Nested apptainer

software/Apptainer/README.md

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+<!--
+   Copyright 2026, Center for High Throughput Computing, University of Wisconsin - Madison
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+-->
+
+# Apptainer
+
+Container definition files for installing Apptainer.
+**This is intended for "nested" containers.**
+
+> [!IMPORTANT]
+> You do not need to do this for the "normal" use of Apptainer containers on CHTC.
+> This is explicitly for the case where you need to be able to launch an Apptainer container ***from inside another container***!
+
+## About nested containers
+
+Normal execution of a container on CHTC has the correct permissions set automatically for everything to work as expected.
+But those permissions do not extend into launching a container from inside of an already running container.
+The result is usually some form of "permission denied" error.
+

software/Apptainer/apptainer-in-apptainer/README.md

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+<!--
+   Copyright 2026, Center for High Throughput Computing, University of Wisconsin - Madison
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+-->
+
+# Apptainer-in-Apptainer
+
+This recipe provides the definition file for the "parent" Apptainer container,
+which has the ability to launch a "child" Apptainer container inside of it.
+
+# Launching inner container
+
+To run the inner container, you need to use the `--unsquash` argument with your `apptainer` command.
+For example,
+
+```
+apptainer exec --unsquash my_inner_container.sif inner_script.sh
+```
+
+## Bare minimum setup
+
+These images have the bare minimum required in order to use Apptainer inside of Apptainer.
+
+* [minimal-ubuntu.def](minimal-ubuntu.def)
+* [minimal-rocky.def](minimal-rocky.def)
+
+## With "nice to have" packages
+
+These images have what is required to use Apptainer inside of Apptainer,
+as well as some additional "common" programs that are useful to have.
+For a full list of additional packages, see the definition file.
+
+* [nice-ubuntu.def](nice-ubuntu.def)
+* [nice-rocky.def](nice-rocky.def)
+
+## [minimal-ubuntu.def](minimal-ubuntu.def)
+
+| | | |
+| ---: | :--- | :--- |
+| *Type* | **Apptainer** | |
+| *OS* | Ubuntu 24.04 (Debian) | |
+| *Base image* | **ubuntu:24.04** | *DockerHub* |
+| *Updated* | 2026-04-27 | *Andrew Owen* |
+| *Last tested on HTC* | 2026-04-27 | *Andrew Owen* |
+| *Last tested on HPC* | - | - |
+
+## [minimal-rocky.def](minimal-rocky.def)
+
+| | | |
+| ---: | :--- | :--- |
+| *Type* | **Apptainer** | |
+| *OS* | Rocky 9 (RHEL) | |
+| *Base image* | **rockylinux:9** | *DockerHub* |
+| *Updated* | 2026-04-27 | *Andrew Owen* |
+| *Last tested on HTC* | 2026-04-27 | *Andrew Owen* |
+| *Last tested on HPC* | - | - |
+
+## [nice-ubuntu.def](nice-ubuntu.def)
+
+| | | |
+| ---: | :--- | :--- |
+| *Type* | **Apptainer** | |
+| *OS* | Ubuntu 24.04 (Debian) | |
+| *Base image* | **ubuntu:24.04** | *DockerHub* |
+| *Updated* | 2026-04-27 | *Andrew Owen* |
+| *Last tested on HTC* | 2026-04-27 | *Andrew Owen* |
+| *Last tested on HPC* | - | - |
+
+## [nice-rocky.def](nice-rocky.def)
+
+| | | |
+| ---: | :--- | :--- |
+| *Type* | **Apptainer** | |
+| *OS* | Rocky 9 (RHEL) | |
+| *Base image* | **rockylinux:9** | *DockerHub* |
+| *Updated* | 2026-04-27 | *Andrew Owen* |
+| *Last tested on HTC* | 2026-04-27 | *Andrew Owen* |
+| *Last tested on HPC* | - | - |
+

software/Apptainer/apptainer-in-apptainer/minimal-rocky.def

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+Bootstrap: docker
+From: rockylinux:9
+
+%post
+    # base dnf/yum setup
+    dnf -y update && \
+        dnf -y install yum-utils && \
+        dnf -y config-manager --set-enabled crb && \
+        dnf -y install epel-release
+
+    dnf -y install --allowerasing \
+            cpio \
+            git \
+            rpm
+
+    # Installing unprivileged apptainer inside of the container
+    # adapted from https://apptainer.org/docs/admin/1.4/installation.html#install-unprivileged-from-pre-built-binaries
+    mkdir -p /opt
+    curl -s https://raw.githubusercontent.com/apptainer/apptainer/main/tools/install-unprivileged.sh | bash -s - /opt/apptainer
+
+%environment
+    export PATH="/opt/apptainer/bin:${PATH}"

software/Apptainer/apptainer-in-apptainer/minimal-ubuntu.def

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+Bootstrap: docker
+From: ubuntu:24.04
+
+%post
+    export DEBIAN_FRONTEND=noninteractive
+    apt update -y
+    apt install -y \
+        bash \
+        cpio \
+        curl \
+        git \
+        rpm2cpio
+
+    # Installing unprivileged apptainer inside of the container
+    # adapted from https://apptainer.org/docs/admin/1.4/installation.html#install-unprivileged-from-pre-built-binaries
+    mkdir -p /opt
+    curl -s https://raw.githubusercontent.com/apptainer/apptainer/main/tools/install-unprivileged.sh | bash -s - /opt/apptainer
+
+%environment
+    export PATH=/opt/apptainer/bin:$PATH

software/Apptainer/apptainer-in-apptainer/nice-rocky.def

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+Bootstrap: docker
+From: rockylinux:9
+
+%post
+    # base dnf/yum setup
+    dnf -y update && \
+        dnf -y install yum-utils && \
+        dnf -y config-manager --set-enabled crb && \
+        dnf -y install epel-release
+
+    # well rounded basic system to support a wide range of user jobs
+    dnf -y groupinstall "Development Tools" "Scientific Support"
+
+    dnf -y install --allowerasing \
+            cpio \
+            git \
+            nano \
+            python3 \
+            python3-pip \
+            python3-devel \
+            rpm \
+            tree \
+            unzip \
+            vim \
+            wget
+
+    # Installing unprivileged apptainer inside of the container
+    # adapted from https://apptainer.org/docs/admin/1.4/installation.html#install-unprivileged-from-pre-built-binaries
+    mkdir -p /opt
+    curl -s https://raw.githubusercontent.com/apptainer/apptainer/main/tools/install-unprivileged.sh | bash -s - /opt/apptainer
+
+%environment
+    export PATH="/opt/apptainer/bin:${PATH}"

software/Apptainer/apptainer-in-apptainer/nice-ubuntu.def

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+Bootstrap: docker
+From: ubuntu:24.04
+
+%post
+    export DEBIAN_FRONTEND=noninteractive
+    apt update -y
+    apt install -y \
+        bash \
+        cpio \
+        curl \
+        git \
+        nano \
+        python3 \
+        python3-pip \
+        rpm2cpio \
+        tar \
+        tree \
+        unzip \
+        vim \
+        wget
+
+    # Installing unprivileged apptainer inside of the container
+    # adapted from https://apptainer.org/docs/admin/1.4/installation.html#install-unprivileged-from-pre-built-binaries
+    mkdir -p /opt
+    curl -s https://raw.githubusercontent.com/apptainer/apptainer/main/tools/install-unprivileged.sh | bash -s - /opt/apptainer
+
+%environment
+    export PATH=/opt/apptainer/bin:$PATH