Example case 4: Large-scale simulations

This study of protein and lipid layer component dynamics requires large systems in the order of few million atoms. Understanding the relations of the system components requires simulating not only one such system, but other similar systems to pinpoint the differences caused by key components. The simulations need to be long in the order of microseconds. In practice, this requires a few simultaneous simulations each taking up tens of computational nodes. Individual simulations are run for a few days at a time, confirmed to proceed as planned, and continued, for a total duration of weeks. The simulations produce a lot of data, which will be stored in Allas but analysed on e.g. Mahti or Puhti.

This can be done by using several CSC services together:

  • Simulations will be performed in Mahti
  • Instructions on available molecular dynamics applications are available on docs.csc.fi/apps/
  • Large simulation result files can be stored in Allas

If the simulations provide datasets that have general interest or applicability, these can be made available using several CSC services together:

  • Allas: Data stored in Allas is available on CSC's supercomputers
  • Fairdata Services: Data preservation for static files after the project is finished. First step is to bring data into IDA, which allows to get identifier (DOI) for the dataset. Digital Preservation Service will require a contract.

There is no personal information in this dataset.

There is no sensitive data in this dataset.

The project will be using CSC computing environments.

Service Getting access Benefits for this case Requirements for the user

 

 

CSC supercomputing environment

Mahti

Mahti is a supercomputer in particular geared towards medium to large scale simulations

Create a CSC user account, CSC project, apply for access right to Mahti and apply for extra storage and billing units

Adhere to General Terms of Use for CSC's Services for Research

Mahti is a supercomputer designed for massively parallel jobs that require large floating point performance and a capable interconnect. 

Mahti is in particular geared towards medium to large scale simulations.

 

 

Using the HPC environments requires basic skills. We recommend you are familiar with basics of Linux command line usage  before starting.

Allas

Create a CSC user account and CSC project, apply for access right to Allas and apply for extra storage and billing units

Adhere to General Terms of Use for CSC's Services for Research

Good accessibility and capacity. Integrity control.

Data stored in Allas is available on CSC's supercomputers and cloud platforms as well as from any location over the Internet.

Responsibility for managing the data, taking backups.