FIX: update README.md

README.md

@@ -3,68 +3,25 @@
 [Official Spack documentation](https://spack.readthedocs.io/en/latest/)
 
 ## How to use on Merlin systems (Merlin6/Merlin7)
-```bash
-module load spack
 
-# If you want to use the unstable software stack do:
+0. Load the spack module:
+
+```bash
+[stable] user@login001:~> module load spack
+```
++ If you want to use the unstable software stack do in addition:
+
+```bash
 spack env activate -p unstable
 ```
 
-### Install your own software
+### Find out what's already installed
-```bash
-# Check if your package is already implemented in Spack
-# You can also use the following website: https://packages.spack.io/
-[stable] user@login001:~> spack list $pkg_name # e.g opal
-
-# Check the package variants you want to set e.g +cuda +openmp ^openmpi ...
-[stable] user@login001:~> spack info $pkg_name # e.g opal
-
-# Add your package to the environment
-[stable] user@login001:~> spack add $pkg_name@version +variant1 ^dep1@version1
-
-# If you want to install from local source clone your source under
-# /afs/psi.ch/sys/spack/user/$USER/spack-environment/$pkg_name
-# and tell Spack you want to use it using:
-[stable] user@login001:~> spack develop $pkg_name@version # Skip this if you don't want to develop from local source
-
-# Check the whole dependency tree of your spec and
-# if you don't need to set more variants
-[stable] user@login001:~> spack concretize
-
-# Install your packages
-[stable] user@login001:~> spack install # -v for verbose
-
-# Load your package
-[stable] user@login001:~> spack load $pkg_name@version +variant1 ^dep1@version1
-
-# Submit your script
-[stable] user@login001:~> sbatch batch.script
-```
-### Switching between environments
-
-There are two environment available to users; stable and unstable. <br/>
-The first one is loaded by default when loading the module. <br/>
-If you want to switch between the two and use different software stack you can use the following command:
 
 ```bash
-spack env activate -p unstable # or stable
+[unstable] user@login001:~>  spack find
-```
-
-### Managing your environments
-
-When adding the following command you actually add a package to your own software stack;
-
-```bash
-[stable] user@login001:~> spack add $pkg_name@version +variant1 ^dep1@version1
-```
-
-You can check which package will be concretized and are in your environment using;
-
-```bash
-[unstable] user@login001:~> spack find
 ==> In environment unstable
 ==> 1 root specs
- -  visit ~adios2+vtkm+gui
+ - []
 
 ==> Included specs
 -- no arch / gcc ------------------------------------------------
@@ -133,13 +90,148 @@ gromacs@2024.1  hwloc@2.9.1  intel-oneapi-mkl@2024.0.0  intel-oneapi-runtime@202
 ==> 257 installed packages
 ```
 
+The included specs and installed packages sections shows you all the packages that are pre-installed for you. </br>
+In case of a package having multiple installations, the following command helps you to find out which software you're interested about.  </br>
+
+For example let's say you are interested in py-alphafold but only in the gpu version; do:
+
+```
+[unstable] user@login001:~> spack find -vl py-alphafold
+==> In environment unstable
+==> 1 root specs
+ -  dpjaszc visit
+
+==> Included specs
+-- no arch / gcc ------------------------------------------------
+------- gromacs%gcc
+
+-- no arch / gcc@12.3.0 -----------------------------------------
+------- cp2k@2024.1%gcc@12.3.0  ------- opal@master%gcc@12.3.0         ------- py-alphafold@2.3.2%gcc@12.3.0
+------- cp2k@2024.1%gcc@12.3.0  ------- py-alphafold@2.3.2%gcc@12.3.0  ------- quantum-espresso@7.3.1%gcc@12.3.0
+
+-- no arch / oneapi@2024.1.0 ------------------------------------
+------- gromacs@2024.1%oneapi@2024.1.0
+
+==> Installed packages
+-- linux-rhel7-x86_64 / gcc@12.3.0 ------------------------------
+rrfdppp py-alphafold@2.3.2~cuda build_system=python_pip  tqziprv py-alphafold@2.3.2+cuda build_system=python_pip cuda_arch=60
+==> 2 installed packages
+```
+
+As you can see there are two installation of py-alphafold, one with +cuda and one without. </br>
+In this particular example, there is only one variant that interests you, so you can do:
+
+``` bash
+spack load py-alphafold +cuda
+```
+
+However if multiple variants are interesting to you and you don't want to have to cite all of them you can do:
+
+``` bash
+spack load /tqziprv # refer to the installation with its hash directly.
+```
+
+### Install your own software
+
+1. Check if your package is already implemented in Spack. <br/>
+ You can also use the following website: https://packages.spack.io/
+
+```bash
+spack list $pkg_name # e.g opal
+```
+
+2. Check the package variants you want to set e.g +cuda +openmp ^openmpi ...
+
+```bash
+spack info $pkg_name # e.g opal
+```
+
+3. Add your package to your personal environment
+
+```bash
+spack add $pkg_name@version +variant1 ^dep1@version1
+```
+
++ If you want to install from local source clone your source under <br/>
+/afs/psi.ch/sys/spack/user/$USER/spack-environment/$pkg_name <br/>
+and tell Spack you want to use it using:
+
+```bash
+spack develop $pkg_name@version # Skip this if you don't want to develop from local source
+```
+4. Check the whole dependency tree of your spec and <br/>
+if you don't need to set more variants
+
+```bash
+spack concretize
+```
+
+5. Install the packages in your environment
+
+```bash
+spack install # -v for verbose
+```
+
+6. Load your package
+
+```bash
+spack load $pkg_name@version +variant1 ^dep1@version1
+```
+
+7. Submit your script
+
+```bash
+sbatch batch.script
+```
+### Switching between environments
+
+There are two environment available to users; stable and unstable. <br/>
+The first one is loaded by default when loading the module. <br/>
+If you want to switch between the two and use different software stack you can use the following command:
+
+```bash
+spack env activate -p unstable # or stable
+```
+
+### Managing your environments
+
+When adding the following command you actually add a package to your own software stack;
+
+```bash
+spack add $pkg_name@version +variant1 ^dep1@version1
+```
+
+You can check which package will be concretized and are in your environment using;
+
+```bash
+[unstable] user@login001:~> spack find
+==> In environment unstable
+==> 1 root specs
+ -  visit ~adios2+vtkm+gui
+
+==> Included specs
+-- no arch / gcc ------------------------------------------------
+gromacs%gcc
+
+-- no arch / gcc@12.3.0 -----------------------------------------
+cp2k@2024.1%gcc@12.3.0  opal@master%gcc@12.3.0         py-alphafold@2.3.2%gcc@12.3.0
+cp2k@2024.1%gcc@12.3.0  py-alphafold@2.3.2%gcc@12.3.0  quantum-espresso@7.3.1%gcc@12.3.0
+
+-- no arch / oneapi@2024.1.0 ------------------------------------
+gromacs@2024.1%oneapi@2024.1.0
+
+==> Installed packages
+...
+==> 257 installed packages
+```
+
 The root spec is the specs that are personal to you and that will be concretized and installed. <br/>
 The installed packages are either packages that were previously installed by admins or packages that you already installed but that are not root. <br/>
 
 If you want to remove this package from your personal env, you can use the following command: <br/>
 
 ```bash
-[stable] user@login001:~> spack rm $pkg_name@version +variant1 ^dep1@version1
+spack rm $pkg_name@version +variant1 ^dep1@version1
 ```
 
 or