Merge branch 'eb-singularity' into 'master'

Eb singularity

See merge request sccs/docs.it4i.cz!208

README.md

@@ -41,33 +41,3 @@ $$
 ```
 
 To enable the MathJX on page you need to enable it by adding line ```---8<--- "mathjax.md"``` at the end of file.
-
-## Development Environment
-
-### MkDocs
-
-Documentation pages are build with [MkDocs](http://www.mkdocs.org/), [MkDocs at GitHub](https://github.com/mkdocs/mkdocs/). You need to install MkDocs locally so that you can build the pages and run development web server.
-
-```bash
-pip install mkdocs pygments pymdown-extensions
-```
-
-You can build the pages with `mkdocs build`.
-
-```bash
-‹hrb33-toshiba› 11:47 $ mkdocs build
-INFO    -  Cleaning site directory
-INFO    -  Building documentation to directory: /home/hrb33/Dokumenty/dev/it4i/docs.it4i.git/site
-```
-
-You can start local server with `mkdocs serve`.
-
-```bash
-✔ ~/Dokumenty/dev/it4i/docs.it4i.git [readme L|✚ 1…6⚑ 1]
-‹hrb33-toshiba› 11:47 $ mkdocs serve
-INFO    -  Building documentation...
-INFO    -  Cleaning site directory
-[I 170124 11:47:27 server:283] Serving on http://127.0.0.1:8000
-[I 170124 11:47:27 handlers:60] Start watching changes
-[I 170124 11:47:27 handlers:62] Start detecting changes
-```

docs.it4i/software/tools/easybuild-images.md

+# Generating Container Recipes & Images
+
+EasyBuild has support for generating container recipes that will use EasyBuild to build and install a specified software stack. In addition, EasyBuild can (optionally) leverage the build tool provided by the container software of choice to create container images.
+
+!!! info
+    The features documented here have been available since **EasyBuild v3.6.0** but are still experimental, which implies they are subject to change in upcoming versions of EasyBuild.
+    You will need to enable the `--experimental` configuration option in order to use them.
+
+## Generating Container Recipes
+
+To generate container recipes, use `eb --containerize`, or `eb -C` for short.
+
+The resulting container recipe will, in turn, leverage EasyBuild to build and install the software that corresponds to the easyconfig files that are specified as arguments to the eb command (and all required dependencies, if needed).
+
+!!! note
+    EasyBuild will refuse to overwrite existing container recipes.
+    To re-generate an already existing recipe file, use the `--force` command line option.
+
+## Base Container Image
+
+In order to let EasyBuild generate a container recipe, it is required to specify which container image should be used as a base, via the `--container-base` configuration option.
+
+Currently, three types of container base images can be specified:
+
+* ** localimage:*path* **: the location of an existing container image file
+* ** docker:*name* **: the name of a Docker container image (to be downloaded from [Docker Hub](https://hub.docker.com/))
+* ** shub:*name* **: the name of a Singularity container image (to be downloaded from [Singularity Hub](https://singularity-hub.org/))
+
+## Building Container Images
+
+To instruct EasyBuild to also build a container image from the generated container recipe, use `--container-build-image` (in combination with `-C` or `--containerize`).
+
+EasyBuild will leverage functionality provided by the container software of choice (see containers_cfg_image_type) to build the container image.
+
+For example, in the case of Singularity, EasyBuild will run `sudo /path/to/singularity build` on the generated container recipe.
+
+The container image will be placed in the location specified by the `--containerpath` configuration option (see Location for generated container recipes & images (`--containerpath`)), next to the generated container recipe that was used to build the image.
+
+## Example Usage
+
+In this example, we will use a pre-built base container image located at `/tmp/example.simg` (see also Base container image (`--container-base`)).
+
+To let EasyBuild generate a container recipe for GCC 6.4.0 + binutils 2.28:
+
+```console
+eb GCC-6.4.0-2.28.eb --containerize --container-base localimage:/tmp/example.simg --experimental
+```
+
+With other configuration options left to default (see output of `eb --show-config`), this will result in a Singularity container recipe using example.simg as base image, which will be stored in `$HOME/.local/easybuild/containers`:
+
+```console
+$ eb GCC-6.4.0-2.28.eb --containerize --container-base localimage:/tmp/example.simg --experimental
+== temporary log file in case of crash /tmp/eb-dLZTNF/easybuild-LPLeG0.log
+== Singularity definition file created at /home/example/.local/easybuild/containers/Singularity.GCC-6.4.0-2.28
+== Temporary log file(s) /tmp/eb-dLZTNF/easybuild-LPLeG0.log* have been removed.
+== Temporary directory /tmp/eb-dLZTNF has been removed.
+```
+
+## Example of a Generated Container Recipe
+
+Below is an example of container recipe for that was generated by EasyBuild, using the following command:
+
+```console
+eb Python-3.6.4-foss-2018a.eb OpenMPI-2.1.2-GCC-6.4.0-2.28.eb -C --container-base shub:shahzebsiddiqui/eb-singularity:centos-7.4.1708 --experimental
+```
+
+It uses the *shahzebsiddiqui/eb-singularity:centos-7.4.1708* base container image that is available from Singularity hub ([see](https://singularity-hub.org/collections/143)).
+
+```
+Bootstrap: shub
+From: shahzebsiddiqui/eb-singularity:centos-7.4.1708
+
+%post
+yum --skip-broken -y install openssl-devel libssl-dev libopenssl-devel
+yum --skip-broken -y install libibverbs-dev libibverbs-devel rdma-core-devel
+
+
+# upgrade easybuild package automatically to latest version
+pip install -U easybuild
+
+# change to 'easybuild' user
+su - easybuild
+
+eb Python-3.6.4-foss-2018a.eb OpenMPI-2.1.2-GCC-6.4.0-2.28.eb --robot --installpath=/app/ --prefix=/scratch --tmpdir=/scratch/tmp
+
+# exit from 'easybuild' user
+exit
+
+# cleanup
+rm -rf /scratch/tmp/* /scratch/build /scratch/sources /scratch/ebfiles_repo
+
+%runscript
+eval "$@"
+
+%environment
+source /etc/profile
+module use /app/modules/all
+module load Python/3.6.4-foss-2018a OpenMPI/2.1.2-GCC-6.4.0-2.28
+
+%labels
+```
+
+!!! note
+    We also specify the easyconfig file for the OpenMPI component of foss/2018a here, because it requires specific OS dependencies to be installed (see the 2nd yum ... install line in the generated container recipe).
+    We intend to let EasyBuild take into account the OS dependencies of the entire software stack automatically in a future update.
+
+    The generated container recipe includes pip install -U easybuild to ensure that the latest version of EasyBuild is used to build the software in the container image, regardless of whether EasyBuild was already present in the container and which version it was.
+
+    In addition, the generated module files will follow the default module naming scheme (EasyBuildMNS). The modules that correspond to the easyconfig files that were specified on the command line will be loaded automatically, see the statements in the %environment section of the generated container recipe.
+
+## Example of Building Container Image
+
+You can instruct EasyBuild to also build the container image by also using `--container-build-image`.
+
+Note that you will need to enter your sudo password (unless you recently executed a sudo command in the same shell session):
+
+```console
+$ eb GCC-6.4.0-2.28.eb --containerize --container-base localimage:/tmp/example.simg --container-build-image --experimental
+== temporary log file in case of crash /tmp/eb-aYXYC8/easybuild-8uXhvu.log
+== Singularity tool found at /usr/bin/singularity
+== Singularity version '2.4.6' is 2.4 or higher ... OK
+== Singularity definition file created at /home/example/.local/easybuild/containers/Singularity.GCC-6.4.0-2.28
+== Running 'sudo /usr/bin/singularity build  /home/example/.local/easybuild/containers/GCC-6.4.0-2.28.simg /home/example/.local/easybuild/containers/Singularity.GCC-6.4.0-2.28', you may need to enter your 'sudo' password...
+== (streaming) output for command 'sudo /usr/bin/singularity build  /home/example/.local/easybuild/containers/GCC-6.4.0-2.28.simg /home/example/.local/easybuild/containers/Singularity.GCC-6.4.0-2.28':
+Using container recipe deffile: /home/example/.local/easybuild/containers/Singularity.GCC-6.4.0-2.28
+Sanitizing environment
+Adding base Singularity environment to container
+...
+== temporary log file in case of crash /scratch/tmp/eb-WnmCI_/easybuild-GcKyY9.log
+== resolving dependencies ...
+...
+== building and installing GCCcore/6.4.0...
+...
+== building and installing binutils/2.28-GCCcore-6.4.0...
+...
+== building and installing GCC/6.4.0-2.28...
+...
+== COMPLETED: Installation ended successfully
+== Results of the build can be found in the log file(s) /app/software/GCC/6.4.0-2.28/easybuild/easybuild-GCC-6.4.0-20180424.084946.log
+== Build succeeded for 15 out of 15
+...
+Building Singularity image...
+Singularity container built: /home/example/.local/easybuild/containers/GCC-6.4.0-2.28.simg
+Cleaning up...
+== Singularity image created at /home/example/.local/easybuild/containers/GCC-6.4.0-2.28.simg
+== Temporary log file(s) /tmp/eb-aYXYC8/easybuild-8uXhvu.log* have been removed.
+== Temporary directory /tmp/eb-aYXYC8 has been removed.
+```
+
+The inspect the container image, you can use `singularity shell` to start a shell session in the container:
+
+```console
+$ singularity shell --shell "/bin/bash --norc" $HOME/.local/easybuild/containers/GCC-6.4.0-2.28.simg
+
+Singularity GCC-6.4.0-2.28.simg:~> source /etc/profile
+
+Singularity GCC-6.4.0-2.28.simg:~> module list
+
+Currently Loaded Modules:
+  1) GCCcore/6.4.0   2) binutils/2.28-GCCcore-6.4.0   3) GCC/6.4.0-2.28
+
+Singularity GCC-6.4.0-2.28.simg:~> which gcc
+/app/software/GCCcore/6.4.0/bin/gcc
+
+Singularity GCC-6.4.0-2.28.simg:~> gcc --version
+gcc (GCC) 6.4.0
+...
+```
+
+Or, you can use `singularity exec` to execute a command in the container.
+
+Compare the output of running which gcc and `gcc --version` locally:
+
+```console
+$ which gcc
+/usr/bin/gcc
+$ gcc --version
+gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
+...
+```
+
+and the output when running the same commands in the container:
+
+```console
+$ singularity exec GCC-6.4.0-2.28.simg which gcc
+/app/software/GCCcore/6.4.0/bin/gcc
+
+$ singularity exec GCC-6.4.0-2.28.simg gcc --version
+gcc (GCC) 6.4.0
+...
+```
+
+## Configuration
+
+### Location for Generated Container Recipes & Images
+
+To control the location where EasyBuild will put generated container recipes & images, use the `--containerpath` configuration setting. Next to providing this as an option to the eb command, you can also define the `$EASYBUILD_CONTAINERPATH` environment variable or specify containerpath in an EasyBuild configuration file.
+
+The default value for this location is `$HOME/.local/easybuild/containers`, unless the `--prefix` configuration setting was provided, in which case it becomes <prefix>/containers (see Overall prefix path (`--prefix`)).
+
+Use `eb --show-full-config | grep containerpath` to determine the currently active setting.
+
+### Container Image Format
+
+The format for container images that EasyBuild is produces via the functionality provided by the container software can be controlled via the `--container-image-format` configuration setting.
+
+For Singularity containers (see Type of container recipe/image to generate (`--container-type`)), three image formats are supported:
+
+* squashfs (default): compressed images using squashfs read-only file system
+* ext3: writable image file using ext3 file system
+* sandbox: container image in a regular directory
+
+[See also](https://singularity.lbl.gov/user-guide#supported-container-formats and http://singularity.lbl.gov/docs-build-container).
+
+## Name for Container Recipe & Image
+
+By default, EasyBuild will use the name of the first easyconfig file (without the .eb suffix) as a name for both the container recipe and image.
+
+You can specify an altername name using the `--container-image-name` configuration setting.
+
+The filename of generated container recipe will be `Singularity`.<name>.
+
+The filename of the container image will be `<name><extension>`, where the value for `<extension>` depends on the image format (see Container image format (`--container-image-format`)):
+
+* ‘.simg’ for squashfs container images
+* ‘.img’ for ext3 container images
+* empty for sandbox container images (in which case the container image is actually a directory rather than a file)
+
+### Temporary Directory for Creating Container Images
+
+The container software that EasyBuild leverages to build container images may be using a temporary directory in a location that doesn’t have sufficient free space.
+
+You can instruct EasyBuild to pass an alternate location via the `--container-tmpdir` configuration setting.
+
+For Singularity, the default is to use /tmp, [see](http://singularity.lbl.gov/build-environment#temporary-folders). If `--container-tmpdir` is specified, the `$SINGULARITY_TMPDIR` environment variable will be defined accordingly to let Singularity use that location instead.
+
+Type of container recipe/image to generate (`--container-type`)
+With the `--container-type` configuration option, you can specify what type of container recipe/image EasyBuild should generated. Possible values are:
+
+* singularity (default): [Singularity](https://singularity.lbl.gov) container recipes & images
+* docker: [Docker](https://docs.docker.com/) container recipe & images
+
+For detailed documentations see [here](http://easybuild.readthedocs.io/en/latest/Containers.html).
+

mkdocs.yml

@@ -156,7 +156,9 @@ pages:
         - Workbench: software/tools/ansys/workbench.md
         - Setting License Preferences: software/tools/ansys/licensing.md
         - Licensing and Available Versions: software/tools/ansys/setting-license-preferences.md
-      - EasyBuild: software/tools/easybuild.md
+      - EasyBuild: 
+        - Introduction: software/tools/easybuild.md
+        - Generating Container Recipes and Images: software/tools/easybuild-images.md
       - Singularity Container:
         - Singularity: software/tools/singularity.md
         - Singularity on IT4Innovations: software/tools/singularity-it4i.md