYSLI_SERVERS=2325@$LICENSE_SERVER
+# [Optional:END]
+
+SOLVER_FILE=/data/user/caubet_m/MAPDL/mysolver.in
+mapdl -b -np ${SLURM_CPUS_PER_TASK} -i "$SOLVER_FILE"
+```
+
+In the above example, one can reduce the number of **cpus per task**. Here
+usually `--exclusive` is recommended if one needs to use the whole memory.
+
+For **SMP** runs, one might try the hyperthreading mode by doubling the proper
+settings (`--cpus-per-task`), in some cases it might be beneficial.
+
+Please notice that `--ntasks-per-core=1` is not defined here, this is because
+we want to run 1 task on many cores! As an alternative, one can explore
+`--ntasks-per-socket` or `--ntasks-per-node` for fine grained configurations.
+
+#### MPI-based example
+
+This example enables Distributed ANSYS for running Mechanical APDL using a Slurm batch script.
+
+```bash
+#!/bin/bash
+#SBATCH --job-name=MAPDL # Job Name
+#SBATCH --partition=hourly # Using 'daily' will grant higher priority than 'general'
+#SBATCH --time=0-01:00:00 # Time needed for running the job. Must match with 'partition' limits.
+#SBATCH --nodes=1 # Number of nodes
+#SBATCH --ntasks=44 # Number of tasks
+#SBATCH --cpus-per-task=1 # Double if hyperthreading enabled
+#SBATCH --ntasks-per-core=1 # Run one task per core
+#SBATCH --hint=nomultithread # Disable Hyperthreading
+#SBATCH --error=slurm-%j.err # Define a file for standard error messages
+##SBATCH --exclusive # Uncomment if you want exclusive usage of the nodes
+
+module use unstable
+module load Pmodules/2.0.4
+module use merlin
+module load ANSYS/2024R2
+
+# [Optional:BEGIN] Specify your license server if this is not 'lic-ansys.psi.ch'
+LICENSE_SERVER=
+export ANSYSLMD_LICENSE_FILE=1055@$LICENSE_SERVER
+export ANSYSLI_SERVERS=2325@$LICENSE_SERVER
+# [Optional:END]
+
+SOLVER_FILE=input.dat
+
+# INTELMPI=no for IBM MPI
+# INTELMPI=yes for INTEL MPI
+INTELMPI=no
+
+if [ "$INTELMPI" == "yes" ]
+then
+ # When using -mpi=intelmpi, KMP Affinity must be disabled
+ export KMP_AFFINITY=disabled
+
+ # INTELMPI is not aware about distribution of tasks.
+ # - We need to define tasks distribution.
+ HOSTLIST=$(srun hostname | sort | uniq -c | awk '{print $2 ":" $1}' | tr '\n' ':' | sed 's/:$/\n/g')
+ mapdl -b -dis -mpi intelmpi -machines $HOSTLIST -np ${SLURM_NTASKS} -i "$SOLVER_FILE"
+else
+ # IBMMPI (default) will be aware of the distribution of tasks.
+ # - In principle, no need to force tasks distribution
+ mapdl -b -dis -mpi ibmmpi -np ${SLURM_NTASKS} -i "$SOLVER_FILE"
+fi
+```
+
+In the above example, one can increase the number of *nodes* and/or *ntasks* if
+needed and combine it with `--exclusive` when necessary. In general, **no
+hypertheading** is recommended for MPI based jobs. Also, one can combine it
+with `--exclusive` when necessary.
diff --git a/docs/merlin7/06-Software-Support/ansys-rsm.md b/docs/merlin7/07-software-support/ansys-rsm.md
similarity index 100%
rename from docs/merlin7/06-Software-Support/ansys-rsm.md
rename to docs/merlin7/07-software-support/ansys-rsm.md
diff --git a/docs/merlin7/06-Software-Support/ansys.md b/docs/merlin7/07-software-support/ansys.md
similarity index 100%
rename from docs/merlin7/06-Software-Support/ansys.md
rename to docs/merlin7/07-software-support/ansys.md
diff --git a/docs/merlin7/06-Software-Support/cp2k.md b/docs/merlin7/07-software-support/cp2k.md
similarity index 100%
rename from docs/merlin7/06-Software-Support/cp2k.md
rename to docs/merlin7/07-software-support/cp2k.md
diff --git a/docs/merlin7/06-Software-Support/cray-module.env.md b/docs/merlin7/07-software-support/cray-module.env.md
similarity index 100%
rename from docs/merlin7/06-Software-Support/cray-module.env.md
rename to docs/merlin7/07-software-support/cray-module.env.md
diff --git a/docs/merlin7/06-Software-Support/dirac.md b/docs/merlin7/07-software-support/dirac.md
similarity index 100%
rename from docs/merlin7/06-Software-Support/dirac.md
rename to docs/merlin7/07-software-support/dirac.md
diff --git a/docs/merlin7/06-Software-Support/gromacs.md b/docs/merlin7/07-software-support/gromacs.md
similarity index 100%
rename from docs/merlin7/06-Software-Support/gromacs.md
rename to docs/merlin7/07-software-support/gromacs.md
diff --git a/docs/merlin7/06-Software-Support/includes/open-ondemand-alternative.md b/docs/merlin7/07-software-support/includes/open-ondemand-alternative.md
similarity index 88%
rename from docs/merlin7/06-Software-Support/includes/open-ondemand-alternative.md
rename to docs/merlin7/07-software-support/includes/open-ondemand-alternative.md
index 5a17d59..1fa9820 100644
--- a/docs/merlin7/06-Software-Support/includes/open-ondemand-alternative.md
+++ b/docs/merlin7/07-software-support/includes/open-ondemand-alternative.md
@@ -1,11 +1,11 @@
-As an alternative to creating an `interactive` session with or without X11 forwarding, you can also use [Open OnDemand on Merlin7](../../05-Open-OnDemand/open-ondemand.md).
+As an alternative to creating an `interactive` session with or without X11 forwarding, you can also use [Open OnDemand on Merlin7](../../06-open-ondemand/open-ondemand.md).
[Open OnDemand](https://www.openondemand.org/) provides web-based access to HPC resources and can be used to start graphical applications such as **VS Code** or **MATLAB** directly from a browser. Sometimes, this can be more convenient than setting up local SSH configuration, X11 forwarding, or VS Code Remote SSH manually.
!!! tip
- If you mainly need a graphical VS Code or MATLAB session, [Open OnDemand on Merlin7](../../05-Open-OnDemand/open-ondemand.md) is often the easiest option.
+ If you mainly need a graphical VS Code or MATLAB session, [Open OnDemand on Merlin7](../../06-open-ondemand/open-ondemand.md) is often the easiest option.
!!! warning
The same login-node rule still applies: **do not run heavy interactive applications directly on login nodes.**
diff --git a/docs/merlin7/06-Software-Support/ippl.md b/docs/merlin7/07-software-support/ippl.md
similarity index 100%
rename from docs/merlin7/06-Software-Support/ippl.md
rename to docs/merlin7/07-software-support/ippl.md
diff --git a/docs/merlin7/06-Software-Support/lammps.md b/docs/merlin7/07-software-support/lammps.md
similarity index 100%
rename from docs/merlin7/06-Software-Support/lammps.md
rename to docs/merlin7/07-software-support/lammps.md
diff --git a/docs/merlin7/06-Software-Support/matlab.md b/docs/merlin7/07-software-support/matlab.md
similarity index 92%
rename from docs/merlin7/06-Software-Support/matlab.md
rename to docs/merlin7/07-software-support/matlab.md
index 086dabc..a1790a9 100644
--- a/docs/merlin7/06-Software-Support/matlab.md
+++ b/docs/merlin7/07-software-support/matlab.md
@@ -3,14 +3,17 @@
## Best practices when running MATLAB
* Use `matlab -batch` for non-interactive production jobs. It is cleaner and better suited for batch execution than starting the full GUI.
-* Prefer `-nodesktop -nosplash` for interactive terminal-based sessions on compute nodes in case of Slurm allocations (e.g. `salloc` or [interactive Slurm sessions](../03-Slurm-General-Documentation/interactive-sessions.md).
+* Prefer `-nodesktop -nosplash` for interactive terminal-based sessions on compute nodes in case of Slurm allocations (e.g. `salloc` or [interactive Slurm sessions](../04-slurm-general-documentation/interactive-sessions.md).
* If using MATLAB parallel features (`parpool`), make sure the number of workers matches the CPUs requested from Slurm.
* Write temporary files to appropriate scratch storage if large I/O is expected.
* For batch jobs, test first with a small input and short walltime before scaling up.
## MATLAB via interactive sessions
-MATLAB for interactive usage **should be always started on a compute node through** an [interactive Slurm session](../03-Slurm-General-Documentation/interactive-sessions.md), and **never directly on a login node**.
+MATLAB for interactive usage **should be always started on a compute node
+through** an [interactive Slurm
+session](../04-slurm-general-documentation/interactive-sessions.md), and
+**never directly on a login node**.
!!! danger "Do not run MATLAB on login nodes"
Do **not** start MATLAB directly on Merlin7 login nodes.
@@ -20,13 +23,13 @@ MATLAB for interactive usage **should be always started on a compute node throug
process **being terminated by administrators**.
For any real computation, start an interactive or batch job with Slurm and run MATLAB inside that allocation.
- Start an [interactive session](../03-Slurm-General-Documentation/interactive-sessions.md) first, then run
+ Start an [interactive session](../04-slurm-general-documentation/interactive-sessions.md) first, then run
MATLAB on the allocated compute node.
There are two common ways to use MATLAB interactively via `interactive` sessions:
-- **Option 1:** [with X11-forwarding](#option-1-matlab-with-x11-forwarding), for the full graphical MATLAB desktop
-- **Option 2:** [without X11-forwarding](#option-2-matlab-without-x11), for terminal-based MATLAB sessions or batch-like interactive testing
+* **Option 1:** [with X11-forwarding](#option-1-matlab-with-x11-forwarding), for the full graphical MATLAB desktop
+* **Option 2:** [without X11-forwarding](#option-2-matlab-without-x11), for terminal-based MATLAB sessions or batch-like interactive testing
Choosing between X11 and non-X11 mode:
@@ -226,5 +229,5 @@ In general, the number of MATLAB workers should not exceed the number of CPUs al
## MATLAB via Open OnDemand
-{% include-markdown "merlin7/06-Software-Support/includes/open-ondemand-alternative.md" %}
+{% include-markdown "merlin7/07-software-support/includes/open-ondemand-alternative.md" %}
diff --git a/docs/merlin7/06-Software-Support/mpich.md b/docs/merlin7/07-software-support/mpich.md
similarity index 100%
rename from docs/merlin7/06-Software-Support/mpich.md
rename to docs/merlin7/07-software-support/mpich.md
diff --git a/docs/merlin7/06-Software-Support/opal-x.md b/docs/merlin7/07-software-support/opal-x.md
similarity index 100%
rename from docs/merlin7/06-Software-Support/opal-x.md
rename to docs/merlin7/07-software-support/opal-x.md
diff --git a/docs/merlin7/06-Software-Support/openmpi.md b/docs/merlin7/07-software-support/openmpi.md
similarity index 100%
rename from docs/merlin7/06-Software-Support/openmpi.md
rename to docs/merlin7/07-software-support/openmpi.md
diff --git a/docs/merlin7/06-Software-Support/pmodules.md b/docs/merlin7/07-software-support/pmodules.md
similarity index 100%
rename from docs/merlin7/06-Software-Support/pmodules.md
rename to docs/merlin7/07-software-support/pmodules.md
diff --git a/docs/merlin7/06-Software-Support/quantum-espresso.md b/docs/merlin7/07-software-support/quantum-espresso.md
similarity index 100%
rename from docs/merlin7/06-Software-Support/quantum-espresso.md
rename to docs/merlin7/07-software-support/quantum-espresso.md
diff --git a/docs/merlin7/06-Software-Support/spack.md b/docs/merlin7/07-software-support/spack.md
similarity index 100%
rename from docs/merlin7/06-Software-Support/spack.md
rename to docs/merlin7/07-software-support/spack.md
diff --git a/docs/merlin7/06-Software-Support/vscode.md b/docs/merlin7/07-software-support/vscode.md
similarity index 81%
rename from docs/merlin7/06-Software-Support/vscode.md
rename to docs/merlin7/07-software-support/vscode.md
index eef4882..a79ce38 100644
--- a/docs/merlin7/06-Software-Support/vscode.md
+++ b/docs/merlin7/07-software-support/vscode.md
@@ -1,15 +1,19 @@
# Visual Studio Code
-Visual Studio Code can be used on Merlin7 with the **Remote - SSH** extension. The recommended workflow is to start a normal non-X11 interactive Slurm session and connect VS Code to the allocated compute node.
+Visual Studio Code can be used on Merlin7 with the **Remote - SSH** extension.
+The recommended workflow is to start a normal non-X11 interactive Slurm session
+and connect VS Code to the allocated compute node.
!!! danger "Do not run VS Code on login nodes"
Do **not** start VS Code directly on Merlin7 login nodes.
- Login nodes are not meant for CPU-intensive, memory-intensive, or long-running VS Code workloads.
- Running VS Code there **can slow down the system for all users** and may lead to your session or
- process **being terminated by administrators**.
+ Login nodes are not meant for CPU-intensive, memory-intensive, or
+ long-running VS Code workloads. Running VS Code there **can slow down the
+ system for all users** and may lead to your session or process **being
+ terminated by administrators**.
- Start an [interactive session](../03-Slurm-General-Documentation/interactive-sessions.md) first,
+ Start an [interactive
+ session](../04-slurm-general-documentation/interactive-sessions.md) first,
then connect VS Code to the allocated compute node.
!!! warning "Do not use X11 mode for VS Code"
@@ -19,7 +23,8 @@ Visual Studio Code can be used on Merlin7 with the **Remote - SSH** extension. T
interactive
```
- Do **not** use `interactive --x11` for VS Code Remote SSH. X11 sessions are not detachable and are intended for foreground graphical applications.
+ Do **not** use `interactive --x11` for VS Code Remote SSH. X11 sessions are
+ not detachable and are intended for foreground graphical applications.
## VS Code via interactive sessions
@@ -40,7 +45,8 @@ interactive -- --cpus-per-task=8 --mem=16G
!!! tip "Request resources with --cpus-per-task"
For most VS Code workflows, request CPUs with `--cpus-per-task`.
- Avoid requesting more CPUs or memory than needed for an editor, terminal, notebook, or compile session.
+ Avoid requesting more CPUs or memory than needed for an editor, terminal,
+ notebook, or compile session.
The allocation is detachable. You may leave the shell with:
@@ -76,7 +82,8 @@ Copy the printed `Host` block into the SSH config file on your **local computer*
!!! tip "Use --print-vscode after each new allocation"
The allocated compute node may change whenever you create a new session.
- Run this command again after creating a new allocation and update your local SSH config:
+ Run this command again after creating a new allocation and update your
+ local SSH config:
```bash
interactive --print-vscode
@@ -140,4 +147,4 @@ If it has ended, create a new allocation and regenerate the VS Code SSH config.
## VS Code via Open OnDemand
-{% include-markdown "merlin7/06-Software-Support/includes/open-ondemand-alternative.md" %}
+{% include-markdown "merlin7/07-software-support/includes/open-ondemand-alternative.md" %}
diff --git a/docs/merlin7/99-support/migration-from-merlin6.md b/docs/merlin7/99-support/migration-from-merlin6.md
index 857dff0..a702e6c 100644
--- a/docs/merlin7/99-support/migration-from-merlin6.md
+++ b/docs/merlin7/99-support/migration-from-merlin6.md
@@ -61,7 +61,7 @@ Before starting the migration, make sure you:
* are **registered on Merlin7**.
- * If not yet registered, please do so following [these instructions](../01-Quick-Start-Guide/requesting-accounts.md)
+ * If not yet registered, please do so following [these instructions](../01-quick-start-guide/requesting-accounts.md)
* **have cleaned up your data to reduce migration time and space usage**.
diff --git a/docs/news/posts/merlin7-preprod-docs.md b/docs/news/posts/merlin7-preprod-docs.md
index ca1cc3e..4a9c2f9 100644
--- a/docs/news/posts/merlin7-preprod-docs.md
+++ b/docs/news/posts/merlin7-preprod-docs.md
@@ -10,6 +10,6 @@ tags:
The Merlin7 cluster is officially in preproduction. This phase will be tested by a few users
and slowly we will contact other users to be part of it. Keep in mind that access is restricted.
-Merlin7 documentation is now available at [Slurm configuration](../../merlin7/03-Slurm-General-Documentation/slurm-configuration.md).
+Merlin7 documentation is now available at [Slurm configuration](../../merlin7/04-slurm-general-documentation/slurm-configuration.md).
More complete documentation will be coming shortly.
diff --git a/docs/support/faq.md b/docs/support/faq.md
index d300959..de056c7 100644
--- a/docs/support/faq.md
+++ b/docs/support/faq.md
@@ -6,7 +6,7 @@ title: "FAQ"
## How do I register for Merlin?
-See [Requesting Merlin Access](../merlin7/01-Quick-Start-Guide/requesting-accounts.md).
+See [Requesting Merlin Access](../merlin7/01-quick-start-guide/requesting-accounts.md).
## How do I get information about downtimes and updates?
@@ -17,7 +17,7 @@ See [Get updated through the Merlin User list!](introduction.md#merlin-user-mail
Merlin projects are placed in the `/data/project` directory. Access to each
project is controlled by Unix group membership. If you require access to an
existing project, please request group membership as described in
-[Requesting Unix Group Membership](../merlin7/01-Quick-Start-Guide/requesting-projects.md#requesting-unix-group-membership).
+[Requesting Unix Group Membership](../merlin7/01-quick-start-guide/requesting-projects.md#requesting-unix-group-membership).
Your project leader or project colleagues will know what Unix group you should
belong to. Otherwise, you can check what Unix group is allowed to access that
@@ -29,7 +29,7 @@ Most software can be installed in user directories without any special
permissions. We recommend using `/data/user/$USER/bin` for software since home
directories are fairly small. For software that will be used by multiple
groups/users you can also [request the admins](introduction.md) install it as a
-[module](../merlin7/06-Software-Support/pmodules.md).
+[module](../merlin7/07-software-support/pmodules.md).
How to install depends a bit on the software itself. There are three common
installation procedures:
diff --git a/docs/support/known-problems.md b/docs/support/known-problems.md
index bbb1adb..8ba0061 100644
--- a/docs/support/known-problems.md
+++ b/docs/support/known-problems.md
@@ -133,9 +133,9 @@ module load paraview
vglrun paraview
```
-Officially, the supported method for running `vglrun` is by using the [NoMachine remote desktop](../merlin7/02-How-To-Use-Merlin/nomachine.md).
+Officially, the supported method for running `vglrun` is by using the [NoMachine remote desktop](../merlin7/02-connecting-to-merlin/nomachine.md).
Running `vglrun` it's also possible using SSH with X11 Forwarding. However, it's very slow and it's only recommended when running
-in Slurm (from [NoMachine](../merlin7/02-How-To-Use-Merlin/nomachine.md)). Please, avoid running `vglrun` over SSH from a desktop or laptop.
+in Slurm (from [NoMachine](../merlin7/02-connecting-to-merlin/nomachine.md)). Please, avoid running `vglrun` over SSH from a desktop or laptop.
## Software
diff --git a/mkdocs.yml b/mkdocs.yml
index 4c05bb0..d92d7c4 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -66,6 +66,8 @@ plugins:
- 'cscs*/*.md'
Support:
- 'support/*.md'
+ News:
+ - 'news/*.md'
# Extensions
markdown_extensions:
@@ -103,53 +105,56 @@ nav:
- news/index.md
- Merlin 7:
- Quick Start Guide:
- - merlin7/01-Quick-Start-Guide/introduction.md
- - merlin7/01-Quick-Start-Guide/code-of-conduct.md
- - merlin7/01-Quick-Start-Guide/requesting-accounts.md
- - merlin7/01-Quick-Start-Guide/requesting-projects.md
- - merlin7/01-Quick-Start-Guide/accessing-interactive-nodes.md
- - merlin7/01-Quick-Start-Guide/accessing-slurm.md
+ - merlin7/01-quick-start-guide/introduction.md
+ - merlin7/01-quick-start-guide/code-of-conduct.md
+ - merlin7/01-quick-start-guide/requesting-accounts.md
+ - merlin7/01-quick-start-guide/requesting-projects.md
+ - merlin7/01-quick-start-guide/accessing-interactive-nodes.md
+ - merlin7/01-quick-start-guide/accessing-slurm.md
+ - Connecting to Merlin7:
+ - merlin7/02-connecting-to-merlin/host-keys.md
+ - SSH:
+ - merlin7/02-connecting-to-merlin/connect-from-linux.md
+ - merlin7/02-connecting-to-merlin/connect-from-windows.md
+ - merlin7/02-connecting-to-merlin/connect-from-macos.md
+ - SSH Key-pairs: merlin7/02-connecting-to-merlin/ssh-keys.md
+ - Remote Desktop: merlin7/02-connecting-to-merlin/nomachine.md
- How To Use Merlin7:
- - merlin7/02-How-To-Use-Merlin/connect-from-linux.md
- - merlin7/02-How-To-Use-Merlin/connect-from-windows.md
- - merlin7/02-How-To-Use-Merlin/connect-from-macos.md
- - merlin7/02-How-To-Use-Merlin/storage.md
- - merlin7/02-How-To-Use-Merlin/transfer-data.md
- - merlin7/02-How-To-Use-Merlin/archive.md
- - merlin7/02-How-To-Use-Merlin/nomachine.md
- - merlin7/02-How-To-Use-Merlin/merlin-rmount.md
- - merlin7/02-How-To-Use-Merlin/merlin_tools.md
- - merlin7/02-How-To-Use-Merlin/ssh-keys.md
- - merlin7/02-How-To-Use-Merlin/kerberos.md
- - merlin7/02-How-To-Use-Merlin/software-repositories.md
+ - merlin7/03-how-to-use-merlin/storage.md
+ - merlin7/03-how-to-use-merlin/transfer-data.md
+ - merlin7/03-how-to-use-merlin/archive.md
+ - merlin7/03-how-to-use-merlin/merlin-rmount.md
+ - merlin7/03-how-to-use-merlin/merlin_tools.md
+ - merlin7/03-how-to-use-merlin/kerberos.md
+ - merlin7/03-how-to-use-merlin/software-repositories.md
- Slurm General Documentation:
- - merlin7/03-Slurm-General-Documentation/merlin7-configuration.md
- - merlin7/03-Slurm-General-Documentation/slurm-configuration.md
- - merlin7/03-Slurm-General-Documentation/interactive-sessions.md
- - merlin7/03-Slurm-General-Documentation/interactive-jobs.md
- - merlin7/03-Slurm-General-Documentation/slurm-examples.md
- - merlin7/03-Slurm-General-Documentation/slurm-mail.md
+ - merlin7/04-slurm-general-documentation/merlin7-configuration.md
+ - merlin7/04-slurm-general-documentation/slurm-configuration.md
+ - merlin7/04-slurm-general-documentation/interactive-sessions.md
+ - merlin7/04-slurm-general-documentation/interactive-jobs.md
+ - merlin7/04-slurm-general-documentation/slurm-examples.md
+ - merlin7/04-slurm-general-documentation/slurm-mail.md
- Jupyterhub:
- - merlin7/04-Jupyterhub/jupyterhub.md
+ - merlin7/05-jupyterhub/jupyterhub.md
- Open OnDemand:
- - merlin7/05-Open-OnDemand/open-ondemand.md
+ - Introduction: merlin7/06-open-ondemand/open-ondemand.md
- Software Support:
- - merlin7/06-Software-Support/pmodules.md
- - merlin7/06-Software-Support/openmpi.md
- - merlin7/06-Software-Support/mpich.md
- - merlin7/06-Software-Support/cray-module.env.md
- - merlin7/06-Software-Support/ansys.md
- - merlin7/06-Software-Support/ansys-rsm.md
- - merlin7/06-Software-Support/cp2k.md
- - merlin7/06-Software-Support/dirac.md
- - merlin7/06-Software-Support/gromacs.md
- - merlin7/06-Software-Support/ippl.md
- - merlin7/06-Software-Support/lammps.md
- - merlin7/06-Software-Support/matlab.md
- - merlin7/06-Software-Support/opal-x.md
- - merlin7/06-Software-Support/quantum-espresso.md
- - merlin7/06-Software-Support/spack.md
- - merlin7/06-Software-Support/vscode.md
+ - merlin7/07-software-support/pmodules.md
+ - merlin7/07-software-support/openmpi.md
+ - merlin7/07-software-support/mpich.md
+ - merlin7/07-software-support/cray-module.env.md
+ - merlin7/07-software-support/ansys.md
+ - merlin7/07-software-support/ansys-rsm.md
+ - merlin7/07-software-support/cp2k.md
+ - merlin7/07-software-support/dirac.md
+ - merlin7/07-software-support/gromacs.md
+ - merlin7/07-software-support/ippl.md
+ - merlin7/07-software-support/lammps.md
+ - merlin7/07-software-support/matlab.md
+ - merlin7/07-software-support/opal-x.md
+ - merlin7/07-software-support/quantum-espresso.md
+ - merlin7/07-software-support/spack.md
+ - merlin7/07-software-support/vscode.md
- Merlin 6:
- Quick Start Guide:
- merlin6/introduction.md