Example Case 4: Large-scale simulations - Services for Research
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 Object Storage
If the simulations provide datasets that have general interest or applicability, these can be made available using several CSC services together:
- Allas Object Storage: 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.
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CSC supercomputing environment
Mahti is a supercomputer in particular geared towards medium to large scale simulations
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.
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.