From 57276fd8548813251d23abc048694b9565b2de59 Mon Sep 17 00:00:00 2001
From: Natasha Pavlovikj <npavlovikj2@unl.edu>
Date: Wed, 20 Jul 2022 18:41:12 -0500
Subject: [PATCH] Update docs for MPI conda packages
---
.../using_anaconda_package_manager.md | 47 +++++++++++++++++++
1 file changed, 47 insertions(+)
diff --git a/content/applications/user_software/using_anaconda_package_manager.md b/content/applications/user_software/using_anaconda_package_manager.md
index 777caf01..13cbb732 100644
--- a/content/applications/user_software/using_anaconda_package_manager.md
+++ b/content/applications/user_software/using_anaconda_package_manager.md
@@ -22,6 +22,7 @@ straightforward.
- [Using /common for environments](#using-common-for-environments)
- [Adding and Removing Packages from an Existing Environment](#adding-and-removing-packages-from-an-existing-environment)
- [Creating custom GPU Anaconda Environment](#creating-custom-gpu-anaconda-environment)
+- [Creating custom MPI Anaconda Environment](#creating-custom-mpi-anaconda-environment)
- [Using an Anaconda Environment in a Jupyter Notebook](#using-an-anaconda-environment-in-a-jupyter-notebook)
### Using Anaconda
@@ -245,6 +246,52 @@ If you have custom GPU Anaconda environment please only use the two lines from a
Using `module load tensorflow-gpu/py36/1.14` and `conda activate tensorflow-gpu-1.14-custom` in the same script is **wrong** and may give you various errors and incorrect results.
{{% /notice %}}
+### Creating Custom MPI Anaconda Environment
+
+Some conda packages available on `conda-forge` and `bioconda` support MPI (via `openmpi` or `mpich`).
+**Currently only packages that were built using `openmpi 4.1` and `mpich 4.0` are supported on HCC clusters.**
+
+In order to be able to correctly use these MPI packages with the MPI libraries installed on our clusters, two steps need to be performed.
+
+First, at install time, besides the package, the package `openmpi=4.1.*=external_*` or `mpich=4.0.*=external_*` needs to be installed for `openmpi` or `mpich` respectively.
+
+Secondly, when activating the conda environment and using the package, the system-wide `openmpi/4.1` or `mpich/4.0` module needs to be loaded depending on the MPI library used.
+
+For example, the steps for creating conda environment with `mpi4py` that supports `openmpi` are:
+{{% panel theme="info" header="Creating Anaconda environment with openmpi" %}}
+{{< highlight bash >}}
+module purge
+module load anaconda
+conda create -n mpi4py-openmpi mpi4py openmpi=4.1.*=external_*
+{{< /highlight >}}
+{{% /panel %}}
+and the steps for using this environment are:
+{{% panel theme="info" header="Using Anaconda environment with openmpi" %}}
+{{< highlight bash >}}
+module purge
+module load compiler/gcc/10 openmpi/4.1 anaconda
+conda activate mpi4py-openmpi
+{{< /highlight >}}
+{{% /panel %}}
+
+
+The steps for creating conda environment with `mpi4py` that supports `mpich` are:
+{{% panel theme="info" header="Creating Anaconda environment with mpich" %}}
+{{< highlight bash >}}
+module purge
+module load anaconda
+conda create -n mpi4py-mpich mpi4py mpich=4.0.*=external_*
+{{< /highlight >}}
+{{% /panel %}}
+and the steps for using this environment are:
+{{% panel theme="info" header="Using Anaconda environment with mpich" %}}
+{{< highlight bash >}}
+module purge
+module load compiler/gcc/10 mpich/4.0 anaconda
+conda activate mpi4py-mpich
+{{< /highlight >}}
+{{% /panel %}}
+
### Using an Anaconda Environment in a Jupyter Notebook
It is not difficult to make an Anaconda environment available to a
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