Added openmpi
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url: /merlin6/jupyterlab.html
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- title: Jupyterhub Troubleshooting
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url: /merlin6/jupyterhub-trouble.html
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- title:
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- title: Software Support
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folderitems:
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- title: OpenMPI
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url: /merlin6/openmpi.html
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- title: Announcements
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folderitems:
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- title: Downtimes
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89
pages/merlin6/05 Software Support/openmpi.md
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89
pages/merlin6/05 Software Support/openmpi.md
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---
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title: OpenMPI Support
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#tags:
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last_updated: 13 March 2020
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keywords: software, openmpi, slurm
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summary: "This document describes how to use OpenMPI in the Merlin6 cluster"
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sidebar: merlin6_sidebar
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permalink: /merlin6/openmpi.html
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---
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## Introduction
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This document describes which set of OpenMPI versions in PModules are supported in the Merlin6 cluster.
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### srun
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We strongly recommend the use of **'srun'** over **'mpirun'** or **'mpiexec'**. Using **'srun'** would properly
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bind tasks in to cores and less customization is needed, while **'mpirun'** and '**mpiexec**' might need more advanced
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configuration and should be only used by advanced users. Please, ***always*** adapt your scripts for using **'srun'**
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before opening a support ticket. Also, please contact us on any problem when using a module.
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{{site.data.alerts.tip}} Always run OpenMPI with the <b>srun</b> command.
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{{site.data.alerts.end}}
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### PModules
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We can find a large number of compilations of OpenMPI modules in the PModules central repositories. However, only
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some of them are suitable for running in a Slurm cluster: ***any OpenMPI versions with suffixes ``_slurm`` or ``_merlin6``
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are suitable for running in the Merlin6 cluster***. Please, ***avoid using any other OpenMPI releases***.
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{{site.data.alerts.tip}} Suitable <b>OpenMPI</b> versions for running in the Merlin6 cluster:
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<p> -
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<span class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">openmpi/<version>_slurm
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</span> <b>[<u>Recommended</u>]</b>
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</p>
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<p> -
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<span class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">openmpi/<version>_merlin6
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</span>
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</p>
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{{site.data.alerts.end}}
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#### 'unstable' repository
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New OpenMPI versions that need to be tested will be compiled first in the **``unstable``** repository, and once validated will be moved to **``stable``**.
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We can not ensure that modules in that repository are production ready, but you can use it *at your own risk*.
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For using *unstable* modules, you might need to load the **``unstable``** PModules repository as follows:
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```bash
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module use unstable
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```
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#### 'stable' repository
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Officially supported OpenMPI versions (https://www.open-mpi.org/) will be available in the **``stable``** repository (which is the *default* loaded repository).
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For further information, please check [https://www.open-mpi.org/software/ompi/ -> Current & Still Supported](https://www.open-mpi.org/software/ompi/)
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versions.
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Usually, not more than 2 minor update releases will be present in the **``stable``** repository. Older minor update releases will be moved to **``deprecated``**
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despite are officially supported. This will ensure that users compile new software with the latest stable versions, but we keep available the old versions
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for software which was compiled with it.
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#### 'deprecated' repository
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Old OpenMPI versions (it is, any official OpenMPI version which has been moved to **retired** or **ancient**) will be
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moved to the ***'deprecated'*** PModules repository.
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For further information, please check [https://www.open-mpi.org/software/ompi/ -> Older Versions](https://www.open-mpi.org/software/ompi/)
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versions.
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Also, as mentioned in [before](/merlin6/openmpi.html#stable-repository), older official supported OpenMPI releases (minor updates) will be moved to ``deprecated``.
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For using *deprecated* modules, you might need to load the **``deprecated``** PModules repository as follows:
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```bash
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module use deprecated
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```
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However, this is usually not needed: when loading directly a specific version in the ``deprecated`` repository, if this is not found in
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``stable`` it try to search and to fallback to other repositories (``deprecated`` or ``unstable``).
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#### About missing versions
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##### Missing OpenMPI versions
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For legacy software, some users might require a different OpenMPI version. **We always encourage** users to try one of the existing stable versions
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(*OpenMPI always with suffix ``_slurm`` or ``_merlin6``!*), as they will contain the latest bug fixes and they usually should work. In the worst case, you
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can also try with the ones in the deprecated repository (again, *OpenMPI always with suffix ``_slurm`` or ``_merlin6``!*), or for very old software which
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was based on OpenMPI v1 you can follow the guide [FAQ: Removed MPI constructs](https://www.open-mpi.org/faq/?category=mpi-removed), which provide
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some easy steps for migrating from OpenMPI v1 to v2 or superior or to find out why your code does not compile properly.
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When, after trying the mentioned versions and workarounds, you are still facing problems, please contact us. Also, please contact us if you require a newer
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version with a different ``gcc`` or ``intel`` compiler (in example, Intel v19).
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