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==Running Programs Within a Container== | ==Running Programs Within a Container== | ||
===<code>sudo</code>=== | |||
Many users ask about <code>sudo</code> since documentation and web sites often discuss using <code>sudo</code>. Know the ability to use <code>sudo</code> to obtain superuser/root permissions which is not available on our clusters. Should you require using <code>sudo</code>, consider the following options: | Many users ask about <code>sudo</code> since documentation and web sites often discuss using <code>sudo</code>. Know the ability to use <code>sudo</code> to obtain superuser/root permissions which is not available on our clusters. Should you require using <code>sudo</code>, consider the following options: | ||
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* Apptainer version 1.1.x has improved support for users using <code>--fakeroot</code> implicitly and explicitly so some things may be possible that were not with Apptainer version 1.0 and Singularity. This includes being able to build some images from <code>.def</code> definition files and building some images without needing to use <code>sudo</code>. That said, know not all images will be able to be built without needing to use <code>sudo</code> or real root. | * Apptainer version 1.1.x has improved support for users using <code>--fakeroot</code> implicitly and explicitly so some things may be possible that were not with Apptainer version 1.0 and Singularity. This includes being able to build some images from <code>.def</code> definition files and building some images without needing to use <code>sudo</code>. That said, know not all images will be able to be built without needing to use <code>sudo</code> or real root. | ||
===When Building Images/Overlays=== | |||
Should you need to build your own container image(s) or overlay(s), be aware of the following: | Should you need to build your own container image(s) or overlay(s), be aware of the following: | ||
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* avoid using Lustre/GPFS filesystems as they don't have the feature set required to properly support building Apptainer containers (including <code>--fakeroot</code>): [https://apptainer.org/docs/admin/main/installation.html#lustre-gpfs link to Apptainer documentation]. | * avoid using Lustre/GPFS filesystems as they don't have the feature set required to properly support building Apptainer containers (including <code>--fakeroot</code>): [https://apptainer.org/docs/admin/main/installation.html#lustre-gpfs link to Apptainer documentation]. | ||
===Important Command Line Options=== | |||
Software that is run inside a container runs in a different environment using different libraries and tools than what is installed on the host system. It is, therefore, important to run programs within containers by '''not''' using any environment settings or software defined outside of the container. Unfortunately, by default, Apptainer will run adopting the shell environment of the host and this can result in issues when running programs. To avoid such issues, when using <code>apptainer run</code>, <code>apptainer shell</code>, <code>apptainer exec</code>, and/or </code>apptainer instance</code>, use one of these options (with more preference to those options listed earlier in the table below): | Software that is run inside a container runs in a different environment using different libraries and tools than what is installed on the host system. It is, therefore, important to run programs within containers by '''not''' using any environment settings or software defined outside of the container. Unfortunately, by default, Apptainer will run adopting the shell environment of the host and this can result in issues when running programs. To avoid such issues, when using <code>apptainer run</code>, <code>apptainer shell</code>, <code>apptainer exec</code>, and/or </code>apptainer instance</code>, use one of these options (with more preference to those options listed earlier in the table below): | ||
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* When using bind mounts, see the [[#Bind_Mounts|section on bind mounts]] below since not all Alliance clusters are the same concerning the exact bind mounts needed to access <code>/home</code>, <code>/project</code>, and <code>/scratch</code>. | * When using bind mounts, see the [[#Bind_Mounts|section on bind mounts]] below since not all Alliance clusters are the same concerning the exact bind mounts needed to access <code>/home</code>, <code>/project</code>, and <code>/scratch</code>. | ||
===Using GPUs=== | |||
When running software inside a container that requires the use of GPUs it is important to do the following: | When running software inside a container that requires the use of GPUs it is important to do the following: | ||
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An example of [[#Using_NVIDIA_GPUs_Within_an_Apptainer_Container|using NVIDIA GPUs within an apptainer container]] appears later on this page. | An example of [[#Using_NVIDIA_GPUs_Within_an_Apptainer_Container|using NVIDIA GPUs within an apptainer container]] appears later on this page. | ||
===Using MPI Programs=== | |||
If you need to run MPI programs inside a container there are things that need to be done in the host environment in order for such to work. Please see the [[#Running_MPI_Programs_Inside_an_Apptainer Container|Running MPI Programs section below]] for an example of how to run MPI programs inside a container. The [http://apptainer.org/docs/user/main/mpi.html official Apptainer documentation] has more information concerning how MPI programs can be run inside a container. | If you need to run MPI programs inside a container there are things that need to be done in the host environment in order for such to work. Please see the [[#Running_MPI_Programs_Inside_an_Apptainer Container|Running MPI Programs section below]] for an example of how to run MPI programs inside a container. The [http://apptainer.org/docs/user/main/mpi.html official Apptainer documentation] has more information concerning how MPI programs can be run inside a container. | ||