From c5b8d9ab4a972d5e29778f4954c1ef4d01ad6a12 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20Hrb=C3=A1=C4=8D?= <david@hrbac.cz>
Date: Thu, 1 Nov 2018 23:50:57 +0100
Subject: [PATCH] Links OK
---
docs.it4i/software/tools/easybuild-images.md | 27 +++++++++++++-------
docs.it4i/software/tools/easybuild.md | 13 +++++++---
docs.it4i/software/tools/singularity-it4i.md | 8 ++++--
docs.it4i/software/tools/singularity.md | 10 +++++---
docs.it4i/software/tools/spack.md | 7 +++--
5 files changed, 45 insertions(+), 20 deletions(-)
diff --git a/docs.it4i/software/tools/easybuild-images.md b/docs.it4i/software/tools/easybuild-images.md
index 215e7e6bc..3a7b0dc16 100644
--- a/docs.it4i/software/tools/easybuild-images.md
+++ b/docs.it4i/software/tools/easybuild-images.md
@@ -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:
-* ** 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/))
+* **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][a].
+* **shub:*name***: the name of a Singularity container image (to be downloaded from [Singularity Hub][b].
## Building Container Images
@@ -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
```
-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
@@ -210,7 +210,7 @@ For Singularity containers (see Type of container recipe/image to generate (`--c
* 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).
+See also [link][d] [link][e].
## Name for Container Recipe & Image
@@ -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.
-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`)
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
+* singularity (default): [Singularity][g] container recipes & 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
diff --git a/docs.it4i/software/tools/easybuild.md b/docs.it4i/software/tools/easybuild.md
index 0fbd09440..cf1e0d721 100644
--- a/docs.it4i/software/tools/easybuild.md
+++ b/docs.it4i/software/tools/easybuild.md
@@ -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
* 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
@@ -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.).
* **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
@@ -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`
-Additional details are available on [here](https://github.com/hpcugent/easybuild-easyconfigs).
+Additional details are available on [here][d].
## EasyBuild on IT4Innovations Clusters
@@ -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
```
+
+[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
diff --git a/docs.it4i/software/tools/singularity-it4i.md b/docs.it4i/software/tools/singularity-it4i.md
index 62523b671..129d97b4b 100644
--- a/docs.it4i/software/tools/singularity-it4i.md
+++ b/docs.it4i/software/tools/singularity-it4i.md
@@ -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.
-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
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)
**image-mpi**
-MPI wrapper - see more in the chapter [Examples MPI](#mpi).
+MPI wrapper - see more in the chapter [Examples MPI][1].
**image-run**
@@ -275,3 +275,7 @@ local:$ scp container.img login@login4.salomon.it4i.cz:/home/login/.singularity/
* Load module Singularity (`ml Singularity`)
* Use your image
+
+[1]: #mpi
+
+[a]: https://code.it4i.cz/sccs/it4i-singularity
diff --git a/docs.it4i/software/tools/singularity.md b/docs.it4i/software/tools/singularity.md
index 288f420a0..e932eb247 100644
--- a/docs.it4i/software/tools/singularity.md
+++ b/docs.it4i/software/tools/singularity.md
@@ -1,6 +1,6 @@
# 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:
@@ -13,7 +13,7 @@ This documentation is for Singularity version 2.4 and newer.
## 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
hra0031@login4:~$ cat /etc/redhat-release
@@ -115,4 +115,8 @@ Singularity ubuntu.img:~> ls /scratch
ddn sys temp work
```
-Comprehensive documentation can be found at the [Singularity](http://singularity.lbl.gov/quickstart) website.
\ No newline at end of file
+Comprehensive documentation can be found at the [Singularity][c] website.
+
+[a]: http://singularity.lbl.gov/
+[b]: https://hub.docker.com/
+[c]: http://singularity.lbl.gov/quickstart
diff --git a/docs.it4i/software/tools/spack.md b/docs.it4i/software/tools/spack.md
index 1dbf2b2d5..f83da8dcf 100644
--- a/docs.it4i/software/tools/spack.md
+++ b/docs.it4i/software/tools/spack.md
@@ -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.
-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
@@ -352,3 +352,6 @@ y
==> 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/
--
GitLab