Announcements, 8th September 2015

KSL Workshop Towards High Efficiency Computing with Allinea

KAUST Supercomputing Laboratory presents the Allinea Software workshop on HPC profiling and debugging: "Towards High Efficiency Computing with Allinea" on October 4th, starting at 9am.

Workshop topics include:

  • How to profile an application on Shaheen II, and how to debug and identify bottlenecks with Allinea Forge.
  • How to optimize and monitor application performance using Allinea Performance Reports. Workshop sessions offer attendees the opportunity to practice using the Allinea tools on Shaheen II with either their own applications or provided examples.

Please register at http://www.hpc.kaust.edu.sa/training/2015/allinea/registrations

When: October 4th, 2015, starting 9am
Where: KAUST Auditorium between Building 4 and 5, Level 0
What: https://www.hpc.kaust.edu.sa/training/2015/allinea/
Contacts: Bilel Hadri (bilel.hadri@kaust.edu.sa) and Samar Aseeri (samar.aseeri@kaust.edu.sa)

Tip of the week: Best Practices for I/O

Efficient I/O is critical for performance with data-intensive applications since parallel file systems are usually a substantial bottleneck on HPC systems.

Here are some simple guidelines that can be used for almost any type of I/O on KSL HPC systems:

  • Avoid frequently opening and closing the same file during code execution.
  • Avoid creating directory hierarchies with thousands of files which causes significant overhead.
  • Aggregate small amounts of data into larger reads and writes.
  • Avoid using ASCII representations of your data since they usually require much more space to store, and require conversion to/from binary when reading/writing.
  • Don’t re-invent the wheel. Using Parallel I/O libraries such as MPI-IO, HDF5 and netCDF can help you to parallelise, aggregate and efficiently manage I/O operations. HDF5 and netCDF use binary file formats that support complex data models and provide portability across multiple systems.

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http://www.hpc.kaust.edu.sa/tip/