Apptainer (Previously known as Singularity)
Background
Singularity Apptainer is a container solution created by necessity for scientific and application-driven workloads. The Singularity Apptainer containers can be used to package entire scientific workflows, software and libraries, and even data. This means that you don’t have to ask your cluster admin to install anything for you - you can put it in a Singularity Apptainer container and run.
(see webpage https://www.sylabs.io and/or httphttps://singularity.lbl.gov/ for apptainer.org/docs/user/latest/ for details)
Build a
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Apptainer Container
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| title | Admin assistance required |
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Singularity Apptainer now requires fakeroot privilege for non-root users to create container images. Please contact an admin to set up your account with fakeroot. |
Build a container from a
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wget https://wiki.ncsa.illinois.edu/download/attachments/82518873/ubuntu1604-cuda92-ompi400.def
singularityapptainer build ubuntu1604-cuda92-ompi400.sif ubuntu1604-cuda92-ompi400.def |
Pull a container from
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Apptainer Hub or Docker Hub
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singularityapptainer pull docker://nvidia/cuda-ppc64le:9.2-cudnn7-devel-ubuntu16.04 |
Run a
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Apptainer Container
| Warning |
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| title | Mounted home filesystem |
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| Unlike docker (which provides an isolated filesystem), Singluarity mounts your home directory into the container. Be aware of this so you don't accidentally delete things in your home directory. |
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Run a container with "exec" command
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mpirun -n 4 singularityapptainer exec --nv /opt/apps/samples-image/ubuntu1604-cuda92-ompi400.sif hostname |
Run a container with shell
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singularityapptainer shell --nv /opt/apps/samples-image/ubuntu1604-cuda92-ompi400.sif |
Build a writable
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Apptainer container
By default, the Singularity Apptainer container filesystem is read-only. There are 2 options to build a writable Singularity Apptainer container.
The "--sandbox" option allows users to create a container within a writable directory (called a sandbox). It’s possible to create a sandbox without root privileges, but to ensure proper file permissions it is recommended to do so as root.
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singularityapptainer build --sandbox cuda-ppc64le/ docker://nvidia/cuda-ppc64le:9.2-cudnn7-devel-ubuntu16.0
singularityapptainer shell --writable cuda-ppc64le/ |
The "--writable" option allows users to create a writable ext3 image. Root privileges are required to create writable containers.
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singularityapptainer build --writable cuda-ppc64le.sif docker://nvidia/cuda-ppc64le:9.2-cudnn7-devel-ubuntu16.04
singularityapptainer shell --writable cuda-ppc64le.sif |
Build a writable
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Apptainer container based on an existing read-only image
Convert it to a writable directory (a sandbox):
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singularityapptainer build --sandbox cuda-ppc64le-mod/ cuda-ppc64le.sif
singularityapptainer shell --writable cuda-ppc64le-mod/ |
Use an existing container as a target to build a new container
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singularityapptainer build --writable cuda-ppc64le-mod.sif cuda-ppc64le.sif
singularityapptainer shell --writable cuda-ppc64le-mod.sif |
Frequently Asked Questions
- Can I run a Singularity Apptainer container with x86 architecture image on an IBM ppc64le system?
A: Singularity Apptainer cannot directly run x86 binaries on an IBM Power system because the bytes of machine code are different. Users need to make sure their own images are built for "ppc64le" rather than "x86". - What is the option "--nv" means?
A: The "--nv" allows the Singularity Apptainer container to leverage the NVIDIA GPU on the host system. Use this option if the container asks for nvidia-docker support.
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