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Commit 2ac0dcc7 authored by Sören Wacker's avatar Sören Wacker
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change link addressing #36

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......@@ -32,7 +32,7 @@ This means that you will sometimes have to wait for other jobs to finish and at
* Do interactive code development, debugging and testing in your local machine, as much as possible. In the cluster, try to organize your code as scripts, instead of working interactively in the command line.
* If you need to test and debug in the cluster, for example, in a GPU node, request an interactive session and do not work in the login node itself (See [Interactive jobs on compute nodes](/docs/manual/job-submission/job-interactive)).
* If you need to test and debug in the cluster, for example, in a GPU node, request an interactive session and do not work in the login node itself (See [Interactive jobs on compute nodes](/docs/manual/job-submission/slurm-basics/#interactive-jobs-on-compute-nodes)).
* Save results frequently: your job can crash, the compute node can become overloaded, or the network shares can become unavailable.
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......@@ -140,7 +140,7 @@ $ apptainer shell -C ubuntu_latest.sif
This is a specialized registry provided by NVIDIA for GPU accelerated applications or GPU software development tools. These images are large, and one is recommended to download them locally in your machine, and only send the downloaded image to DAIC. _For this, you need to have Apptainer locally installed first_. To install Apptainer in your machine, follow the official [Installing Apptainer instructions](https://apptainer.org/docs/admin/main/installation.html). Apptainer needs a Linux kernel to run, if you create your container on a MacBook, or a computer with a different CPU architecture than the target system, there is a good chance that the container will not run.
{{% alert title="Warning" color="warning" %}}
By default, Apptainer images are saved to `~/.singularity`. Ideally, to avoid quota issues, you'd set the environment variable `SINGULARITY_CACHEDIR` to a different location. At present, both the `bulk` and `umbrella` filesystems do not support pulling images, so you are advised to pull these to your local machine and then copy over the image file to DAIC.
By default, Apptainer images are saved to `~/.singularity`. Ideally, to avoid quota issues, you'd set the environment variable `APPTAINER_CACHEDIR` to a different location. At present, both the `bulk` and `umbrella` filesystems do not support pulling images, so you are advised to pull these to your local machine and then copy over the image file to DAIC.
{{% /alert %}}
```bash
......@@ -391,8 +391,8 @@ From: condaforge/miniforge3:latest
mamba clean --all -y
# Now add the script to activate the Conda environment
echo '. "/opt/conda/etc/profile.d/conda.sh"' >> $SINGULARITY_ENVIRONMENT
echo 'conda activate __apptainer-env__' >> $SINGULARITY_ENVIRONMENT
echo '. "/opt/conda/etc/profile.d/conda.sh"' >> $APPTAINER_ENVIRONMENT
echo 'conda activate __apptainer-env__' >> $APPTAINER_ENVIRONMENT
```
This file is similar to the file in the [Building images](#building-images), with the addition of `%files` area. `%files` specifies the files in the host system (ie, your machine) that need to be copied to the container image, and optionally, where should they be available. In the previous example, the `environment.yml` file will be available in `/opt/` in the container.
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