From 419b1b8c25d5bd66fba2d71a988d7c70595b4ff6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 16 Nov 2023 21:28:43 +0100
Subject: [PATCH] improve commands for building Apptainer image from Docker
 container

---
 mkdocs/docs/HPC/apptainer.md | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/mkdocs/docs/HPC/apptainer.md b/mkdocs/docs/HPC/apptainer.md
index 6b255f0502d..f06d943b90a 100644
--- a/mkdocs/docs/HPC/apptainer.md
+++ b/mkdocs/docs/HPC/apptainer.md
@@ -55,13 +55,20 @@ Due to the nature of `--fakeroot` option, we recommend to write your
 Apptainer/Singularity image to a globally writable location, like
 `/tmp`, or `/local` directories. Once the image is created, you should
 move it to your desired destination. An example to make an
-Apptainer/Singularity container:
-
-<pre><code>$ <b>APPTAINER_CACHEDIR=/tmp/ \
-APPTAINER_TMPDIR=/tmp/ \
-apptainer build --fakeroot /tmp/tensorflow-21.10-tf1-py3.sif \
-docker://nvcr.io/nvidia/tensorflow:21.10-tf1-py3</b>
-</code></pre>
+Apptainer/Singularity container image:
+
+```shell
+# avoid that Apptainer uses $HOME/.cache
+export APPTAINER_CACHEDIR=/tmp/$USER/apptainer/cache
+# instruct Apptainer to use temp dir on local filessytem
+export APPTAINER_TMPDIR=/tmp/$USER/apptainer/tmpdir
+# specified temp dir must exist, so create it
+mkdir -p $APPTAINER_TMPDIR
+# convert Docker container to Apptainer container image
+apptainer build --fakeroot /tmp/$USER/tf.sif docker://nvcr.io/nvidia/tensorflow:21.10-tf1-py3
+# mv container image to $VSC_SCRATCH
+mv /tmp/$USER/tf.sif $VSC_SCRATCH/tf.sif
+```
 
 ### Converting Docker images