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Singularity: Difference between revisions
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(Added troubleshooting for tmpfs issues in some modern linux distributions. Added sandbox use in building containers. Added troubleshooting for using CUDA with singularity. I did not add any reference number, as I didn't want to break anything.) |
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'''NOTE:''' Any image you create on your own computer needs to be uploaded to the cluster before you can use that image. | '''NOTE:''' Any image you create on your own computer needs to be uploaded to the cluster before you can use that image. | ||
====Build error when building on a Linux distribution==== | ====Build error when building on a Linux distribution==== <!--T:122--> | ||
When building on certain Linux distributions, you may get this error despite having enough memory on your device. | When building on certain Linux distributions, you may get this error despite having enough memory on your device. | ||
<!--T:123--> | |||
<source>$ WARNING: 'nodev' mount option set on /tmp, it could be a source of failure during build process | <source>$ WARNING: 'nodev' mount option set on /tmp, it could be a source of failure during build process | ||
$FATAL: no memory left on device</source> | $FATAL: no memory left on device</source> | ||
<!--T:124--> | |||
Many modern Linux distributions, use an in-memory <tt>tmpfs</tt> filesystem, which may limit the size of the container you can build. | Many modern Linux distributions, use an in-memory <tt>tmpfs</tt> filesystem, which may limit the size of the container you can build. | ||
The [https://sylabs.io/guides/3.6/user-guide/build_env.html#temporary-folders Singularity Documentation] gives a more detailed explanation. | The [https://sylabs.io/guides/3.6/user-guide/build_env.html#temporary-folders Singularity Documentation] gives a more detailed explanation. | ||
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If that is the case, you can solve the problem by setting SINGULARITY_TMPDIR to a disk location. | If that is the case, you can solve the problem by setting SINGULARITY_TMPDIR to a disk location. | ||
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<source>$ SINGULARITY_TMPDIR="disk/location" singularity build IMAGE_NAME.sif docker://DOCKER-IMAGE-NAME</source> | <source>$ SINGULARITY_TMPDIR="disk/location" singularity build IMAGE_NAME.sif docker://DOCKER-IMAGE-NAME</source> | ||
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$ singularity build gqcp.sif docker-archive://gqcp.tar</source> | $ singularity build gqcp.sif docker-archive://gqcp.tar</source> | ||
===Creating a custom image with sandbox=== | ===Creating a custom image with sandbox=== <!--T:127--> | ||
<!--T:128--> | |||
The <tt>--sandbox</tt> flag allows you to create a container within a writable directory. | The <tt>--sandbox</tt> flag allows you to create a container within a writable directory. | ||
this allows for easy modifications of existing containers. | this allows for easy modifications of existing containers. | ||
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* clusters using Infiniband need UCX. | * clusters using Infiniband need UCX. | ||
=== Using CUDA on Compute Canada clusters === | === Using CUDA on Compute Canada clusters === <!--T:129--> | ||
<!--T:130--> | |||
If you are running programs which use the CUDA library, you must make sure that your Singularity container has CUDA installed. | If you are running programs which use the CUDA library, you must make sure that your Singularity container has CUDA installed. | ||
<!--T:131--> | |||
The <tt>--nv</tt> flag needs to be added to make CUDA work. | The <tt>--nv</tt> flag needs to be added to make CUDA work. | ||
<!--T:132--> | |||
<source> | <source> | ||
$ srun singularity run --nv container-name.sif [job to do] | $ srun singularity run --nv container-name.sif [job to do] | ||