Merge pull request #250 from boegel/main

update docs for release of EasyBuild v4.9.1

docs/common-toolchains.md

@@ -51,8 +51,8 @@ graph LR
   A --> |binutils| C[intel-compilers];
   B --> |OpenMPI| E[gompi];
   C --> |impi| F[iimpi];
-  B --> |FlexiBLAS + FFTW + ScaLAPACK| D[gfbf];
-  D --> |OpenMPI| G[foss];
+  B --> |FlexiBLAS (incl. LAPACK) + FFTW| D[gfbf];
+  D --> |OpenMPI + ScaLAPACK| G[foss];
   E --> |FlexiBLAS + FFTW + ScaLAPACK| G[foss];
   F --> |imkl| Z[intel];
   C --> |imkl| H[iimkl];

docs/configuration.md

@@ -620,7 +620,9 @@ output of `type -f module` (in a `bash` shell), or `alias module` (in a `tcsh` s
 
 The actual module command (i.e., `modulecmd`, `modulecmd.tcl`,
 `lmod`, ...) must be available via `$PATH` (which is not standard), except when using Lmod
-(in that case the `lmod` binary can also be located via `$LMOD_CMD`).
+(in that case the `lmod` binary can also be located via `$LMOD_CMD`) or when using
+Environment Modules (in that case the `modulecmd.tcl` binary can also be located via
+`$MODULES_CMD`).
 
 For example, to indicate that EasyBuild should be using `Lmod` as modules tool:
 

docs/easybuild-v5/changes-in-default-configuration.md

@@ -0,0 +1,52 @@
+# Changes in default configuration in EasyBuild v5.0
+
+*(for a full overview of changes in EasyBuild v5.0, see [here](overview-of-changes.md))*
+
+Various changes in default configuration included in EasyBuild v5.0, including:
+
+* [Enable RPATH linking by default][rpath]
+* [Enable `--trace` by default][trace]
+
+---
+
+## Enable RPATH linking by default {: #rpath }
+
+[RPATH linking][rpath_support] is enabled by default in EasyBuild v5.0 (see [easybuild-framework PR #4448](https://github.com/easybuilders/easybuild-framework/pull/4448)).
+
+The benefits for enabling RPATH are explained in [Why RPATH?][rpath_support_why].
+
+This enhancement **does not** add any filtering of environment variables. This means `$LD_LIBRARY_PATH`
+will continue to be appended by the environment module files EasyBuild generates,
+unless it is configured to filter these variables (via `--filter-env-vars`,
+see also [Relation to `$LD_LIBRARY_PATH`][rpath_support_LD_LIBRARY_PATH]).
+
+To disable RPATH linking, either:
+
+* Use the `--disable-rpath` command line option;
+* Set the `$EASYBUILD_DISABLE_RPATH` environment variable;
+* Disable RPATH linking in an EasyBuild [configuration file](../configuration.md#configuration_file):
+
+    ``` ini
+    [override]
+    rpath=0
+    ```
+
+
+---
+
+## Enable `--trace` by default {: #trace }
+
+The [`--trace` option](../tracing-progress.md) is enabled by default (see [easybuild-framework PR #4250](https://github.com/easybuilders/easybuild-framework/pull/4250)).
+
+This makes the output produced by the `eb` command more informative, by providing more information about what's going on in the background.
+
+To disable trace output, either:
+
+* Use the `--disable-trace` command line option;
+* Set the `$EASYBUILD_DISABLE_TRACE` environment variable;
+* Disable trace mode in a [configuration file](../configuration.md#configuration_file):
+
+    ``` ini
+    [override]
+    trace=0
+    ```

docs/easybuild-v5/enhancements.md

@@ -5,29 +5,10 @@
 Various significant enhancements are included in EasyBuild v5.0, including:
 
 * [`run_shell_cmd` function][run_shell_cmd]
-* [Enable `--trace` by default][trace]
 
 ---
 
 ## `run_shell_cmd` function { : #run_shell_cmd }
 
 See dedicated page on the new [`run_shell_cmd` function](run_shell_cmd.md).
 
----
-
-## Enable `--trace` by default {: #trace }
-
-The [`--trace` option](../tracing-progress.md) is enabled by default (see [easybuild-framework PR #4250](https://github.com/easybuilders/easybuild-framework/pull/4250)).
-
-This makes the output produced by the `eb` command more informative, by providing more information about what's going on in the background.
-
-To disable trace output, either:
-
-* Use the `--disable-trace` command line option;
-* Set the `$EASYBUILD_DISABLE_TRACE` environment variable;
-* Disable trace mode in a [configuration file](../configuration.md#configuration_file):
-
-    ``` ini
-    [override]
-    trace=0
-    ```

docs/easybuild-v5/index.md

@@ -2,6 +2,7 @@
 
 - [Overview of changes](overview-of-changes.md)
     - [Backwards-incompatible changes](backwards-incompatible-changes.md)
+    - [Changes in default configuration](changes-in-default-configuration.md)
     - [Enhancements](enhancements.md)
         - [`run_shell_cmd` function](run_shell_cmd.md)
     - [Deprecated functionality](deprecated-functionality.md)

docs/easybuild-v5/overview-of-changes.md

@@ -3,16 +3,15 @@
 !!! warning
     EasyBuild 5.0 is currently still under development, via the `5.0.x` branches in the EasyBuild GitHub repositories.
 
-    We intend to update this section of the documentation regularly as the planned changes are being implemented,
-    and when there are [proposed changes](proposed-changes.md) where we are requesting community feedback.
+    We intend to update this section of the documentation regularly as the planned changes are being implemented.
 
 This page provides a concise overview of the most prominent changes in EasyBuild version 5.0,
 which can be categorized as:
 
 * [Enhancements](enhancements.md)
+* [Changes in default configuration](changes-in-default-configuration.md)
 * [Backward-incompatible changes](backwards-incompatible-changes.md)
 * [Deprecated functionality](deprecated-functionality.md)
-* [Proposed changes](proposed-changes.md)
 * [Policies](policies.md)
 
 For in-depth details on a particular change, see the pull requests that are linked

docs/installation.md

@@ -69,11 +69,11 @@ This is EasyBuild 4.8.0 (framework: 4.8.0, easyblocks: 4.8.0) on host example.lo
 ```
 
 !!! tip
-    The Tcl-based or Lmod implementations of environment modules do their default sorting differently.
-    The former will normally sort in the lexicographic order, while Lmod follows
-    an approach that is closer to Python's construct `LooseVersion` way of ordering. Such aspects
-    may make a big difference, if you have installed both versions 1.9.0 and 1.15.2,
-    with respect to what is the version being loaded by default.
+    The Tcl/C Environment Modules (version <= 3.2.10) does its default sorting differently than
+    newer versions of Environment Modules and Lmod. The former will normally sort in the
+    lexicographic order, while the latters follow an approach that is closer to Python's construct
+    `LooseVersion` way of ordering. Such aspects may make a big difference, if you have installed
+    both versions 1.9.0 and 1.15.2, with respect to what is the version being loaded by default.
 
 You can also run `eb --show-system-info` to see system information relevant to EasyBuild,
 or run`eb --show-config` to see the default EasyBuild configuration (see also [Configuring EasyBuild][configuring_easybuild]).
@@ -356,12 +356,16 @@ Supported module tools:
     the `module` function; for example, using `type module` or `type -f module`.
 
 !!! note
-    For Lmod specifically, EasyBuild will try to fall back to finding the `lmod` binary via the `$LMOD_CMD`
+    For Lmod, EasyBuild will try to fall back to finding the `lmod` binary via the `$LMOD_CMD`
     environment variable, in case `lmod` is not available in `$PATH`.
 
     In EasyBuild versions *prior* to 2.1.1, the path specified by `$LMOD_CMD` was (erroneously) preferred over the
     (first) `lmod` binary available via `$PATH`.
 
+    For modern Tcl-only environment modules (version >= 4.0.0), EasyBuild will try to fall back to finding the
+    `modulecmd.tcl` binary via the `$MODULES_CMD` environment variable, in case `modulecmd.tcl` is not available
+    in `$PATH`.
+
 
 Additional notes:
 

docs/manipulating-dependencies.md

@@ -85,8 +85,8 @@ $ eb HDF5-1.8.13-intel-2015a.eb --hide-deps=zlib,Szip -D
 ```
 
 !!! note
-    Using Lmod (version >= 5.7.5), hidden modules can be made visible in the output of '`module avail`' using the
-    `--show-hidden` option.
+    Using Lmod (version >= 5.7.5) or Environment Modules (version >= 4.6.0), hidden modules can be made
+    visible in the output of '`module avail`' using respectively the `--show-hidden` or `--all` option.
 
     For example: