|9:00 – 9:15||Welcome and introduction|
|9:15 – 10:00||Introduction to HPC concepts (theoretical part)|
|10:00 – 10:30||Connecting and copying files from/to the execution cluster|
|10:30 – 11:00||Introduction to SLURM and job submission|
|11:00 – 11:30||Coffee break|
|11:30 – 12:30||Introduction to OpenMP and Practical session on introductory shared memory exercises:|
|12:30 – 13:30||Introduction to MPI and Practical session on introductory distributed memory exercises:|
|13:30 – 14:30||Lunch|
|14:30 – 15:00||Introduction to sequence database search and dynamic data distribution|
|15:00 – 16:00||Practical session on sequence database search with MPI and with static and dynamic data distribution (part 1)|
|16:00 – 16:30||Coffee break|
|16:30 – 18:00||Practical session on sequence database search with MPI and with static and dynamic data distribution (part 2)|
|08:00 – 8:15||Summary of the first day|
|8:15 – 8:45||Second day presentation.|
Background on pairwise and multiple genome comparison.
Introduction to GECKO.
|08:45 – 9:45|| Practical session:|
|09:45 – 10:30||Description and pseudo-code of the implemented parallel strategy. Coarse-grained at the pairwise comparison level and fine-grained inside each module composing GECKO. Measuring application speedup and efficiency|
|10:30 – 11:00||Coffee break|
|11:00 – 13:00||Groups organization and start working with the parallel strategy.|
Practical session: Self-organized group work to benchmark the described parallel strategy
|13:00 – 14:00||Lunch|
|14:00 – 14:30||Motivational discussion about parallelisation and its costs and benefits in GECKO:|
|14:30 – 14:45||Quick recapitulation of the course|
All material is also available in the ELIXIR-SI eLearning platform web
The course will be streamed (live) in the following web (Google chrome required)
This course to be held 6-7 April 2017 in Malaga, Spain is part of the Train-the-Researcher (TtR) subtask of the ELIXIR-EXCELERATE project. The course is organised as a two-day mini-symposium, and aims at introducing the participants in the complexities of parallel programming with emphasis on genome-scale comparison algorithms.
- The theoretical aspects of this course cover (a) the parallel programing background, with a quick overview in the architectures and programming models; and (b) the basis for genome-scale sequence comparison algorithms.
- The practical aspects are organised to master the concepts of data distribution and balancing using a Map-Reduce strategy and internal coding with MPI.
This course has been prepared for two days including theoretical and practical parts. The first day will start with a brief introduction to HPC condensed during the morning. A practical introductory part to HPC will complete the first day. The second day will firstly provide the necessary background on the multiple genome comparison application GECKO. Secondly, on the same day, we will motivate the potential HPC techniques to be applied to this application and will let the students organize in groups to start thinking about a parallelization approach and later on implementing it. At the end of the day each group will briefly describe how they have implemented it and will present their results (i.e. speedup).
The course is comprised of practical exercises preceded by short lectures. Exercises will be conducted primarily in the C programming language using the MPI library.
This course is open to bioinformatics users and developers that aim at using HPC resources to extend their activity beyond the limitations of sequential applications on commodity hardware. This course will not suit participants that are looking for entry-level concepts in HPC.
20 participants will be selected by CV and motivation. Gender equality will be an additional aspect to select the participants. As an applicant to this course you need to fill out your personal information, attach your CV and provide a short paragraph to explain why you want to apply for this course. Optionally if you are part of an ELIXIR node you can also attach a letter of endorsement from the node manager. The last application day will be March 16th, the result of the candidate selection will be notified March 17th. The course registration is free, but by sending this participation you commit to attend the course in case you are selected as it is stated in the conditions/policy document of the registration form.
This course has a broad technical scope and hence programming skills are required. Experience in the command-line, writing and compiling C code would make the course easier to follow.
From the city center (Alameda principal) to the course venue (room 2.0.10, indications will be provided in-place) . Bus line 11 operates every 10 minutes
From the the course venue to the city center. Bus line 11 operates every 10 minutes
From Hotel Tribuna (C/ Carretería) to the bus stop (Alameda principal. Bus line 11)