Ex 12.) Mini-Challenge: Running your first HPC simulation

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With all what you learned so far, you should be now able to compile, set up and run your first HPC simulation. We have picked GADGET-4, a state-of-the-art N-Body cosmological simulation code.

  1. Download/clone the latest version of GADGET-4 from HERE onto SCIAMA (Tip: git may be helpful)
  2. Create a Makefile.systype with the correct system (Generic-intel) uncommented (Tip: check the Makefile for details/instructions)
  3. Try to execute the make-examples.sh script to build the example simulation codes. You will notice that you will run into errors due to missing libraries. Identify and load the correct versions of the missing libraries (for the compiler use intel_comp/2019.2 and for mpi use openmpi/4.0.1) (Tip: you can solve this by either deducing the correct libraries from the error messages or studying the online documentation of Gadget-4)
  4. Pick an example (recommended: DM-L50-N128) and go into the respective subfolder in the examples folder. If the building process in the previous step was successful, you should find there a Gadget4 binary file among other files.
  5. Adapt the submission script (job.sh) in the folder i.e. set the partition to training.q, reduce the number of tasks to 16 and set up the module environment to match the one you used for building (Tip: module list -t gives you a list of the currently loaded modules without any decorations around them for easy copy & paste)
  6. Submit the job script to slurm. It may fail due to one more additional library (HDF5) required at runtime (it is listed in the docs but not required at compile time). Identify it and add it to the modules loaded in the job script. You then also have to load it into your current environment, delete the Gadget4 binary and build folder in your example folder and build the example again.
  7. Submit again. Now it should run successfully within a couple of minutes.
  8. ????
  9. Profit!!! (well, you mastered the content of the first day successfully ;))
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