[et_pb_section fb_built=”1″ fullwidth=”on” _builder_version=”4.16″ _module_preset=”default” global_colors_info=”{}”][et_pb_fullwidth_menu menu_id=”15″ menu_style=”centered” fullwidth_menu=”on” active_link_color=”#d80b8c” dropdown_menu_line_color=”#221f72″ _builder_version=”4.16″ _module_preset=”default” menu_font=”|600|||||||” menu_text_color=”#FFFFFF” menu_font_size=”16px” background_color=”#221f72″ background_layout=”dark” sticky_position=”top” global_colors_info=”{}”][\/et_pb_fullwidth_menu][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”4.16″ custom_padding=”0px||0px||false|false” global_colors_info=”{}”][et_pb_row _builder_version=”4.16″ background_size=”initial” background_position=”top_left” background_repeat=”repeat” custom_padding=”||3px||false|false” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||”][et_pb_text admin_label=”Breadcrumb” _builder_version=”4.16″ _module_preset=”default” custom_padding=”||0px|||” global_colors_info=”{}”]<\/p>\n
Scientific Computing and Data<\/a> \/ High Performance Computing<\/a> \/ Documentation<\/a> \/ Running Container: Apptainer\/Singularity<\/p>\n [\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”4.16″ _module_preset=”default” global_colors_info=”{}”][et_pb_row _builder_version=”4.16″ _module_preset=”default” global_colors_info=”{}”][et_pb_column type=”4_4″ _builder_version=”4.16″ _module_preset=”default” global_colors_info=”{}”][et_pb_text admin_label=”Introduction” _builder_version=”4.16″ _module_preset=”default” header_font=”|600|||||||” header_text_color=”#221f72″ header_font_size=”26px” header_2_text_color=”#221f72″ header_2_font_size=”24px” custom_margin=”10px||20px||false|false” custom_padding=”10px||20px||false|false” global_colors_info=”{}”]<\/p>\n <\/p>\n On the Minerva HPC cluster, Apptainer (formerly known as Singularity) is the supported container runtime environment, known for its compatibility with high-performance computing (HPC) systems and enhanced security model. Unlike Docker, which requires root privileges and runs persistent daemons\u2014posing potential security risks on multi-user HPC clusters\u2014Apptainer was designed from the ground up to support secure, non-privileged container execution.<\/p>\n Although Docker is not available directly on Minerva for these reasons, existing Docker container images can be seamlessly converted and executed using Apptainer. This compatibility allows users to leverage the vast ecosystem of Docker containers while adhering to the stricter security and user access controls required on shared compute infrastructure.<\/p>\n Apptainer enables you to create and execute containers that encapsulate complex software environments into a single portable and reproducible image file (typically with a You may choose to use Apptainer on Minerva when:<\/p>\n The software you need has complex dependencies that are difficult or impossible to install on your local machine or the HPC cluster.<\/p>\n<\/li>\n The application requires newer kernel versions or system-level libraries that are not supported by the cluster\u2019s operating system.<\/p>\n<\/li>\n You need to reproduce a past analysis, share workflows with collaborators, or maintain long-term reproducibility of scientific pipelines.<\/p>\n<\/li>\n<\/ul>\n [\/et_pb_text][et_pb_text admin_label=”How to use apptainer on Minerva” _builder_version=”4.16″ _module_preset=”default” header_font=”|600|||||||” header_text_color=”#221f72″ header_font_size=”26px” header_2_text_color=”#221f72″ header_2_font_size=”24px” custom_margin=”10px||20px||false|false” custom_padding=”10px||||false|false” global_colors_info=”{}”]<\/p>\n Search for available Apptainer and Singularity Modules on Minerva:<\/p>\n [\/et_pb_text][et_pb_image src=”https:\/\/scpublic.dmz.hpc.mssm.edu\/HPC\/apptainer\/ml_av_apptainer.png” _builder_version=”4.16″ _module_preset=”default” width=”60%” max_width=”60%” module_alignment=”center” global_colors_info=”{}”][\/et_pb_image][et_pb_image src=”https:\/\/scpublic.dmz.hpc.mssm.edu\/HPC\/apptainer\/ml_av_singularity.png” _builder_version=”4.16″ _module_preset=”default” width=”60%” max_width=”60%” module_alignment=”center” custom_margin=”||10px||false|false” custom_padding=”||10px||false|false” global_colors_info=”{}”][\/et_pb_image][et_pb_text admin_label=”How to use apptainer on Minerva” _builder_version=”4.16″ _module_preset=”default” header_font=”|600|||||||” header_text_color=”#221f72″ header_font_size=”26px” header_2_text_color=”#221f72″ header_2_font_size=”24px” custom_margin=”10px||20px||false|false” custom_padding=”10px||20px||false|false” hover_enabled=”0″ global_colors_info=”{}” sticky_enabled=”0″]<\/p>\n Since Singularity and Apptainer share nearly identical command-line interfaces, the following sections will exclusively refer to Apptainer for consistency, but these commands are compatible with Singularity.\u00a0<\/p>\n Load the apptainer module:<\/p>\n You can use \u201capptainer pull\u201d to download a container image from a give URI, such as pull the image from Sylabs Cloud library:\/\/, Singularity Hub shub:\/\/ and Docker Hub docker:\/\/<\/p>\n To pull a docker image:<\/p>\n To create a container within a writable directory (called a sandbox):<\/p>\n [\/et_pb_text][et_pb_text admin_label=”Running an Apptainer Container on Minerva” _builder_version=”4.16″ _module_preset=”default” header_font=”|600|||||||” header_text_color=”#221f72″ header_font_size=”26px” header_2_text_color=”#221f72″ header_2_font_size=”24px” custom_margin=”10px||20px||false|false” custom_padding=”10px||20px||false|false” global_colors_info=”{}”]<\/p>\n When running within an Apptainer container, a user has the same permissions and privileges that he or she would have outside the container.<\/p>\n Once you have the images, you can shell into it (The shell subcommand is useful for interactive work)<\/p>\n To run a container with the default runscript command:<\/p>\n Or run a custom command with exec, or pipes for batch processing (e.g. within a LSF job), For example:<\/p>\n Where [\/et_pb_text][et_pb_image src=”https:\/\/scpublic.dmz.hpc.mssm.edu\/HPC\/apptainer\/apptainer_os.png” _builder_version=”4.16″ _module_preset=”default” width=”60%” max_width=”60%” module_alignment=”center” custom_margin=”||20px||false|false” custom_padding=”||20px||false|false” global_colors_info=”{}”][\/et_pb_image][et_pb_text admin_label=”Building External Directories” _builder_version=”4.16″ _module_preset=”default” header_font=”|600|||||||” header_text_color=”#221f72″ header_font_size=”26px” header_2_text_color=”#221f72″ header_2_font_size=”24px” custom_margin=”10px||20px||false|false” custom_padding=”10px||20px||false|false” global_colors_info=”{}”]<\/p>\n Binding a directory to your Apptainer container allows you to access files in a host system directory from within your container.<\/p>\n By default, \u00a0 Warning: Sometimes libraries or packages in\u00a0 Apptainer supports running on GPUs from within containers. The\u00a0 IMPORTANT:<\/b> [\/et_pb_text][et_pb_text admin_label=”Build your own containers” _builder_version=”4.16″ _module_preset=”default” header_font=”|600|||||||” header_text_color=”#221f72″ header_font_size=”26px” header_2_text_color=”#221f72″ header_2_font_size=”24px” custom_margin=”10px||20px||false|false” custom_padding=”10px||20px||false|false” global_colors_info=”{}”]<\/p>\n Although there are a lot of container images contributed by various users on Docker Hub and Singularity Hub, there is time that you want to create\/build your own containers. You can build your own container images either use Singularity Remote Builder<\/a> or your local Linux workstation with which you have the root access. If you don’t have a Linux system you could easily install one in a virtual machine using software like VirtualBox<\/a>, Vagrant<\/a>, VMware<\/a>, or Parallels<\/a>.<\/p>\n [\/et_pb_text][et_pb_text admin_label=”Useful Links” _builder_version=”4.16″ _module_preset=”default” header_font=”|600|||||||” header_text_color=”#221f72″ header_font_size=”26px” header_2_text_color=”#221f72″ header_2_font_size=”24px” custom_margin=”10px||20px||false|false” custom_padding=”10px||20px||false|false” global_colors_info=”{}”]<\/p>\n [\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":" Scientific Computing and Data \/ High Performance Computing \/ Documentation \/ Running Container: Apptainer\/SingularityApptainer\/Singularity On the Minerva HPC cluster, Apptainer (formerly known as Singularity) is the supported container runtime environment, known for its compatibility with high-performance computing (HPC) systems and enhanced security model. Unlike Docker, which requires root privileges and runs persistent daemons\u2014posing potential […]<\/p>\n","protected":false},"author":624,"featured_media":0,"parent":35,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"","footnotes":""},"class_list":["post-11139","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages\/11139","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/users\/624"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/comments?post=11139"}],"version-history":[{"count":12,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages\/11139\/revisions"}],"predecessor-version":[{"id":13298,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages\/11139\/revisions\/13298"}],"up":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages\/35"}],"wp:attachment":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/media?parent=11139"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Apptainer\/Singularity<\/h1>\n
.sif<\/code> extension). These images are self-contained, making them ideal for consistent and repeatable workflows across different environments.<\/p>\n\n
Apptainer\/Singularity Modules on Minerva HPC<\/h2>\n
<\/strong><\/a><\/code><\/p>\nHow to use Apptainer\/Singularity on Minerva HPC<\/h2>\n
$ module load apptainer\/1.3.6<\/code><\/pre>\n$ apptainer pull --name hello-world_latest.sif shub:\/\/vsoch\/hello-world<\/code><\/pre>\n$ apptainer pull ubuntu_latest.sif docker:\/\/ubuntu:latest<\/code><\/pre>\n$ apptainer build --sandbox lolcow\/ shub:\/\/GodloveD\/lolcow<\/code><\/pre>\n<\/strong><\/a><\/code><\/p>\nRunning an Apptainer Container<\/h2>\n
# From the cluster\r\n$ apptainer shell ubuntu_latest.sif<\/code><\/pre>\n$ apptainer run hello-world_latest.sif<\/code><\/pre>\n$ apptainer exec ubuntu_latest.sif \/path\/to\/my\/script.sh<\/code><\/pre>\nscript.sh<\/code> contains the processing steps to be executed within the LSF batch job. Alternatively, you can pass any standard Linux command directly to the exec<\/code> subcommand. The exec<\/code> subcommand also supports features like pipes and output redirection. Below is a simple example demonstrating a change in the Linux distribution environment:<\/p>\nBuilding External Directories<\/h2>\n
\/tmp<\/code>, current working directory $PWD<\/code>, user home directory $HOME<\/code>, and \/sc\/arion\/\u00a0<\/code>is automatically mounted into an Apptainer container, which should be enough for most of the cases. You can also bind other directories into your Apptainer container yourself. To get a shell with a specified ‘dir’ mounted in the image.<\/span><\/p>\n\n
$ apptainer run -B \/user\/specified\/dir ubuntu_latest.sif<\/code><\/pre>\n<\/blockquote>\n$HOME <\/code>got picked up in container, especially for python packages at ~\/.local <\/code>and R library $_LIBS_USER at ~\/.Rlib)<\/code>.[\/et_pb_text][et_pb_text admin_label=”Running GPU-enabled containers” _builder_version=”4.16″ _module_preset=”default” header_font=”|600|||||||” header_text_color=”#221f72″ header_font_size=”26px” header_2_text_color=”#221f72″ header_2_font_size=”24px” custom_margin=”10px||20px||false|false” custom_padding=”10px||20px||false|false” global_colors_info=”{}”]<\/p>\nRunning GPU-Enabled Containers<\/h2>\n
--nv\u00a0<\/code>option must be passed to the exec or shell subcommand. For example:<\/p>\n\n
$ module load apptainer\/1.3.6 \r\n$ apptainer pull docker:\/\/tensorflow\/tensorflow:latest-gpu \r\n$ apptainer shell --nv -B \/run tensorflow_latest-gpu-jupyter.sif<\/code><\/pre>\n<\/blockquote>\n
Apptainer gives you the ability to install and run applications in your own Linux environment with your own customized software stack. While the HPC staff can provide guidance on how to create and use Apptainer containers, we do not have the resources to manage containers for individual users. If you decide to use Apptainer, it is your responsibility to build and manage your own containers, and software within your own Linux environment.<\/p>\nBuilding Your Own Containers<\/h2>\n
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sudo<\/code> privileges for users<\/li>\n
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$ ml python \r\n$ spython recipe Dockerfile Singularity<\/code><\/pre>\n<\/blockquote>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\nSome Helpful External Web Sites<\/h2>\n
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