HPCE/gitea-pages
0
0
Fork 0
Code Issues 2 Pull Requests Actions Packages Projects Activity

Update docs

Browse Source
This commit is contained in:
caubet_m
2025-01-21 12:02:02 +01:00
parent 2cc87f6f44
commit 5fc6adc5ab
10 changed files with 283 additions and 341 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
pages/merlin7/05-Software-Support/ansys.md
View File

@ -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/using-modules.html)**.
The ANSYS software can be loaded through **[PModules](/merlin7/pmodules.html)**.
The default ANSYS versions are loaded from the central PModules repository.

64
pages/merlin7/05-Software-Support/cray-module.env.md Normal file
View File

@ -0,0 +1,64 @@
---
title: Cray Programming Environment
#tags:
keywords: cray, module
last_updated: 24 Mai 2023
summary: "This document describes how to use the Cray Programming Environment on Merlin7."
sidebar: merlin7_sidebar
permalink: /merlin7/cray-module-env.html
---
## Loading the Cray module
The Cray Programming Environment, with Cray's compilers and MPI, is not loaded by default.
To load it, one has to run the following command:
```bash
module load cray
```
The Cray Programming Environment will load all the necessary dependencies. In example:
```bash
🔥 [caubet_m@login001:~]# module list
Currently Loaded Modules:
1) craype-x86-rome 2) libfabric/1.15.2.0
3) craype-network-ofi
4) xpmem/2.9.6-1.1_20240510205610__g087dc11fc19d 5) PrgEnv-cray/8.5.0
6) cce/17.0.0 7) cray-libsci/23.12.5
8) cray-mpich/8.1.28 9) craype/2.7.30
10) perftools-base/23.12.0 11) cpe/23.12
12) cray/23.12
```
You will notice an unfamiliar `PrgEnv-cray/8.5.0` that was loaded. This is a meta-module that Cray provides to simplify the switch of compilers and their associated dependencies and libraries,
as a whole called Programming Environment. In the Cray Programming Environment, there are 4 key modules.
* `cray-libsci` is a collection of numerical routines tuned for performance on Cray systems.
* `libfabric` is an important low-level library that allows you to take advantage of the high performance Slingshot network.
* `cray-mpich` is a CUDA-aware MPI implementation, optimized for Cray systems.
* `cce` is the compiler from Cray. C/C++ compilers are based on Clang/LLVM while Fortran supports Fortran 2018 standard. More info: https://user.cscs.ch/computing/compilation/cray/
You can switch between different programming environments. You can check the available module with the `module avail` command, as follows:
```bash
🔥 [caubet_m@login001:~]# module avail PrgEnv
--------------------- /opt/cray/pe/lmod/modulefiles/core ---------------------
PrgEnv-cray/8.5.0 PrgEnv-gnu/8.5.0
PrgEnv-nvhpc/8.5.0 PrgEnv-nvidia/8.5.0
```
## Switching compiler suites
Compiler suites can be exchanged with PrgEnv (Programming Environments) provided by HPE-Cray. The wrappers call the correct compiler with appropriate options to build
and link applications with relevant libraries, as required by the loaded modules (only dynamic linking is supported) and therefore should replace direct calls to compiler
drivers in Makefiles and build scripts.
To swap the the compiler suite from the default Cray to GNU compiler, one can run the following.
```bash
🔥 [caubet_m@login001:~]# module swap PrgEnv-cray/8.5.0 PrgEnv-gnu/8.5.0
Lmod is automatically replacing "cce/17.0.0" with "gcc-native/12.3".
```

4
pages/merlin7/05-Software-Support/openmpi.md
View File

@ -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/using-modules.html) and [Spack](/merlin7/spack.html), ensuring compatibility and reliability for production use.
These versions are available via [Pmodules](/merlin7/pmodules.html) and [Spack](/merlin7/spack.html), 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/using-modules.html) or [Spack](/merlin7/spack.html)), the corresponding PMIx version will be automatically loaded.
When loading an OpenMPI module (via [Pmodules](/merlin7/pmodules.html) or [Spack](/merlin7/spack.html)), the corresponding PMIx version will be automatically loaded.
* Users do not need to manually manage PMIx compatibility.
{{site.data.alerts.warning}}

153
pages/merlin7/05-Software-Support/pmodules.md Normal file
View File

@ -0,0 +1,153 @@
---
title: PSI Modules
#tags:
keywords: Pmodules, software, stable, unstable, deprecated, overlay, overlays, release stage, module, package, packages, library, libraries
last_updated: 07 September 2022
#summary: ""
sidebar: merlin7_sidebar
permalink: /merlin7/pmodules.html
---
## PSI Environment Modules
On top of the operating system stack we provide different software using the PSI developed PModule system.
PModules is the official supported way and each package is deployed by a specific expert. Usually, in PModules
software which is used by many people will be found.
If you miss any package/versions or a software with a specific missing feature, contact us. We will study if is feasible or not to install it.
### Module Release Stages
To ensure proper software lifecycle management, PModules uses three release stages: unstable, stable, and deprecated.
1. **Unstable Release Stage:**
* Contains experimental or under-development software versions.
* Not visible to users by default. Use explicitly:
```bash
module use unstable
```
* Software is promoted to **stable** after validation.
2. **Stable Release Stage:**
* Default stage, containing fully tested and supported software versions.
* Recommended for all production workloads.
3. **Deprecated Release Stage:**
* Contains software versions that are outdated or discontinued.
* These versions are hidden by default but can be explicitly accessed:
```bash
module use deprecated
```
* Deprecated software can still be loaded directly without additional configuration to ensure user transparency.
## PModules commands
Below is listed a summary of common `module` commands:
```bash
module use # show all available PModule Software Groups as well as Release Stages
module avail # to see the list of available software packages provided via pmodules
module use unstable # to get access to a set of packages not fully tested by the community
module load <package>/<version> # to load specific software package with a specific version
module search <string> # to search for a specific software package and its dependencies.
module list # to list which software is loaded in your environment
module purge # unload all loaded packages and cleanup the environment
```
Please refer to the **external [PSI Modules](https://pmodules.gitpages.psi.ch/chap3.html) document** for
detailed information about the `module` command.
### module use/unuse
Without any parameter, `use` **lists** all available PModule **Software Groups and Release Stages**.
```bash
module use
```
When followed by a parameter, `use`/`unuse` invokes/uninvokes a PModule **Software Group** or **Release Stage**.
```bash
module use EM # Invokes the 'EM' software group
module unuse EM # Uninvokes the 'EM' software group
module use unstable # Invokes the 'unstable' Release stable
module unuse unstable # Uninvokes the 'unstable' Release stable
```
### module avail
This option **lists** all available PModule **Software Groups and their packages**.
Please run `module avail --help` for further listing options.
### module search
This is used to **search** for **software packages**. By default, if no **Release Stage** or **Software Group** is specified
in the options of the `module search` command, it will search from the already invoked *Software Groups* and *Release Stages*.
Direct package dependencies will be also showed.
```bash
🔥 [caubet_m@login001:~]# module search openmpi
Module Rel.stage Group Overlay Requires
--------------------------------------------------------------------------------
openmpi/4.1.6 stable Compiler Alps gcc/12.3.0
openmpi/4.1.6 stable Compiler Alps gcc/13.3.0
openmpi/4.1.6 stable Compiler Alps gcc/14.2.0
openmpi/4.1.6 stable Compiler Alps intelcc/22.2
openmpi/5.0.5 stable Compiler Alps gcc/8.5.0
openmpi/5.0.5 stable Compiler Alps gcc/12.3.0
openmpi/5.0.5 stable Compiler Alps gcc/14.2.0
openmpi/5.0.5 stable Compiler Alps intelcc/22.2
```
Please run `module search --help` for further search options.
### module load/unload
This loads/unloads specific software packages. Packages might have direct dependencies that need to be loaded first. Other dependencies
will be automatically loaded.
In the example below, the ``openmpi/5.0.5`` package will be loaded, however ``gcc/14.2.0`` must be loaded as well as this is a strict dependency. Direct dependencies must be loaded in advance. Users can load multiple packages one by one or at once. This can be useful for instance when loading a package with direct dependencies.
```bash
# Single line
module load gcc/14.2.0 openmpi/5.0.5
# Multiple line
module load gcc/14.2.0
module load openmpi/5.0.5
```
#### module purge
This command is an alternative to `module unload`, which can be used to unload **all** loaded module files.
```bash
module purge
```
## Requesting New PModules Packages
The PModules system is designed to accommodate the diverse software needs of Merlin7 users. Below are guidelines for requesting new software or versions to be added to PModules.
### 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.
* **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.
### Requesting a Missing Version
If the currently available versions of a package do not meet your requirements:
* **New Versions:** Requests for newer versions are generally supported, especially if there is interest from multiple users.
* **Intermediate Versions:** Installation of intermediate versions (e.g., versions between the current stable and deprecated versions)
can be considered if there is a strong justification, such as specific features or compatibility requirements.
### General Notes
* New packages or versions are prioritized based on their relevance and usage.
* For any request, providing detailed information about the required software or version (e.g., name, version, features) will help
expedite the process.

18
pages/merlin7/05-Software-Support/spack.md Normal file
View File

@ -0,0 +1,18 @@
---
title: Spack
keywords: spack, python, software, compile
summary: "Spack the HPC package manager documentation"
sidebar: merlin7_sidebar
toc: false
permalink: /merlin7/spack.html
---
For Merlin7 the *package manager for supercomputing* [Spack](https://spack.io/) is available. It is meant to compliment the existing PModules
solution, giving users the opertunity to manage their own software environments.
Documentation for how to use Spack on Merlin7 is provided [here](https://gitlab.psi.ch/lsm-hpce/spack-psi/-/blob/main/README.md).
## The Spack PSI packages
An initial collection of packages (and Spack reciepes) are located at **[Spack PSI](https://gitlab.psi.ch/lsm-hpce/spack-psi)**, users can directly use these
through calls like `spack add ...`.