User:Edu159

Public application template

A: An introduction

• Please describe yourself in three sentences, one of them regarding your current studies.

I am Eduardo, a 24 years old guy that is passionated about science and computers. I have a BSc in computer science and I am currently finishing a 4 year degree in Materials Engineering. I love all that is related with numerical methods and simulations since the last year (I took a course Simulation of materials) and currently I am doing my final project about simulation of heat diffusion + Joule effect in a nano-wire using FEM. I am a very friendly and teamworking person.

• Which languages do you speak?

Spanish is my mother tongue but I can write and speak English relatively fluid.

• What's your overall background? The general field you work in or are studying, e.g. computer science, physics, artificial intelligence, control theory...

I think that I have a nice multidisciplinary background that comes from my two distinct university degrees(and self-teaching). I like to get my hands dirty with lots of different things coming from different fields of science. Despite of that fact, I am interested to focus my professional career in numerical methods and/or simulations related with materials science.

• Why do you want to participate in the Google Summer of Code? What do you hope to gain by doing so?

GSOC is an amazing program for people that like to code, and the key thing is that you can be involved in a serious free software project with the supervision and help of a mentor! It is a privilege to have a person that can guide you and help you in such a thing. I do not know other program that offers that kind of support.

• Please also describe your previous experience with the GSoC, if any. Includes any community-bonding, mentor experience or application, not necessarily accepted. We use this subquestion to identify which students are unfamiliar with how the program goes, providing further support. It has no negative impact on your rating!

No experience at all.

• Why are you choosing Octave?

When I decided trying to be selected for a project for the GSOC I checked the 192 organisations looking for keywords like, science, maths, numerical methods, etc... because I wanted to dedicate my time to something I am really interested in. Octave along with CGAL were the only two organisations that I found that really appeal to me. And with no doubt OCTAVE was the chosen one. I wanted to do only a proposal so I could prepare it well enough to have a chance. Other strong reason is that I have used Octave for quite long and it would be nice to contribute to it.

C: Contact

• Please state the (unique and identical where possible) nick you use on IRC and any other communication channel related to Octave. We really want unique nicks. You might want to bold it.

nick: edu159

• Which time zone do you live in? Will that change over GSoC duration? Perhaps DST adjustment or a relocation. Note that both UTC and GMT are not aware of daylight saving time! Please state UTC+x or -x.

Time zone: UTC+0. It won't change during GSoC.

• Please state the timeframe (in UTC+0) when you feel most comfortable working during GSoC. Where are your time buffers? Example: I usually code around 9.00 to 18.00 and could also try to start earlier (~7.00) for few days ;-)

I can code from 7:00-13:00 in May, June and first half of July from Monday to Thursday. On Fridays, Saturdays and Sundays I have almost the whole day free for coding. In the second half of July and August I have no timeframe restrictions.

E: Coding experience

• Please describe your experience with C++, Octave or Matlab m-scripts, OpenGL and Qt.

I have programmed in C++ along with the STL and Boost libraries, from small to medium large projects. . With octave I have worked for quite long and in different fields: robotics (path finding algorithms), signal processing (signal modulation and filtering), FEM (2D fem solver for static structural problems), and programming of several basic numerical methods (Forward-Backward Euler, LU decomposition, Newton-Raphson...). With openGL I have done a few things in the past and I know how its work, but I am not very interested in graphical programming right now. Qt happens to be the same.

• Please describe your experience with other programming languages.

I like developing code with Python the most. I love Django framework. I have touched Java and assembler for the x86 platform, AVR and Motorolla microcontrollers.

• Please describe your experience with being in a development team. Do you have experience working with open source or free projects?

I have only that kind of experience while doing some personal projects with a friend of mine, so I have not experience with such a large project and free software community.

• Please describe the biggest project you have written code for and what you learned by doing so. Also describe your role in that project over time.

I have dealt with projects with around 2.5-3k lines of code, not more. I don't have a extraordinary successful story about a project I have been in although I have been in lots of small ones. I worked the last year while in college with a friend on a website for informal job seeking done in PHP+MySQL (around 3K lines of PHP code). We even sent the idea to Ycombinator to get funding. Unfortunately we were not selected and the idea was not as good as we thought. I learned a lot with that project, particularly combining both college and a project at the same time, working regularly and establishing deadlines.

• Please state the commits and patches you already contributed to Octave. This question (one of the most important parts by the way) is the only part of your application our wiki admins will edit for you even after the application deadline. Code sometimes speaks louder than many words do.

• Contributions to Octave:
  • Patch submitted for bug #41839.(m-file) UPDATE: The patch has been accepted.
  • Patch submitted for bug #41796.(c++)
• Others:
  • Code that implements partial functionality of ilu function("no-fill option") : file

F: Feeling fine

• Please describe (in short) your experience with the following tools: We only use this question to determine where you need guidance, not for rating! We by no means expect you to be familiar with all of these and you'll won't necessarily need them while working with us.
• IRC and mailing lists

I have experience with both worlds.

• Mercurial or other source code management systems

I have worked with git and svn

• Mediawiki or other wiki software

Not at all.

• make, gcc, gdb or other development tools

I have worked with them many times but I have not a deep knowledge of them.

• What will make you actively stay in our community after this GSoC is over? You can also tell us after applications close and we'll happily try to fulfill :-)

It's an easy one. The fun and personal satisfaction that I can achieve during my time here. UPDATE: I have been around for three weeks, and I had fun and a rewarding experience. The community is very active and helps newbies without hesitation.

O: Only out of interest

• Did you ever hear about Octave before?

Yeah, long time ago...

• If so, when and where? How far have you been involved already?

In 2007 when I used it in a subject called "Pattern recognition"

• If not, where would you expect or advise us to do advertising?

Do you really need that? At least here in Spain not many people/universities can afford to get a Matlab license (actually I don't know why they should do that xD). You are well advertised just because octave is a quality software.

• What was the first question concerning Octave you could not find an answer to rather quickly? Of course more than one question can be stated. We try to improve based on this each year! Includes learning how to use it, code, website, GSoC application, …

In my opinion some ideas on the website have very little information. In fact I am interested in sparse matrices as a project for my proposal (taken the idea from the ideas page) but there is almost no explanation of some points.

P: Prerequisites

• Please state the operating system you work with.

I like programming on Linux.

• If you have access to more than one, please state them and the conditions under which you are granted this access.

I own also a Windows native installation.

• Please estimate an average time per day you will be able to (if separated) access
  • an internet connection --> ~18 hours a day
  • a computer -> 24 hours a day
  • a computer with your progressing work on -> 24 hours a day

* Please describe the degree up to which you can install new software on computers you have access to.

With total freedom.

S: Self-assessment

• Please describe how useful criticism looks from your point of view as committing student.

I think its totally necessary in a free software community. You have to be prepared to be criticized, in fact is a duty of the community to do it in a constructive way for the goodness of the project.

• How autonomous are you when developing?

Personally I don't like to bother others unless necessary, in fact I sometimes said to my dad when he has an issue with the computer... "first search on Google then ask me" and he always gets really mad.

• Do you like to discuss changes intensively and not start coding until you know what you want to do?

I have to confess that sometimes I spent too much time designing before programming. That is why I like to set deadlines. They help me to get things done.

• Do you like to code a proof of concept to 'see how it turns out', modifying that and taking the risk of having work thrown away if it doesn't match what the project or original proponent had in mind?

It is not what I like but what is maybe necessary to be done. Just as easy.

Y: Your task

Introduction

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My intention is to implement the missing ilu and ichol functions and to continue last year's GSoC project developed by Kai Torben. The goal is the complete integration in the core of Octave. Those functions will have a direct impact on quite a few functions that solve sparse linear systems as ilu and ichol are known to be good algorithms for generating preconditioners. Some of the functions that will take advantage of them are pcg, bicg or gmres among others. Bottom line, performance of sparse linear system solvers in Octave will be raised.

Approach

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• ilu: This function has a big chunk of options and the last year was almost implemented by Kai despite of the fact that he could not finally integrate it into Octave . His approach was interfacing Octave with ITSOL/ZITSOL libraries but in the end there were some issues with that direction:

1. ILUTP algorithm did not work for him
2. He had to patch the library to get things work. Not nice for achieve integration.
3. modified versions of algorithms ("milu" option) were not implemented in the libraries
4. That "ugly" scenario lead to finally not being able to include ITSOL as a dependency with Octave. Bottom line, the integration of the function with the development\n repository could not be achieved.

I have been in contact with Kai by mail and agrees that writing from scratch all the functions needed as oct-files (ILUTP, ILU0, ILUC and ILUT) would be a harder but safer way to go if integration want to be achieved. This way no dependencies are needed to be added and the overhead of translating the data from Octave to ITSOL and vice verse is eliminated. Algorithms will be taken from Yousef Saad's book "Iterative methods for sparse linear systems Ed. 2". Moreover, I can use some of the code that Kai wrote, mostly the tests, documentation and the m-file "ilu.m" that glue together all the functions. ITSOL source code is also a good place to look for some help.

I have implemented the ILU0 algorithm so far and benchmarked it against Matlab and Kai's last GsOC version(using ITSOL). The performance is great. You can check the code and see a table with the execution times in a blog I have created to inform about my achievements in the project. Here is the link to the source code I have written so far. I has not got any doc-strings nor tests, but is functional.

• ichol: In this case things should be easier at first glance. Kai implemented the functions related with ichol from Fortran prototypes and they work as expected. In theory would be only necessary to code the complex versions and the modified versions of the algorithms. On the other hand, there is an issue here with licenses I did not know at first and Kai pointed me out (see here). Authors should be contact in order to ask for a permission, but if they are not in favor of giving to us then functions will be implemented from scracth.

The road map of what and how I want to do the project is clear to me, but I don't know for sure if it will be enough for the GSoC period. Because I am concerned about that there are other functions that I would like to implement if it would be necessary like lsqr and minres, both highly related with ichol and ilu. I have already done some search and found that this website [lsqr] [minres]. The website is from the people that wrote the papers given as references in Matlab documentation. In the website there are several codes that can be used. I have mailed professor Michael Saunders about adapting them into Octave versions and he answered me that I am welcome to do while I respect the license (CPL or BSD licenses). He claimed that they are very unrestrictive but I've been told that they are not compatible with GPL3. I will need some insights about that if I happen to have time for implementing them.

Project structure

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These are the main files that will be needed for the project:

• ilu.m -- Act as a wrapper for the rest of ilu functions
  • ilu0.cc -- Implements ilu decomposition zero level of fill
  • ilut.cc -- Implements ilu decomposition with threshold
  • iluc.cc -- Implements Crout version of ilu decomposition
  • ilutp.cc-- Implements the ilu decomposition with threshold and pivoting

• ichol.m -- Act as a wraper for the rest of functions
  • ichol0.cc -- Implements ichol decomposition with zero level of fill
  • icholt.cc -- Implements ichol decomposition with threshold
  • icholt0jp.cc -- Implements ichol decomposition following Jones and Plassmann strategy

NOTE: All the algorithms could be used with real and complex numbers and "modifified versions" will be implemented as well.

Estimated timeline:

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• FIRST PERIOD:

19 May-20 June: Implement ilu related functions. In that order ilu0, ilut, iluc , ilutp.

20-25 June: Write ilut, iluc, ilutp automated tests, documentation and benchmarking.

27 June: (Millstone 1) ilu.m is fully functional and ready to be integrated with Octave core.

27 June: Mid-term evaluation

• SECOND PERIOD:

28 June-2 July: Strategy for ichol will be fully established in those days. Better to plan wisely before code.

2 July-5 August: Implement ichol related functions. In that order ichol0, icholt. ichol0jp if there is time left.

5-10 August: Write automated tests, documentation and benchmarking for those functions.

10 August: (Millstone 2) ichol.m is fully functional and ready for integration.

10-18 August: Buffer week for any unexpected situation or minor changes that should be done. If there is time left, then I will work on minres and lsqr functions.

Note: I set schedule starting on May 19th but I would like to start coding since I know I am selected (22 April), so maybe goals would be reached before stated above. So that dates should be taken as top limits. In June 3 college exams are scheduled that still not have fixed dates. I am not worried about them since I have a lot of time for studying.