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Merged Natasha Pavlovikj requested to merge update into master
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@@ -248,8 +248,7 @@ Using `module load tensorflow-gpu/py36/1.14` and `conda activate tensorflow-gpu-
@@ -248,8 +248,7 @@ Using `module load tensorflow-gpu/py36/1.14` and `conda activate tensorflow-gpu-
### Creating Custom MPI Anaconda Environment
### Creating Custom MPI Anaconda Environment
Some conda packages available on `conda-forge` and `bioconda` support MPI (via `openmpi` or `mpich`).
Some conda packages available on `conda-forge` and `bioconda` support MPI (via `openmpi` or `mpich`). However, just using the `openmpi` and `mpich` packages from `conda-forge` often does not work on HPC systems. More information about this can be found [here](https://conda-forge.org/docs/user/tipsandtricks.html#using-external-message-passing-interface-mpi-libraries).
**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.
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.
@@ -257,6 +256,7 @@ First, at install time, besides the package, the "dummy" package `openmpi=4.1.*=
@@ -257,6 +256,7 @@ First, at install time, besides the package, the "dummy" package `openmpi=4.1.*=
These "dummy" packages are empty, but allow the solver to create correct environments and use the system-wide modules when the environment is activated.
These "dummy" packages are empty, but allow the solver to create correct environments and use the system-wide modules when the environment is activated.
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.
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.
 
**Currently only packages that were built using `openmpi 4.1` and `mpich 4.0` are supported on HCC clusters.**
For example, the steps for creating conda environment with `mpi4py` that supports `openmpi` are:
For example, the steps for creating conda environment with `mpi4py` that supports `openmpi` are:
{{% panel theme="info" header="Creating Anaconda environment with openmpi" %}}
{{% panel theme="info" header="Creating Anaconda environment with openmpi" %}}
@@ -275,7 +275,6 @@ conda activate mpi4py-openmpi
@@ -275,7 +275,6 @@ conda activate mpi4py-openmpi
{{< /highlight >}}
{{< /highlight >}}
{{% /panel %}}
{{% /panel %}}
The steps for creating conda environment with `mpi4py` that supports `mpich` are:
The steps for creating conda environment with `mpi4py` that supports `mpich` are:
{{% panel theme="info" header="Creating Anaconda environment with mpich" %}}
{{% panel theme="info" header="Creating Anaconda environment with mpich" %}}
{{< highlight bash >}}
{{< highlight bash >}}
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