Merge pull request #60 from ARCTraining/jhodrien-2025-fixes-2

Update to Spack 1.1.0

Author: murphyqm

book/course/conda.md

@@ -450,7 +450,7 @@ We've discovered we also need the `statsmodels` package for some extra work we w
 
 ````{admonition} Searching for packages
 
-Conda has a command-line search functionality that we describe below in the section [Use Conda to search for a package](#searching-for-packages); you can also use the [`conda-forge` repository](https://anaconda.org/conda-forge) or [`bioconda` repository](https://anaconda.org/bioconda) to search for packages.
+Conda has a command-line search functionality that we describe below in the section [Using Conda to search for a package](searching-for-packages); you can also use the [`conda-forge` repository](https://anaconda.org/conda-forge) or [`bioconda` repository](https://anaconda.org/bioconda) to search for packages.
 ````
 
 Once you have the name (and possibly version) of the package you want to install, again there are two different ways to add these packages, much like there were two ways to create the environment to begin with.

book/course/spack/advanced.md

@@ -8,7 +8,7 @@ Spack install software within.
 To define your container, you create a YAML file that describes what you want.
 Here's I'm saying I want spack to install gromacs with MPI enabled, and
 OpenMPI.  I want it to create the container for Singularity/Apptainer, and I
-want it to make sure the libgomp1 package is installed onto the OS.
+want it to make sure the libgomp package is installed onto the OS.
 
 spack.yaml:
 
@@ -21,10 +21,13 @@ spack:
 # What I want it to create
   container:
     format: singularity
+    images:
+      os: almalinux:9
+      spack: 1.1.0
 # Bonus OS packages I'd like installed
     os_packages:
       final:
-      - libgomp1
+      - libgomp
 # Additional config for the build process
   config:
     mount proc: yes
@@ -57,18 +60,10 @@ As a proof of life, let's run gromacs from within that container:
 
 ```bash
 $ apptainer run gromacs-openmpi.sif mpirun -np 4 gmx_mpi
-                    :-) GROMACS - gmx_mpi, 2024.4-spack (-:
+                    :-) GROMACS - gmx_mpi, 2025.3-spack (-:
 
-Executable:   /opt/software/linux-zen4/gromacs-2024.4-af5srsrjr7w2alftldvyek2chqu4rtls/bin/gmx_mpi
-Data prefix:  /opt/software/linux-zen4/gromacs-2024.4-af5srsrjr7w2alftldvyek2chqu4rtls
-Working dir:  /users/example/hpc2
-Command line:
-  gmx_mpi
-
-SYNOPSIS
-
-gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice <int>]
-    [-[no]backup]
+Executable:   /opt/software/linux-zen4/gromacs-2025.3-ipqq3w22geizv4y6pdroneco3hq33xkj/bin/gmx_mpi
+Data prefix:  /opt/software/linux-zen4/gromacs-2025.3-ipqq3w22geizv4y6pdroneco3hq33xkj
 ...
 ```
 

book/course/spack/containers.md

@@ -4,6 +4,10 @@ Environments in Spack feel a whole lot like environments in Conda; they allow
 you to bundle up a number of different pieces of software into a single entity,
 making a single coherent collection.
 
+This is a very simple introduction, and really doesn't cover all the things
+you can do with environments, so if you're interested in these, please read
+the main documentation links in the [References](environments:references) section.
+
 ## Creating an environment
 
 Here's a minimal workflow for creating an environment:
@@ -13,17 +17,21 @@ Here's a minimal workflow for creating an environment:
   ```bash
   spack env create myenv
   ```
+- Activate it
+  ```bash
+  spack env activate myenv
+  ```
 
 - Add a list of software to it
 
   ```bash
-  spack -e myenv add bash@5 python py-numpy py-scipy py-matplotlib openssl@3.0.15
+  spack add bash@5 python py-numpy py-scipy py-matplotlib openssl@3.0.7
   ```
 
 - Tweak the config if required
 
   ```bash
-  spack -e myenv config edit
+  spack config edit
   ```
 
   Please review the references for more information on options here, but nothing
@@ -32,7 +40,7 @@ Here's a minimal workflow for creating an environment:
 - Validate the installation
 
   ```bash
-  spack -e myenv concretize
+  spack concretize
   ```
 
   [Concretizing](https://spack.readthedocs.io/en/latest/environments.html#spec-concretization)
@@ -42,7 +50,7 @@ Here's a minimal workflow for creating an environment:
 - Build and install the software
 
   ```bash
-  spack -e myenv install
+  spack install
   ```
 
 Note this follows the normal behaviour of Spack, reusing previously built
@@ -51,7 +59,8 @@ software, and external software you've told it to use.
 ## Using an environment
 
 Again, this feels very familiar to people used to Conda; you have to activate
-an environment before using it:
+an environment before using it (although we did actually do this earlier when
+we created it):
 
 ```bash
 spack env activate myenv
@@ -63,8 +72,8 @@ Once activated, you can confirm that it's really live:
 $ which bash
 ~/spack/var/spack/environments/myenv/.spack-env/view/bin/bash
 $ bash --version
-GNU bash, version 5.2.26(1)-release (x86_64-pc-linux-gnu)
-Copyright (C) 2022 Free Software Foundation, Inc.
+GNU bash, version 5.3.3(1)-release (x86_64-pc-linux-gnu)
+Copyright (C) 2025 Free Software Foundation, Inc.
 License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
 
 This is free software; you are free to change and redistribute it.
@@ -79,7 +88,8 @@ You can leave an environment using:
 spack env deactivate
 ```
 
+(environments:references)=
 ## References
 
-- [Using Spack to Replace Homebrew/Conda](https://spack.readthedocs.io/en/latest/replace_conda_homebrew.html)
+- [Environment Basics](https://spack.readthedocs.io/en/latest/environments_basics.html)
 - [Environments](https://spack.readthedocs.io/en/latest/environments.html)