Singularity - Revision history

Derek: Redirected page to Apptainer

2022-10-14T16:57:53Z

Redirected page to Apptainer

Mbaney at 16:33, 5 May 2022

2022-05-05T16:33:18Z

← Older revision		Revision as of 16:33, 5 May 2022
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	[https://sylabs.io/docs/ Singularity] is a container platform that doesn't elevate the privileges of a user running the container. This is important as UMIACS runs many multi-tenant ~~computer systems~~ and doesn't provide administrative control to users in them.		[https://sylabs.io/docs/ Singularity] is a container platform that doesn't elevate the privileges of a user running the container. This is important as UMIACS runs many multi-tenant hosts and doesn't provide administrative control to users on them.

	You can find out what the current version is that we provide by running the '''singularity --version''' command. If this instead says <code>singularity: command not found</code> please contact staff and we will ensure that the software is available on the host you are looking for it on.		You can find out what the current version is that we provide by running the '''singularity --version''' command. If this instead says <code>singularity: command not found</code> please contact staff and we will ensure that the software is available on the host you are looking for it on.
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	</pre>		</pre>

	Singularity can run a variety of images including its own format and Docker images. To create images you ~~however~~ need to have administrative rights ~~and therefore~~ you will need to do this on a host that you have access to (laptop or personal desktop).		Singularity can run a variety of images including its own format and [https://sylabs.io/guides/3.0/user-guide/singularity_and_docker.html Docker images]. To create images, you need to have administrative rights. Therefore, you will need to do this on a host that you have administrative access to (laptop or personal desktop) rather than a UMIACS-supported host.

	~~If you are going to pull large images you may run out of space in your home directory so we suggest you run the following commands to setup~~ a ~~alternate cache directory~~.

			If you are going to pull large images, you may run out of space in your home directory. We suggest you run the following commands to setup a alternate cache directory.
	<pre>		<pre>
	export WORKDIR=/scratch0/username		export WORKDIR=/scratch0/username
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	</pre>		</pre>

	We do suggest you pull images down into an intermediate file ('''SIF''' file) as you ~~can~~ then not have to worry about re-caching the image.		We do suggest you pull images down into an intermediate file ('''SIF''' file) as you then do not have to worry about re-caching the image.

	<pre>		<pre>
	$ singularity pull cuda10.2.sif docker://nvidia/cuda:10.2-devel		$ singularity pull cuda10.2.sif docker://nvidia/cuda:10.2-devel
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	</pre>		</pre>

	Now you can run the local image with the '''run''' command or start a shell with the '''shell''' command. Please note that if you are in an environment with GPUs and you want to access them inside the container you do need to specify the '''--nv''' flag.		Now you can run the local image with the '''run''' command or start a shell with the '''shell''' command. Please note that if you are in an environment with GPUs and you want to access them inside the container you need to specify the '''--nv''' flag.

	<pre>		<pre>
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	==Example==		==Example==
			We have a [https://gitlab.umiacs.umd.edu/derek/gpudocker gpudocker] example workflow using our [[GitLab]] as a Docker registry. You can clone the repository and further customize this to your needs. The workflow is:
	We have a [https://gitlab.umiacs.umd.edu/derek/gpudocker gpudocker] example workflow using our [[GitLab]] as a ~~docker~~ registry. You can ~~for~~ the repository and further customize this to your needs. The workflow is ~~that you have~~ a ~~local~~ laptop or desktop ~~you can run Docker~~ on to create the image~~, tag it~~ and and push it to the repository. ~~Then you pull~~ the image down onto one of our workstations/clusters and run with your data.		# Run Docker on a laptop or personal desktop on to create the image.
			# Tag the image and and push it to the repository.
			# Pull the image down onto one of our workstations/clusters and run it with your data.

	<pre>		<pre>

Mbaney at 16:50, 7 May 2021

2021-05-07T16:50:45Z

← Older revision		Revision as of 16:50, 7 May 2021
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	<pre>		<pre>
	export WORKDIR=/~~scatch0~~/~~derek~~		export WORKDIR=/scratch0/username
	export SINGULARITY_CACHEDIR=${WORKDIR}/.cache		export SINGULARITY_CACHEDIR=${WORKDIR}/.cache
	mkdir -p $SINGULARITY_CACHEDIR		mkdir -p $SINGULARITY_CACHEDIR

Mbaney at 13:47, 4 September 2020

2020-09-04T13:47:36Z

← Older revision		Revision as of 13:47, 4 September 2020
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	[https://sylabs.io/docs/ Singularity] is a container platform that doesn't elevate the privileges of a user running the container. This is important as UMIACS runs many multi-tenant computer systems and doesn't provide administrative control to users in them.		[https://sylabs.io/docs/ Singularity] is a container platform that doesn't elevate the privileges of a user running the container. This is important as UMIACS runs many multi-tenant computer systems and doesn't provide administrative control to users in them.

	You can find out what the current version is that we provide by running the '''singularity''' command. If this says <tt>command not found</tt> please contact staff and we will ensure that the software is available on the host you are looking for.		You can find out what the current version is that we provide by running the '''singularity --version''' command. If this instead says <code>singularity: command not found</code> please contact staff and we will ensure that the software is available on the host you are looking for it on.

	<pre>		<pre>

Liam at 15:24, 20 April 2020

2020-04-20T15:24:00Z

← Older revision		Revision as of 15:24, 20 April 2020
Line 1:		Line 1:
	[https://sylabs.io/docs/ Singularity] is a container platform that doesn't elevate the privileges of a user running the container. This is important as UMIACS runs many multi-tenant computer systems and doesn't provide administrative control to users in them.		[https://sylabs.io/docs/ Singularity] is a container platform that doesn't elevate the privileges of a user running the container. This is important as UMIACS runs many multi-tenant computer systems and doesn't provide administrative control to users in them.

	You can find out what the current version that we provide by running the '''singularity''' command. If this says command not found please contact staff and we will ensure that the software is available on the host you are looking for.		You can find out what the current version is that we provide by running the '''singularity''' command. If this says <tt>command not found</tt> please contact staff and we will ensure that the software is available on the host you are looking for.

	<pre>		<pre>

Mbaney at 15:16, 20 April 2020

2020-04-20T15:16:28Z

← Older revision		Revision as of 15:16, 20 April 2020
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	==Example==		==Example==

	We have a [https://gitlab.umiacs.umd.edu/derek/gpudocker gpudocker] example workflow using our [[~~Gitlab~~]] as a docker registry. You can for the repository and further customize this to your needs. The workflow is that you have a local laptop or desktop you can run Docker on to create the image, tag it and and push it to the repository. Then you pull the image down onto one of our workstations/clusters and run with your data.		We have a [https://gitlab.umiacs.umd.edu/derek/gpudocker gpudocker] example workflow using our [[GitLab]] as a docker registry. You can for the repository and further customize this to your needs. The workflow is that you have a local laptop or desktop you can run Docker on to create the image, tag it and and push it to the repository. Then you pull the image down onto one of our workstations/clusters and run with your data.

	<pre>		<pre>

Derek at 16:33, 14 April 2020

2020-04-14T16:33:53Z

@@ Line 10: / Line 10: @@
 Singularity can run a variety of images including its own format and Docker images.  To create images you however need to have administrative rights and therefore you will need to do this on a host that you have access to (laptop or personal desktop).
-If you are going to pull large images you may run out of space in your home directory so we suggest you run the following commands to setup a alternate cache directory:
+If you are going to pull large images you may run out of space in your home directory so we suggest you run the following commands to setup a alternate cache directory.
 <pre>
@@ Line 65: / Line 65: @@
 $ singularity run --nv cuda10.2.sif nvidia-smi -L
 GPU 0: GeForce GTX 1080 Ti (UUID: GPU-9ee980c3-8746-08dd-8e14-82fbaf88367e)
 </pre>

Derek at 16:12, 14 April 2020

2020-04-14T16:12:50Z

← Older revision		Revision as of 16:12, 14 April 2020
Line 1:		Line 1:
	[https://sylabs.io/docs/ Singularity] is a container platform that doesn't elevate the privileges of a user running the container. This is important as UMIACS runs many multi-tenant computer systems and doesn't provide administrative control to users in them.		[https://sylabs.io/docs/ Singularity] is a container platform that doesn't elevate the privileges of a user running the container. This is important as UMIACS runs many multi-tenant computer systems and doesn't provide administrative control to users in them.

	It can ~~run a variety of images including its own format and Docker images~~. ~~To create images you however need to have administrative rights~~ and ~~therefore you~~ will ~~need to do this~~ on a host ~~that~~ you ~~have access to (laptop or personal desktop)~~.		You can find out what the current version that we provide by running the '''singularity''' command. If this says command not found please contact staff and we will ensure that the software is available on the host you are looking for.

	~~First if~~ you are going to pull large images you may run out of space in your home directory so we suggest you run the following commands to setup a alternate cache directory:		<pre>
			$ singularity --version
			singularity version 3.4.2-1.1.el7
			</pre>

			Singularity can run a variety of images including its own format and Docker images. To create images you however need to have administrative rights and therefore you will need to do this on a host that you have access to (laptop or personal desktop).

			If you are going to pull large images you may run out of space in your home directory so we suggest you run the following commands to setup a alternate cache directory:

	<pre>		<pre>

Derek at 16:11, 14 April 2020

2020-04-14T16:11:11Z

← Older revision		Revision as of 16:11, 14 April 2020
Line 1:		Line 1:
	Singularity is a container platform that doesn't elevate the privileges of a user running the container. This is important as UMIACS runs many multi-tenant computer systems and doesn't provide administrative control to users in them.		[https://sylabs.io/docs/ Singularity] is a container platform that doesn't elevate the privileges of a user running the container. This is important as UMIACS runs many multi-tenant computer systems and doesn't provide administrative control to users in them.

	It can run a variety of images including its own format and Docker images. To create images you however need to have administrative rights and therefore you will need to do this on a host that you have access to (laptop or personal desktop).		It can run a variety of images including its own format and Docker images. To create images you however need to have administrative rights and therefore you will need to do this on a host that you have access to (laptop or personal desktop).

Derek: Created page with "Singularity is a container platform that doesn't elevate the privileges of a user running the container. This is important as UMIACS runs many multi-tenant computer systems a..."

2020-04-14T16:09:56Z

Created page with "Singularity is a container platform that doesn't elevate the privileges of a user running the container. This is important as UMIACS runs many multi-tenant computer systems a..."

New page

Singularity is a container platform that doesn't elevate the privileges of a user running the container. This is important as UMIACS runs many multi-tenant computer systems and doesn't provide administrative control to users in them.

It can run a variety of images including its own format and Docker images. To create images you however need to have administrative rights and therefore you will need to do this on a host that you have access to (laptop or personal desktop).

First if you are going to pull large images you may run out of space in your home directory so we suggest you run the following commands to setup a alternate cache directory:

<pre>
export WORKDIR=/scatch0/derek
export SINGULARITY_CACHEDIR=${WORKDIR}/.cache
mkdir -p $SINGULARITY_CACHEDIR
</pre>

We do suggest you pull images down into an intermediate file ('''SIF''' file) as you can then not have to worry about re-caching the image.

<pre>
$ singularity pull cuda10.2.sif docker://nvidia/cuda:10.2-devel
INFO: Converting OCI blobs to SIF format
INFO: Starting build...
Getting image source signatures
Copying blob sha256:7ddbc47eeb70dc7f08e410a6667948b87ff3883024eb41478b44ef9a81bf400c
25.45 MiB / 25.45 MiB [====================================================] 0s
Copying blob sha256:c1bbdc448b7263673926b8fe2e88491e5083a8b4b06ddfabf311f2fc5f27e2ff
34.53 KiB / 34.53 KiB [====================================================] 0s
Copying blob sha256:8c3b70e3904492c753652606df4726430426f42ea56e06ea924d6fea7ae162a1
845 B / 845 B [============================================================] 0s
Copying blob sha256:45d437916d5781043432f2d72608049dcf74ddbd27daa01a25fa63c8f1b9adc4
162 B / 162 B [============================================================] 0s
Copying blob sha256:d8f1569ddae616589c5a2dabf668fadd250ee9d89253ef16f0cb0c8a9459b322
6.88 MiB / 6.88 MiB [======================================================] 0s
Copying blob sha256:902fc5ce82298797e09dc1b28ed942da3892a354321725fad6955ee651557e98
9.00 MiB / 9.00 MiB [======================================================] 0s
Copying blob sha256:ae1bb79c5cfc1c10948684c3a2964ec7444b19cae7edc487aa474804336b52c1
184 B / 184 B [============================================================] 0s
Copying blob sha256:fa6605c8fe7a3779c56b4768ac46738f160f005067f22c03e3cf5e87ad5d19d0
674.37 MiB / 674.37 MiB [==================================================] 8s
Copying blob sha256:0508a679d3397b66fdf6cd56db9a99e2b7af5a8519e9f9534d2dff07779f2482
783.58 MiB / 783.58 MiB [=================================================] 10s
Copying config sha256:44b5f1390c8715653c6488b3cb4fbee875c30cacadc827b2b4372b18318b2fa0
7.28 KiB / 7.28 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
2020/04/14 11:52:55 info unpack layer: sha256:7ddbc47eeb70dc7f08e410a6667948b87ff3883024eb41478b44ef9a81bf400c
2020/04/14 11:52:56 info unpack layer: sha256:c1bbdc448b7263673926b8fe2e88491e5083a8b4b06ddfabf311f2fc5f27e2ff
2020/04/14 11:52:56 info unpack layer: sha256:8c3b70e3904492c753652606df4726430426f42ea56e06ea924d6fea7ae162a1
2020/04/14 11:52:56 info unpack layer: sha256:45d437916d5781043432f2d72608049dcf74ddbd27daa01a25fa63c8f1b9adc4
2020/04/14 11:52:56 info unpack layer: sha256:d8f1569ddae616589c5a2dabf668fadd250ee9d89253ef16f0cb0c8a9459b322
2020/04/14 11:52:57 info unpack layer: sha256:902fc5ce82298797e09dc1b28ed942da3892a354321725fad6955ee651557e98
2020/04/14 11:52:57 info unpack layer: sha256:ae1bb79c5cfc1c10948684c3a2964ec7444b19cae7edc487aa474804336b52c1
2020/04/14 11:52:57 info unpack layer: sha256:fa6605c8fe7a3779c56b4768ac46738f160f005067f22c03e3cf5e87ad5d19d0
2020/04/14 11:53:14 info unpack layer: sha256:0508a679d3397b66fdf6cd56db9a99e2b7af5a8519e9f9534d2dff07779f2482
INFO: Creating SIF file...
INFO: Build complete: cuda10.2.sif
</pre>

Now you can run the local image with the '''run''' command or start a shell with the '''shell''' command. Please note that if you are in an environment with GPUs and you want to access them inside the container you do need to specify the '''--nv''' flag.

<pre>
$ singularity run --nv cuda10.2.sif nvidia-smi -L
GPU 0: GeForce GTX 1080 Ti (UUID: GPU-9ee980c3-8746-08dd-8e14-82fbaf88367e)
</pre>