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Commit c5b8d9ab authored by David Hrbáč's avatar David Hrbáč
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5 merge requests!368Update prace.md to document the change from qprace to qprod as the default...,!367Update prace.md to document the change from qprace to qprod as the default...,!366Update prace.md to document the change from qprace to qprod as the default...,!323extended-acls-storage-section,!219Virtual environment, upgrade MKdocs, upgrade Material design
...@@ -22,9 +22,9 @@ In order to let EasyBuild generate a container recipe, it is required to specify ...@@ -22,9 +22,9 @@ In order to let EasyBuild generate a container recipe, it is required to specify
Currently, three types of container base images can be specified: Currently, three types of container base images can be specified:
* ** localimage:*path* **: the location of an existing container image file * **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/)) * **docker:*name***: the name of a Docker container image (to be downloaded from [Docker Hub][a].
* ** shub:*name* **: the name of a Singularity container image (to be downloaded from [Singularity Hub](https://singularity-hub.org/)) * **shub:*name***: the name of a Singularity container image (to be downloaded from [Singularity Hub][b].
## Building Container Images ## Building Container Images
...@@ -64,7 +64,7 @@ Below is an example of container recipe for that was generated by EasyBuild, usi ...@@ -64,7 +64,7 @@ Below is an example of container recipe for that was generated by EasyBuild, usi
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 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)). It uses the *shahzebsiddiqui/eb-singularity:centos-7.4.1708* base container image that is available from Singularity hub ([see][c].
``` ```
Bootstrap: shub Bootstrap: shub
...@@ -210,7 +210,7 @@ For Singularity containers (see Type of container recipe/image to generate (`--c ...@@ -210,7 +210,7 @@ For Singularity containers (see Type of container recipe/image to generate (`--c
* ext3: writable image file using ext3 file system * ext3: writable image file using ext3 file system
* sandbox: container image in a regular directory * 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). See also [link][d] [link][e].
## Name for Container Recipe & Image ## Name for Container Recipe & Image
...@@ -232,13 +232,22 @@ The container software that EasyBuild leverages to build container images may be ...@@ -232,13 +232,22 @@ The container software that EasyBuild leverages to build container images may be
You can instruct EasyBuild to pass an alternate location via the `--container-tmpdir` configuration setting. 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 `$SINGULARITY_TMPDIR` environment variable will be defined accordingly to let Singularity use that location instead. For Singularity, the default is to use /tmp, [see][f]. If `--container-tmpdir` is specified, the `$SINGULARITY_TMPDIR` environment variable will be defined accordingly to let Singularity use that location instead.
Type of container recipe/image to generate (`--container-type`) 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: 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 * singularity (default): [Singularity][g] container recipes & images
* docker: [Docker](https://docs.docker.com/) container recipe & images * docker: [Docker][h] container recipe & images
For detailed documentations see [here](http://easybuild.readthedocs.io/en/latest/Containers.html). For detailed documentations see [here][i].
[a]: https://hub.docker.com/
[b]: https://singularity-hub.org/
[c]: https://singularity-hub.org/collections/143
[d]: https://singularity.lbl.gov/user-guide#supported-container-formats
[e]: http://singularity.lbl.gov/docs-build-container
[f]: http://singularity.lbl.gov/build-environment#temporary-folders
[g]: https://singularity.lbl.gov
[h]: https://docs.docker.com/
[i]: http://easybuild.readthedocs.io/en/latest/Containers.html
...@@ -13,9 +13,9 @@ All builds and installations are performed at user level, so you don't need the ...@@ -13,9 +13,9 @@ All builds and installations are performed at user level, so you don't need the
EasyBuild relies on two main concepts EasyBuild relies on two main concepts
* Toolchains * Toolchains
* EasyConfig file (our easyconfigs is [here](https://code.it4i.cz/sccs/easyconfigs-it4i)) * EasyConfig file (our easyconfigs is [here][a])
Detailed documentations is available [here](http://easybuild.readthedocs.io). Detailed documentations is available [here][b].
## Toolchains ## Toolchains
...@@ -24,7 +24,7 @@ A toolchain corresponds to a compiler and a set of libraries which are commonly ...@@ -24,7 +24,7 @@ A toolchain corresponds to a compiler and a set of libraries which are commonly
* **foss** is based on the GCC compiler and on open-source libraries (OpenMPI, OpenBLAS, etc.). * **foss** is based on the GCC compiler and on open-source libraries (OpenMPI, OpenBLAS, etc.).
* **intel** is based on the Intel compiler and on Intel libraries (Intel MPI, Intel Math Kernel Library, etc.). * **intel** is based on the Intel compiler and on Intel libraries (Intel MPI, Intel Math Kernel Library, etc.).
Additional details are available on [here](https://github.com/hpcugent/easybuild/wiki/Compiler-toolchains). Additional details are available on [here][c].
## EasyConfig File ## EasyConfig File
...@@ -34,7 +34,7 @@ By default, EasyConfig files and generated modules are named using the following ...@@ -34,7 +34,7 @@ By default, EasyConfig files and generated modules are named using the following
`software-name-software-version-toolchain-name-toolchain-version(-suffix).eb` `software-name-software-version-toolchain-name-toolchain-version(-suffix).eb`
Additional details are available on [here](https://github.com/hpcugent/easybuild-easyconfigs). Additional details are available on [here][d].
## EasyBuild on IT4Innovations Clusters ## EasyBuild on IT4Innovations Clusters
...@@ -437,3 +437,8 @@ Job ID Username Queue Jobname S ...@@ -437,3 +437,8 @@ Job ID Username Queue Jobname S
------------------------------ --------------- --------------- --------------- -------- ---- ----- ------ ----- - ----- ------------------------------ --------------- --------------- --------------- -------- ---- ----- ------ ----- - -----
1319314.dm2 username qprod git-2.11.0-GNU- 85605 1 16 -- 24:00 R 00:00:17 1319314.dm2 username qprod git-2.11.0-GNU- 85605 1 16 -- 24:00 R 00:00:17
``` ```
[a]: https://code.it4i.cz/sccs/easyconfigs-it4i
[b]: http://easybuild.readthedocs.io
[c]: https://github.com/hpcugent/easybuild/wiki/Compiler-toolchains
[d]: https://github.com/hpcugent/easybuild-easyconfigs
...@@ -19,7 +19,7 @@ On our clusters, the Singularity images of main linux distributions are prepared ...@@ -19,7 +19,7 @@ On our clusters, the Singularity images of main linux distributions are prepared
Current information about available Singularity images can be obtained by the `ml av` command. The Images are listed in the `OS` section. Current information about available Singularity images can be obtained by the `ml av` command. The Images are listed in the `OS` section.
The bootstrap scripts, wrappers, features, etc. are located [here](https://code.it4i.cz/sccs/it4i-singularity). The bootstrap scripts, wrappers, features, etc. are located [here][a].
!!! note !!! note
The images with graphic card support are marked as **-GPU** and images with Intel Xeon Phi support are marked as **-MIC** The images with graphic card support are marked as **-GPU** and images with Intel Xeon Phi support are marked as **-MIC**
...@@ -77,7 +77,7 @@ CentOS Linux release 7.3.1708 (Core) ...@@ -77,7 +77,7 @@ CentOS Linux release 7.3.1708 (Core)
**image-mpi** **image-mpi**
MPI wrapper - see more in the chapter [Examples MPI](#mpi). MPI wrapper - see more in the chapter [Examples MPI][1].
**image-run** **image-run**
...@@ -275,3 +275,7 @@ local:$ scp container.img login@login4.salomon.it4i.cz:/home/login/.singularity/ ...@@ -275,3 +275,7 @@ local:$ scp container.img login@login4.salomon.it4i.cz:/home/login/.singularity/
* Load module Singularity (`ml Singularity`) * Load module Singularity (`ml Singularity`)
* Use your image * Use your image
[1]: #mpi
[a]: https://code.it4i.cz/sccs/it4i-singularity
# Singularity Container # Singularity Container
[Singularity](http://singularity.lbl.gov/) enables users to have full control of their environment. A non-privileged user can "swap out" the operating system on the host for one they control. So if the host system is running RHEL6 but your application runs in Ubuntu/RHEL7, you can create an Ubuntu/RHEL7 image, install your applications into that image, copy the image to another host, and run your application on that host in it’s native Ubuntu/RHEL7 environment. [Singularity][a] enables users to have full control of their environment. A non-privileged user can "swap out" the operating system on the host for one they control. So if the host system is running RHEL6 but your application runs in Ubuntu/RHEL7, you can create an Ubuntu/RHEL7 image, install your applications into that image, copy the image to another host, and run your application on that host in it’s native Ubuntu/RHEL7 environment.
Singularity also allows you to leverage the resources of whatever host you are on. This includes HPC interconnects, resource managers, file systems, GPUs and/or accelerators, etc. Singularity does this by enabling several key facets: Singularity also allows you to leverage the resources of whatever host you are on. This includes HPC interconnects, resource managers, file systems, GPUs and/or accelerators, etc. Singularity does this by enabling several key facets:
...@@ -13,7 +13,7 @@ This documentation is for Singularity version 2.4 and newer. ...@@ -13,7 +13,7 @@ This documentation is for Singularity version 2.4 and newer.
## Using Docker Images ## Using Docker Images
Singularity can import, bootstrap, and even run Docker images directly from [Docker Hub](https://hub.docker.com/). You can easily run RHEL7 container like this: Singularity can import, bootstrap, and even run Docker images directly from [Docker Hub][b]. You can easily run RHEL7 container like this:
```console ```console
hra0031@login4:~$ cat /etc/redhat-release hra0031@login4:~$ cat /etc/redhat-release
...@@ -115,4 +115,8 @@ Singularity ubuntu.img:~> ls /scratch ...@@ -115,4 +115,8 @@ Singularity ubuntu.img:~> ls /scratch
ddn sys temp work ddn sys temp work
``` ```
Comprehensive documentation can be found at the [Singularity](http://singularity.lbl.gov/quickstart) website. Comprehensive documentation can be found at the [Singularity][c] website.
\ No newline at end of file
[a]: http://singularity.lbl.gov/
[b]: https://hub.docker.com/
[c]: http://singularity.lbl.gov/quickstart
...@@ -2,9 +2,9 @@ ...@@ -2,9 +2,9 @@
Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine. Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.
Homepage is at [https://spack.io/](https://spack.io/) Homepage is [here][a].
Documentation is at [https://spack.readthedocs.io/en/latest/](https://spack.readthedocs.io/en/latest/) Documentation is [here][b].
## Spack on IT4Innovations Clusters ## Spack on IT4Innovations Clusters
...@@ -352,3 +352,6 @@ y ...@@ -352,3 +352,6 @@ y
==> Successfully uninstalled git@2.11.0%gcc@4.4.7 arch=linux-centos6-x86_64 -xmh3hmb ==> Successfully uninstalled git@2.11.0%gcc@4.4.7 arch=linux-centos6-x86_64 -xmh3hmb
``` ```
[a]: https://spack.io/
[b]: https://spack.readthedocs.io/en/latest/
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