Optimization
PIs and users can request support on technical or scientific topics by emailing our help system (help@rockfish.jhu.edu). This support is limited to 8 hours, free of cost. If the project needs more support PIs can request dedicated support, which usually includes paying for part of an FTE.
All users are strongly encouraged to optimize the use of Rockfish. This can be done in different ways. If unsure on how to proceed, please send email to help@rockfish.jhu.edu and ask for assistance.
- Optimize your application using compiler flags
- Use the proper compiler
- Benchmark your code. If it runs in parallel find out the best number of cores to use.
- Optimize your data access/read and writes
- Batch scripts best practices
- Using job arrays
- Using GNU parallel
- Optimizing workflows and data manipulation
- Selection of most appropriate file system