ssh <username>@puhti.csc.fi # replace <username> with your CSC username, e.g. email@example.com
modulecommand! Check out which modules are loaded as default as you login to Puhti:
💬 Let’s imagine that you want to do some molecular dynamics simulations using the Gromacs application.
module spider gromacs
☝🏻 This might take a while as the command searches through all the available modules.
💬 The list can be quite long. You can go to the next line with Enter, or stop viewing by typing
module avail gromacs
💡 Tip: Another quick way to list the available versions is by typing the load command until the module name and then hit
$ module load gromacs # and here double press TAB gromacs gromacs/2022.3 gromacs-env/2021-gpu gromacs/2021.4-plumed gromacs/2022.4 gromacs-env/2022 gromacs/2021.5 gromacs-env gromacs-env/2022-gpu gromacs/2021.6 gromacs-env/2020 gromacs/2022.2 gromacs-env/2021
module load gromacs
module listcompared to the first try? Try this again:
☝🏻 If no version is given in the module command, the default version is loaded.
module load gromacs/2021.6 module list
module purge # Purge all (non-sticky) modules module list # List the loaded modules module load StdEnv # Load the default module environment module list # List the loaded modules
💭 If actually using Gromacs in Puhti, you would run the application as a batch job through the queueing system, which will be discussed in detail later.
💭 Check out an example batch job script for Gromacs to see how the module is recommended to be loaded (
module load gromacs-env loads the latest minor release of a specific year).
💬 Using an older version of a module is usually possible
💬 As an example, you can try to load an old version of Gromacs from 2020.
gromacs/2020.5module cannot be loaded in the default environment since it has different dependencies. Check with the
module spidercommand which other modules are needed for the older version:
module spider gromacs/2020.5
module purge module load gcc/9.4.0 module load openmpi/4.1.4 module load gromacs/2020.5 module list
☝🏻 It is generally best to use the latest versions since they typically are more performant than old ones and may have useful new features.