diff --git a/README.md b/README.md index e7d5cf5..a032b7a 100644 --- a/README.md +++ b/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 -```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.
-The first one is loaded by default when loading the module.
-If you want to switch between the two and use different software stack you can use the following command: +### Find out what's already installed ```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 -[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 +[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.
+In case of a package having multiple installations, the following command helps you to find out which software you're interested about.
+ +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.
+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.
+ 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 $pkg_name@version +variant1 ^dep1@version1 +``` + ++ If you want to install from local source clone your source under
+/afs/psi.ch/sys/spack/user/$USER/spack-environment/$pkg_name
+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
+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.
+The first one is loaded by default when loading the module.
+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.
The installed packages are either packages that were previously installed by admins or packages that you already installed but that are not root.
If you want to remove this package from your personal env, you can use the following command:
```bash -[stable] user@login001:~> spack rm $pkg_name@version +variant1 ^dep1@version1 +spack rm $pkg_name@version +variant1 ^dep1@version1 ``` or