SingularityContainerCreation - Revision history

ROMAIN ROUGNY rrougny@vub.ac.be: /* Creation of a container using a definition file */

2019-10-15T13:39:38Z

Creation of a container using a definition file

← Older revision		Revision as of 13:39, 15 October 2019
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	From: centos:latest		From: centos:latest
	</pre>		</pre>
	The first line indicates that we will use a container from [https://hub.docker.com/explore/ Docker hub], the second line specifies which container (the latest release of CentOS).		The first line indicates that we will use a container from [https://hub.docker.com/explore/ Docker hub], the second line specifies which container (the latest release of CentOS). You can also replace '''latest''' by the version number, like '''7''' or '''8'''.

	Now, if you issue the following command :		Now, if you issue the following command :

STEPHANE GERARD stgerard@vub.ac.be at 17:48, 30 October 2018

2018-10-30T17:48:19Z

← Older revision		Revision as of 17:48, 30 October 2018
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	mkdir /scratch		mkdir /scratch
	</pre>		</pre>
	'''Note''' : We may have noticed the absence of the "-B /user" option in the previous example. This is not a mistake : the home directory /user/<login> is always mounted by default inside the container. But again (sorry to insist) : the /user directory must exist beforehand in the container !		'''Note''' : We may have noticed the absence of the "-B /user" option in the previous example. This is not a mistake : the home directory of the user who launches the container (in this case : /user/<login>) is always mounted by default inside the container. But again (sorry to insist) : the /user directory must exist beforehand in the container !

	= Sources =		= Sources =
	* [https://www.sylabs.io/docs/ Singularity website] -> explanations to build a container on this [https://www.sylabs.io/guides/2.6/user-guide/build_a_container.html page].		* [https://www.sylabs.io/docs/ Singularity website] -> explanations to build a container on this [https://www.sylabs.io/guides/2.6/user-guide/build_a_container.html page].

STEPHANE GERARD stgerard@vub.ac.be at 17:43, 30 October 2018

2018-10-30T17:43:51Z

@@ Line 58: / Line 58: @@
 To discover the other possibilities of definition files, please consult this [https://www.sylabs.io/guides/2.6/user-guide/container_recipes.html page].
 = Sources =
 * [https://www.sylabs.io/docs/ Singularity website] -> explanations to build a container on this [https://www.sylabs.io/guides/2.6/user-guide/build_a_container.html page].

STEPHANE GERARD stgerard@vub.ac.be at 17:32, 30 October 2018

2018-10-30T17:32:27Z

← Older revision		Revision as of 17:32, 30 October 2018
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	</pre>		</pre>
	Here, the tarball 'foobar.tgz' from the host will be copied into the container in the /root directory before the %post section. This is useful when you need to install some programs from a tarball.		Here, the tarball 'foobar.tgz' from the host will be copied into the container in the /root directory before the %post section. This is useful when you need to install some programs from a tarball.

			To discover the other possibilities of definition files, please consult this [https://www.sylabs.io/guides/2.6/user-guide/container_recipes.html page].

	= Sources =		= Sources =
	* [https://www.sylabs.io/docs/ Singularity website] -> explanations to build a container on this [https://www.sylabs.io/guides/2.6/user-guide/build_a_container.html page].		* [https://www.sylabs.io/docs/ Singularity website] -> explanations to build a container on this [https://www.sylabs.io/guides/2.6/user-guide/build_a_container.html page].

STEPHANE GERARD stgerard@vub.ac.be at 17:27, 30 October 2018

2018-10-30T17:27:34Z

← Older revision		Revision as of 17:27, 30 October 2018
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	</pre>		</pre>

	If you need to include files		If you need to include files in the container before the commands of the %post section are executed, add a %file section like in this example :
			<pre>
			%files
			foobar.tgz /root/foobar.tgz
			</pre>
			Here, the tarball 'foobar.tgz' from the host will be copied into the container in the /root directory before the %post section. This is useful when you need to install some programs from a tarball.

	= Sources =		= Sources =
	* [https://www.sylabs.io/docs/ Singularity website] -> explanations to build a container on this [https://www.sylabs.io/guides/2.6/user-guide/build_a_container.html page].		* [https://www.sylabs.io/docs/ Singularity website] -> explanations to build a container on this [https://www.sylabs.io/guides/2.6/user-guide/build_a_container.html page].

STEPHANE GERARD stgerard@vub.ac.be at 17:20, 30 October 2018

2018-10-30T17:20:17Z

@@ Line 10: / Line 10: @@
 <pre>
 Bootstrap: docker
 From: centos:latest
 </pre>
@@ Line 33: / Line 32: @@
 If you want to transform the sandbox into a single image file, run the following command :
 <pre>
-sudo singularity build test1.simg test1.img
+$ sudo singularity build test1.simg test1.img
 </pre>
 = Sources =
 * [https://www.sylabs.io/docs/ Singularity website] -> explanations to build a container on this [https://www.sylabs.io/guides/2.6/user-guide/build_a_container.html page].

STEPHANE GERARD stgerard@vub.ac.be at 17:08, 30 October 2018

2018-10-30T17:08:42Z

← Older revision		Revision as of 17:08, 30 October 2018
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	If you want to transform the sandbox into a single image file, run the following command :		If you want to transform the sandbox into a single image file, run the following command :
	<pre>		<pre>
	~~blabla~~		sudo singularity build test1.simg test1.img
	</pre>		</pre>
	= Sources =		= Sources =
	* [https://www.sylabs.io/docs/ Singularity website] -> explanations to build a container on this [https://www.sylabs.io/guides/2.6/user-guide/build_a_container.html page].		* [https://www.sylabs.io/docs/ Singularity website] -> explanations to build a container on this [https://www.sylabs.io/guides/2.6/user-guide/build_a_container.html page].

STEPHANE GERARD stgerard@vub.ac.be at 15:58, 30 October 2018

2018-10-30T15:58:21Z

← Older revision		Revision as of 15:58, 30 October 2018
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	Singularity test1.img:~>		Singularity test1.img:~>
	</pre>		</pre>
	The "--writable" flag is really important if you want to bring modifications inside the image.		The "--writable" flag is really important if you want to bring modifications inside the image. Now, you can do "yum install -y vim" and log out.

			If you want to transform the sandbox into a single image file, run the following command :
			<pre>
			blabla
			</pre>
	= Sources =		= Sources =
	* [https://www.sylabs.io/docs/ Singularity website] -> explanations to build a container on this [https://www.sylabs.io/guides/2.6/user-guide/build_a_container.html page].		* [https://www.sylabs.io/docs/ Singularity website] -> explanations to build a container on this [https://www.sylabs.io/guides/2.6/user-guide/build_a_container.html page].

STEPHANE GERARD stgerard@vub.ac.be at 15:54, 30 October 2018

2018-10-30T15:54:25Z

← Older revision		Revision as of 15:54, 30 October 2018
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	after one or two minutes, you get an container ready to be used under the form of a directory test1.img.		after one or two minutes, you get an container ready to be used under the form of a directory test1.img.

	Now, let's say you want to install vim inside the container. Issue the following command :		Now, let's say you want to install vim inside the container. Issue the following command to open a shell as root inside the container :
	<pre>		<pre>
	$ sudo singularity shell --writable test1.img		$ sudo singularity shell --writable test1.img

STEPHANE GERARD stgerard@vub.ac.be at 15:46, 30 October 2018

2018-10-30T15:46:44Z

← Older revision		Revision as of 15:46, 30 October 2018
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	<pre>		<pre>
	sudo singularity build --sandbox test1.img test1.def		$ sudo singularity build --sandbox test1.img test1.def
	</pre>		</pre>
	after one or two minutes, you get an container ready to be used under the form of a directory test1.img.		after one or two minutes, you get an container ready to be used under the form of a directory test1.img.

			Now, let's say you want to install vim inside the container. Issue the following command :
			<pre>
			$ sudo singularity shell --writable test1.img
			Singularity: Invoking an interactive shell within container...

			Singularity test1.img:~>
			</pre>
			The "--writable" flag is really important if you want to bring modifications inside the image.

	= Sources =		= Sources =
	* [https://www.sylabs.io/docs/ Singularity website] -> explanations to build a container on this [https://www.sylabs.io/guides/2.6/user-guide/build_a_container.html page].		* [https://www.sylabs.io/docs/ Singularity website] -> explanations to build a container on this [https://www.sylabs.io/guides/2.6/user-guide/build_a_container.html page].