This repo contains Singularity definition file generated by easybuild to build containers. The containers are built on Sylabs Cloud
There is a Singularity recipe for Easybuild Base contaienr for Centos 7 called Singularity.Easybuild-CentOS-7. The easybuild base container is meant to configure easybuild environment so we can build Singularity containers with easybuild. We can extend the base container concept for other distributions
The easybuild base container can be fetched by running:
singularity pull --arch amd64 library://shahzebmsiddiqui/default/easybuild:centos-7
The top-level proposal directory contains a few ways we can organize Singularity Recipe files. Once this is decided by the easybuild community we
can enforce this when building the container library.
The apps directory contains the Easybuild Singularity Recipe that were successfully built in Sylabs Cloud into containers. The recipe
files were auto-generated by easybuild and tweaked manually afterwards.
The easybuild container stack can be found at Sylabs at https://cloud.sylabs.io/library/shahzebmsiddiqui/easybuild-centos7
You can pull one of the easybuild containers from Sylabs let's say java:1.8.0_92 as follows:
singularity pull --arch amd64 library://shahzebmsiddiqui/easybuild-centos7/java:1.8.0_92
Once we have the container locally we can shell into container and see the modules loaded:
ssi29@ag-mxg-hulk090> singularity shell java-1.8.0_92.sif Singularity java-1.8.0_92.sif:~/gpfs/eb-images> module av -------------------------------- /app/modules/all ---------------------------------------- Java/1.8.0_92 (L) Where: L: Module is loaded Use "module spider" to find all possible modules and extensions. Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
The java binary is accessible in the container $PATH so you can use this container to build your Java program such as a helloworld.java as follows:
ssi29@ag-mxg-hulk090> singularity exec java-1.8.0_92.sif javac helloworld.java ssi29@ag-mxg-hulk090> singularity exec java-1.8.0_92.sif java HelloWorld Hello, World
Currently, we don't have a central repository for building easybuild containers. Building a container registry on-prem using Singularity Enterprise would limit the open source community from contributing back. According to Sylabs, Singularity Enterprise is on-prem version of Sylabs Cloud.
When you build containers on Sylabs Cloud, you can only push containers to your library (i.e https://cloud.sylabs.io/library/shahzebmsiddiqui/). This
prevents others from contributing because their is no concept of shared namespace for a library with Access Control List (ACLs) to control permission
on a library. I foresee easybuild maintainers have the following ACLs Push, Update, Delete on containers and everyone has Pull access
to all containers in a library.
If you are interested in contributing back, fork the repo https://github.com/shahzebsiddiqui/eb-singularity and generate your recipe and issue a PR and I will build and publish the container in my library at https://cloud.sylabs.io/library/shahzebmsiddiqui/easybuild-centos7
You should build your containers using the base container provided in this repo, this means you should have the following line set in your recipe:
Bootstrap: library From: shahzebmsiddiqui/default/easybuild:centos-7
The quickest way to get started is copy one of the recipe files in apps. To demonstrate we will try building M4-1.4.19 by using one
of the existing recipes.
First navigate to your fork and go to the m4 directory and copy the file as follows:
cd apps/m/m4 cp Singularity.M4-1.4.18 Singularity.M4-1.4.19
The format of the recipe file is Singularity.<easyconfig> without the .eb extension. Next we change the following lines
eb M4-1.4.18.eb --robot-->eb M4-1.4.19.eb --robotmodule load M4/1.4.18-->module load M4/1.4.19
There will be some containers that can't be built on Sylabs either due to timeout (60min) or eb can't fetch source files (Java). In those
cases we need to build container locally and push it to Sylabs. For example, the java:1.8.0_92 container found at https://cloud.sylabs.io/library/shahzebmsiddiqui/easybuild-centos7/java was
built locally and pushed to Sylabs.
Certainly there will be some applications that require additional dependencies to be installed in %post section, so copy-paste and build
container won't work, you will need to work through the details and build container successfully before we can accept it.
When you are building containers, please reuse existing containers as a base image to satisfy all the dependency. For example ant-1.9.7-Java-1.8.0_92.eb has
a dependency on Java-1.8.0.92.eb so we set the base image to the following:
Bootstrap: library From: shahzebmsiddiqui/easybuild-centos7/java:1.8.0_92
See recipe file for Singularity.ant-1.9.7-Java-1.8.0_92 for more details.
If you were to build ant with the easybuild base image we would end up building the entire dependency tree including Java-1.8.0_92. We can
confirm this by running a dry run -D to see all the modules built:
$ eb ant-1.9.7-Java-1.8.0_92.eb -D == temporary log file in case of crash /scratch/eb-dYEUtq/easybuild-fC51To.log Dry run: printing build status of easyconfigs and dependencies CFGS=/mxg-hpc/users/ssi29/easybuild/software/EasyBuild/4.1.0/easybuild/easyconfigs * [ ] $CFGS/j/Java/Java-1.8.0_92.eb (module: Java/1.8.0_92) * [ ] $CFGS/j/JUnit/JUnit-4.12-Java-1.8.0_92.eb (module: JUnit/4.12-Java-1.8.0_92) * [ ] $CFGS/a/ant/ant-1.9.7-Java-1.8.0_92.eb (module: ant/1.9.7-Java-1.8.0_92) == Temporary log file(s) /scratch/eb-dYEUtq/easybuild-fC51To.log* have been removed. == Temporary directory /scratch/eb-dYEUtq has been removed.