Advanced School on Scientific Software Development: Concepts and Tools | (smr 2330) (20 February 2012

Administration

Material

Announcement (poster) External website for participants (moodle platform) Final list of participants Group photo Reference tutorial material by K. Huff and R.T. Guy thehackerwithin (The Hacker Within) Research project questionnaire - case to work on during the School

Advanced School on Scientific Software Development: Concepts and Tools | (smr 2330)

Go to day

Monday, 20 February 2012

08:30 - 10:00 REGISTRATION at the Adriatico Guesthouse, outside the Kastler Lecture Hall (Lower Level 1)
- 08:30 REGISTRATION at the Adriatico Guesthouse, outside the Kastler Lecture Hall (Lower Level 1) 1h30'
10:00 - 10:30 Introduction to the School
- 10:00 Introduction to the School 30'
  
  Speaker: Organizers (S. Cozzini, A. Balaz, G. Giuliani)
10:30 - 11:00 Coffee break
- 10:30 Coffee break 30'

11:00 - 11:45 Basic concepts of software engineering and maintenance

11:00 Basic concepts of software engineering and maintenance 45'

Speaker:	Graziano Giuliani (ICTP Trieste/University of L'Aquila)
Material:	Lesson notes

11:45 - 12:45 Software lifecycle and writing of scientific codes
- 11:45 Software lifecycle and writing of scientific codes 1h0'
  
  Material: Lesson notes
12:45 - 14:00 Lunch break
- 12:45 Lunch break 1h15'

14:00 - 15:00 Unix shell 1

Location:

Adriatico Guest House Informatics Lab.

14:00 Unix shell 1 1h0'

Speaker:	R.T. Guy (Dept of Computer Science, University of Toronto)
Material:	Lesson notes

15:00 - 16:00 Unix shell 2

Location: Adriatico Guest House Informatics Lab.
- 15:00 Unix shell 2 1h0'
  
  Speaker: R.T. Guy (Dept of Computer Science, University of Toronto)
16:00 - 16:30 Coffee break
- 16:00 Coffee break 30'

16:30 - 17:30 Version control 1

Location:

Adriatico Guest House Informatics Lab.

16:30 Version control 1 1h0'

Speaker:	K. Huff (University of Wisconsin - Madison and Argonne National Laboratory)
Material:	Lesson notes

17:30 - 18:30 Version control 2

Location:

Adriatico Guest House Informatics Lab.

17:30 Version control 2 1h0'

Speaker:	K. Huff (University of Wisconsin - Madison and Argonne National Laboratory)
Material:	Lesson notes

Tuesday, 21 February 2012

09:00 - 09:45 Compiling scientific codes: Basic concepts and tools (compilers & make)

09:00 Compiling scientific codes: Basic concepts and tools (compilers & make) 45'

Speaker:	A. Balaz (Scientific Computing Laboratory, Institute of Physics Belgrade)
Material:	Lesson notes

09:45 - 10:30 Debugging scientific codes: Basic concepts and tools (gdb/ddd)

09:45 Debugging scientific codes: Basic concepts and tools (gdb/ddd) 45'

Speaker:	A. Balaz (Scientific Computing Laboratory, Institute of Physics Belgrade)
Material:	Lesson notes

10:30 - 11:00 Coffee break
- 10:30 Coffee break 30'

11:00 - 11:45 Python 1: Shell and variables

11:00 Python 1: Shell and variables 45'

Speaker:	K. Huff (University of Wisconsin - Madison and Argonne National Laboratory)
Material:	Lesson notes

11:45 - 12:30 Python 2: Sets/dicts/lists/tuples

Location:

Adriatico Guest House Informatics Lab.

11:45 Python 2: Sets/dicts/lists/tuples 45'

Speaker:	R.T. Guy (Dept of Computer Science, University of Toronto)
Material:	Lesson notes

12:30 - 14:00 Lunch break
- 12:30 Lunch break 1h30'

14:00 - 15:00 Python 3: Flow control and lists

Location:

Adriatico Guest House Informatics Lab.

14:00 Python 3: Flow control and lists 1h0'

Speaker:	K. Huff (University of Wisconsin - Madison and Argonne National Laboratory)
Material:	Lesson notes

15:00 - 16:00 Python 4: Functions/standard modules

Location:

Adriatico Guest House Informatics Lab.

15:00 Python 4: Functions/standard modules 1h0'

Speaker:	R.T. Guy (Dept of Computer Science, University of Toronto)
Material:	Lesson notes

16:00 - 16:30 Coffee break
- 16:00 Coffee break 30'
16:30 - 18:30 Laboratory sessions: Python exercises

Location: Adriatico Guest House Informatics Lab.
- 16:30 Laboratory sessions: Python exercises 2h0'
  
  Material: Python exercises 1
19:30 - 21:00 WELCOME RECEPTION
```
Cafeteria, Adriatico Guest House
```
- 19:30 WELCOME RECEPTION 1h30'

Wednesday, 22 February 2012
- 09:00 - 09:45 Python 5: File I/O
  - 09:00 Python 5: File I/O 45'
    
    Speaker: R.T. Guy (Dept of Computer Science, University of Toronto)
- 09:45 - 10:30 Python 6: OO design
  - 09:45 Python 6: OO design 45'
    
    Speaker: R.T. Guy (Dept of Computer Science, University of Toronto)
- 10:30 - 11:00 Coffee break
  - 10:30 Coffee break 30'
- 11:00 - 11:45 Python 7: Matplolib
  - 11:00 Python 7: Matplolib 45'
    
    Speaker: K. Huff (University of Wisconsin - Madison and Argonne National Laboratory)
- 11:45 - 12:30 Python 8: Scipy
  - 11:45 Python 8: Scipy 45'
    
    Speaker: K. Huff (University of Wisconsin - Madison and Argonne National Laboratory)
- 12:30 - 14:00 Lunch break
  - 12:30 Lunch break 1h30'
- 14:00 - 15:00 Python 9: Numpy
  
  Location: Adriatico Guest House Informatics Lab.
  - 14:00 Python 9: Numpy 1h0'
    
    Speaker: K. Huff (University of Wisconsin - Madison and Argonne National Laboratory)
- 15:00 - 16:00 Python 10: Nose Testing
  
  Location: Adriatico Guest House Informatics Lab.
  - 15:00 Python 10: Nose Testing 1h0'
    
    Speaker: R.T. Guy (Dept of Computer Science, University of Toronto)
- 16:00 - 16:30 Coffee break
  - 16:00 Coffee break 30'
- 16:30 - 18:30 Laboratory sessions: Python exercises
  
  Location: Adriatico Guest House Informatics Lab.
  - 16:30 Laboratory sessions: Python exercises 2h0'

Thursday, 23 February 2012

09:00 - 10:30 Introduction to testing scientific software

09:00 Introduction to testing scientific software 1h30'

Speaker:	S. Cozzini (CNR/IOM/Uos/SISSA Trieste)
Material:	Lesson notes

10:30 - 11:00 Coffee break
- 10:30 Coffee break 30'

11:00 - 12:30 How to setup regression tests for codes (Buildbot usage)

11:00 How to setup regression tests for codes (Buildbot usage) 1h30'

Speaker:	S. Cozzini (CNR/IOM/Uos/SISSA Trieste)
Material:	Lesson notes

12:30 - 14:00 Lunch break
- 12:30 Lunch break 1h30'
14:00 - 16:00 Laboratory sessions: Exercises on software testing

Location: Adriatico Guest House Informatics Lab.
- 14:00 Laboratory sessions: Exercises on software testing 2h0'
16:00 - 16:30 Coffee break
- 16:00 Coffee break 30'

16:30 - 17:00 GDB tutorial and hands-on

Location:

Adriatico Guest House Informatics Lab.

16:30 GDB tutorial and hands-on 30'

Speaker:	V. Slavnic (Scientific Computing Laboratory, Institute of Physics Belgrade)
Material:	Examples

17:00 - 18:30 Laboratory sessions: Exercises on software testing

Location: Adriatico Guest House Informatics Lab.
- 17:00 Laboratory sessions: Exercises on software testing 1h30'

Friday, 24 February 2012

09:00 - 09:45 Managing sustainability into software

09:00 Managing sustainability into software 45'

Speaker:	S. Crouch (School of Electronics and Computer Science, University of Southampton)
Material:	Lesson notes

09:45 - 10:30 Adopting open source software for longer-term use

09:45 Adopting open source software for longer-term use 45'

Speaker:	S. Crouch (School of Electronics and Computer Science, University of Southampton)
Material:	Lesson notes

10:30 - 11:00 Coffee break
- 10:30 Coffee break 30'

11:00 - 11:45 Ticketing, trac pages, documentation

11:00 Ticketing, trac pages, documentation 45'

Speaker:	S. Crouch (School of Electronics and Computer Science, University of Southampton)
Material:	Lesson notes

12:30 - 14:00 Lunch break
- 12:30 Lunch break 1h30'
14:00 - 16:00 Laboratory sessions: Exercises on software development

Location: Adriatico Guest House Informatics Lab.
- 14:00 Laboratory sessions: Exercises on software development 2h0'
  
  Material: Exercises
16:00 - 16:30 Coffee break
- 16:00 Coffee break 30'
16:30 - 18:30 Students' projects presentations and discussion

Location: Adriatico Guest House Informatics Lab.
- 16:30 Students' projects presentations and discussion 2h0'

Saturday, 25 February 2012
- 09:00 - 09:30 Wrap-up of the first week activities
  - 09:00 Wrap-up of the first week activities 30'
- 09:30 - 10:30 Students' projects presentations and discussion
  - 09:30 Students' projects presentations and discussion 1h0'
- 10:30 - 11:00 Coffee break
  - 10:30 Coffee break 30'
- 11:00 - 12:30 Students' projects presentations and discussion
  - 11:00 Students' projects presentations and discussion 1h30'
- 12:30 - 14:00 Lunch break
```
Lunch, and free afternoon
```
  - 12:30 Lunch break 1h30'

Monday, 27 February 2012

09:00 - 09:45 Optimizing scientific codes: profiling and optimizing (gprof/perfview)

09:00 Optimizing scientific codes: profiling and optimizing (gprof/perfview) 45'

Speaker:	A. Balaz (Scientific Computing Laboratory, Institute of Physics Belgrade)
Material:	Lesson notes

09:45 - 10:30 Merging and mixing different languages: code wrapping and the coding glue

09:45 Merging and mixing different languages: code wrapping and the coding glue 45'

Speaker:	A. Balaz (Scientific Computing Laboratory, Institute of Physics Belgrade)
Material:	Lesson notes

10:30 - 11:00 Coffee break
- 10:30 Coffee break 30'

11:00 - 11:45 Mixing Python, C and Fortran

11:00 Mixing Python, C and Fortran 45'

Speaker:	K. Huff (University of Wisconsin - Madison and Argonne National Laboratory)
Material:	Lesson notes

11:45 - 12:30 Exercises related to topics of the first week

Location: Adriatico Guest House Informatics Lab.
- 11:45 Exercises related to topics of the first week 45'
12:30 - 14:00 Lunch break
- 12:30 Lunch break 1h30'
14:00 - 15:00 Catching memory leaks with Valgrind
- 14:00 Catching memory leaks with Valgrind 1h0'
  
  Speaker: R.T. Guy (Dept of Computer Science, University of Toronto)
15:00 - 16:00 Laboratory sessions: Work on individual/group projects

Location: Adriatico Guest House Informatics Lab.
- 15:00 Laboratory sessions: Work on individual/group projects 1h0'
16:00 - 16:30 Coffee break
- 16:00 Coffee break 30'
16:30 - 18:30 Laboratory sessions: Work on individual/group projects

Location: Adriatico Guest House Informatics Lab.
- 16:30 Laboratory sessions: Work on individual/group projects 2h0'

Tuesday, 28 February 2012

09:00 - 09:45 HPC Infrastructures for Scienfific Computing - 1

09:00 HPC Infrastructures for Scienfific Computing - 1 45'

Speaker:	A. Ali (Bahauddin Zakariya University)
Material:	Lesson notes

09:45 - 10:30 Scientific Data Formats

09:45 Scientific Data Formats 45'

Speaker:	G. Giuliani (ICTP Trieste/University of L'Aquila)
Material:	Lesson notes

10:30 - 11:00 Coffee break
- 10:30 Coffee break 30'
11:00 - 11:45 Laboratory sessions: Work on individual/group projects

Location: Adriatico Guest House Informatics Lab.
- 11:00 Laboratory sessions: Work on individual/group projects 45'
11:45 - 12:30 Laboratory sessions: Hands on NetCDF: Examples

Location: Adriatico Guest House Informatics Lab.
- 11:45 Laboratory sessions: Hands on NetCDF: Examples 45'
  
  Material: Examples
12:30 - 14:00 Lunch break
- 12:30 Lunch break 1h30'
14:00 - 15:00 How to compile Matlab codes
- 14:00 How to compile Matlab codes 1h0'
  
  Speaker: R.T. Guy (Dept of Computer Science, University of Toronto)
15:00 - 16:00 Laboratory sessions: Work on individual/group projects

Location: Adriatico Guest House Informatics Lab.
- 15:00 Laboratory sessions: Work on individual/group projects 1h0'
16:00 - 16:30 Coffee break
- 16:00 Coffee break 30'
16:30 - 18:30 Laboratory sessions: Work on individual/group projects

Location: Adriatico Guest House Informatics Lab.
- 16:30 Laboratory sessions: Work on individual/group projects 2h0'

Wednesday, 29 February 2012

09:00 - 09:45 HPC Infrastructures for Scienfific Computing - 2

09:00 HPC Infrastructures for Scienfific Computing - 2 45'

Speaker:	A. Ali (Bahauddin Zakariya University)
Material:	Lesson notes

09:45 - 10:30 Introduction to porting scientific codes to different computational infrastructures

09:45 Introduction to porting scientific codes to different computational infrastructures 45'

Speaker:	S.Cozzini (CNR/IOM/Uos/SISSA Trieste)
Material:	Lesson notes

10:30 - 11:00 Coffee break
- 10:30 Coffee break 30'
11:00 - 12:30 Laboratory sessions: Work on individual/group projects

Location: Adriatico Guest House Informatics Lab.
- 11:00 Laboratory sessions: Work on individual/group projects 1h30'
12:30 - 14:00 Lunch break
- 12:30 Lunch break 1h30'
14:00 - 16:00 Laboratory sessions: Work on individual/group projects

Location: Adriatico Guest House Informatics Lab.
- 14:00 Laboratory sessions: Work on individual/group projects 2h0'
16:00 - 16:30 Coffee break
- 16:00 Coffee break 30'
16:30 - 18:30 Laboratory sessions: Work on individual/group projects

Location: Adriatico Guest House Informatics Lab.
- 16:30 Laboratory sessions: Work on individual/group projects 2h0'

Thursday, 1 March 2012

09:00 - 09:45 Hands-on on scientific data formats
- 09:00 Hands-on on scientific data formats 45'
  
  Speaker: G. Giuliani (ICTP Trieste/University of L'Aquila)

09:45 - 10:30 On floating point representation of real numbers in computers

09:45 On floating point representation of real numbers in computers 45'

Speaker:	A. Ali (Bahauddin Zakariya University)
Material:	Lesson notes

10:30 - 11:00 Coffee break
- 10:30 Coffee break 30'

11:00 - 11:30 PRACE Research Infrastructure

11:00 PRACE Research Infrastructure 30'

Speaker:	A. Balaz (Scientific Computing Laboratory, Institute of Physics Belgrade)
Material:	Presentation

11:30 - 12:30 Laboratory sessions: Work on individual/group projects

Location: Adriatico Guest House Informatics Lab.
- 11:30 Laboratory sessions: Work on individual/group projects 1h0'
12:30 - 14:00 Lunch break
- 12:30 Lunch break 1h30'
14:00 - 16:00 Laboratory sessions: Work on individual/group projects

Location: Adriatico Guest House Informatics Lab.
- 14:00 Laboratory sessions: Work on individual/group projects 2h0'
16:00 - 16:30 Coffee break
- 16:00 Coffee break 30'
16:30 - 18:30 Laboratory sessions: Work on individual/group projects

Location: Adriatico Guest House Informatics Lab.
- 16:30 Laboratory sessions: Work on individual/group projects 2h0'

Friday, 2 March 2012
- 09:00 - 10:30 Selected presentations by participants
  - 09:00 Selected presentations by participants 1h30'
- 10:30 - 11:00 Coffee break
  - 10:30 Coffee break 30'
- 11:00 - 12:30 Selected presentations by participants
  - 11:00 Selected presentations by participants 1h30'
- 12:30 - 13:00 Wrap-up and closing remarks
  - 12:30 Wrap-up and closing remarks 30'
    
    Speaker: Organizers