User:Antonio Pino: Difference between revisions

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* Which time zone do you live in? Will that change over GSoC duration?
* Which time zone do you live in? Will that change over GSoC duration?
In Spain we are at UTC+1 (DST UTC+2), although there have been talks to change to an UTC+0 (DST UTC+1) frame, I am not aware of those taking place soon, nor do I plan to travel outside UTC+2 this summer.
In Spain we are at UTC+1 (DST UTC+2), although there have been talks to change to an UTC+0 (DST UTC+1) frame, I am not aware of those taking place soon, nor do I plan to travel outside UTC+2 this summer.
* Please state the timeframe (in UTC+0) when you feel most comfortable working during GSoC. Where are your time buffers?
* Please state the time frame (in UTC+0) when you feel most comfortable working during GSoC. Where are your time buffers?
I am really a morning person, so a eight to six (UTC+0) schedule will do for me.
I am really a morning person, so a eight to six (UTC+0) schedule will do for me.


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* 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.
* 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.


The biggest project I have worked on was the VHDL discrete filter, carried out along with two colleagues. The idea was to make use of all we learned about digital circuits so we implemented a RAM, adders, various types of registers, finite state machines, and we all went through the nightmare of 'looking for the bug' and creating testbenchs for vhdl. But more importantly that an innocent looking modification may break others' job.
The biggest project I have worked on was the VHDL discrete filter, carried out along with two colleagues. The idea was to make use of all we learned about digital circuits so we implemented a RAM, adders, various types of registers, finite state machines, and we all went through the nightmare of 'looking for the bug' and creating test benchs for vhdl. But more importantly that an innocent looking modification may break others' job.


By the way, knowing about the nuts and bolts of how are numbers stored in the bare metal gave me an appreciation for what are the differences between an idealized (almighty) function and the ''real'' poor man's version of it.
By the way, knowing about the nuts and bolts of how are numbers stored in the bare metal gave me an appreciation for what are the differences between an idealized (almighty) function and the ''real'' poor man's version of it.
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The project I intend to do is [http://wiki.octave.org/Summer_of_Code_Project_Ideas#Improve_logm.2C_sqrtm.2C_funm Improve logm, sqrtm, funm]; its aim is to improve the existing implementations of [https://en.wikipedia.org/wiki/Matrix_function Matrix Functions] in Octave based on the algorithms developed by [http://www.maths.manchester.ac.uk/~higham/NAMF/#People a team lead by Prof. Higham] (project entitled Numerical Analysis of Matrix Functions, NAMF) at the University of Manchester. At this point in time, in Octave there are the following: [http://hg.savannah.gnu.org/hgweb/octave/file/9a8be23d2c05/scripts/linear-algebra/expm.m expm] makes use of Padé approximant, [http://hg.savannah.gnu.org/hgweb/octave/file/9a8be23d2c05/scripts/linear-algebra/logm.m logm] uses a Schur-Parlett algorithm, and [http://hg.savannah.gnu.org/hgweb/octave/file/9a8be23d2c05/libinterp/corefcn/sqrtm.cc sqrtm] using a variant of the algorithm in A New sqrtm for MATLAB[1]. On the other hand, in Octave-Forge there are [http://sourceforge.net/p/octave/linear-algebra/ci/default/tree/inst/funm.m funm] and [http://sourceforge.net/p/octave/linear-algebra/ci/default/tree/inst/thfm.m trigonometric and hyperbolic matrix functions]. For a general survey-introduction to matrix functions (or matrix computation in general) refer to Golub & Van Loan[2].
The project I intend to do is [http://wiki.octave.org/Summer_of_Code_Project_Ideas#Improve_logm.2C_sqrtm.2C_funm Improve logm, sqrtm, funm]; its aim is to improve the existing implementations of [https://en.wikipedia.org/wiki/Matrix_function Matrix Functions] in Octave based on the algorithms developed by [http://www.maths.manchester.ac.uk/~higham/NAMF/#People a team lead by Prof. Higham] (project entitled Numerical Analysis of Matrix Functions, NAMF) at the University of Manchester. At this point in time, in Octave there are the following: [http://hg.savannah.gnu.org/hgweb/octave/file/9a8be23d2c05/scripts/linear-algebra/expm.m expm] makes use of Padé approximant, [http://hg.savannah.gnu.org/hgweb/octave/file/9a8be23d2c05/scripts/linear-algebra/logm.m logm] uses a Schur-Parlett algorithm, and [http://hg.savannah.gnu.org/hgweb/octave/file/9a8be23d2c05/libinterp/corefcn/sqrtm.cc sqrtm] using a variant of the algorithm in A New sqrtm for MATLAB[1]. On the other hand, in Octave-Forge there are [http://sourceforge.net/p/octave/linear-algebra/ci/default/tree/inst/funm.m funm] and [http://sourceforge.net/p/octave/linear-algebra/ci/default/tree/inst/thfm.m trigonometric and hyperbolic matrix functions]. For a general survey-introduction to matrix functions (or matrix computation in general) refer to Golub & Van Loan[2].


I believe this is of interest to Gnu Octave first, due to the goal of overall MATLAB compatibility and second, because more and more systems are being described by a matrix equation lately.
I believe this is of interest to GNU Octave first, due to the goal of overall MATLAB compatibility and second, because more and more systems are being described by a matrix equation lately.


Upon completion Gnu Octave should have a working funm based on the Schur-Parlett algorithms by Higham et al., that calls to specific matrix functions if these have an instance of their own: expm, logm, sqrtm etc.
Upon completion GNU Octave should have a working funm based on the Schur-Parlett algorithms by Higham et al., that calls to specific matrix functions if these have an instance of their own: expm, logm, sqrtm etc.


'''Update:'''
'''Update:'''
Part of the work is already done by Prof. N.J. Higham and is available under a GPLv3+ license: [http://www.ma.man.ac.uk/~higham/mftoolbox/ The Matrix Function Toolbox][3] which is closely related to the book by the same author[4]. A [http://www.ma.man.ac.uk/~higham/mctoolbox toolbox for matrix computations][4] (The Matrix Computation Toolbox) is also provided by the same author, under the same license. Finally, a funm function is provided in the page of the NAMF project under GPLv3+. One might suggest that there is still room for improvement; because as Marco Caliari noted the toolboxes are from 2008. A review of the literature needs to be done in order to use more recent algorithms when writing the new functions.
Part of the work is already done by Prof. N.J. Higham and is available under a GPLv3+ license: [http://www.ma.man.ac.uk/~higham/mftoolbox/ The Matrix Function Toolbox][3] which is closely related to the book by the same author[4]. A [http://www.ma.man.ac.uk/~higham/mctoolbox toolbox for matrix computations][5] (The Matrix Computation Toolbox) is also provided by the same author, under the same license. Finally, a funm function is provided in the page of the NAMF project under GPLv3+. One might suggest that there is still room for improvement; because as Marco Caliari noted the toolboxes are from 2008. A review of the literature needs to be done in order to use more recent algorithms when writing the new functions.


'''May the 25th Update:'''
After the community bonding period and before starting today the coding period, I will briefly list the transformation that has undergone my initial proposal: from just implementing new algorithms and then add them to GNU Octave, to various modifications of GNU Octave itself so that Higham's toolboxes run smoothly and in the end add the new algorithms. Sticking to what I said before, I expect to be doing the modifications (e.g. new bugs, patches, toolboxes) most of the first half of the coding period. From there we aim to go as far as we can about matrix functions, I will do so.


'''TENTATIVE TIMELINE'''
On the side, I reckon that fast-running matrix manipulation involves C++, a weakness I will cure with a quick refreshment and reading lots of GNU Octave code.


'''weeks 1-2'''
I hope everyone pleasantly codes their summer away!
 
PS: a final thank goes to the project in general and my mentors in particular for the opportunity.
 
 
==='''TENTATIVE TIME LINE'''===
 
1st week, May 25-31. Last/14th week, August 24-30.
 
Important dates: all of them, but specially the ''Midterm'' on the 3rd of July (week 6), the ''Firm Pencils Down'' on the 21st of August, and the ''Final Evaluation'' on the 28th of August.
 
'''preceding weeks (community bonding)'''
 
First meeting.
 
Start the blog.
 
Set up the working environment.
 
Create an hg repository with the toolboxes.
 
Second meeting.
 
Start writing tests for NAMF software and get acquainted with the bug reporting in Savannah.
 
'''week 1'''
 
The start should be soft for I am having the finals in this period. At this point the list of algorithms to be used must be completely defined; that is, a final review of the literature is to be done.
 
Work on the toolboxes starts here. NAMF software shall tested now, so that a first funm works well within Octave.


The start should be soft for I am having the finals in this period. At this point the list of algorithms to be used must be completely defined; that is, a final review of the literature will be done. For that purpose, the access to my university's bibliographical will be used.
'''weeks 2-4'''


Work with the toolboxes starts here.
Keep working in the toolboxes proceeding in chronological order:


'''weeks 3-4'''
::Test Matrix Toolbox (1995)
::Matrix Computation Toolbox (2002)
::Matrix Function Toolbox (2008).


''Milestone 0'': the toolboxes are working and packaged.
Start refreshing C++ knowledge.


'''weeks 4-7'''
'''weeks 4-7'''
''Milestone 0'': the toolboxes are ready.
''' ''Midterm'' on the 3rd of July (week 6)'''
End the C++ refreshing.


funm  
funm  
''Milestone 1'': general purpose funm based on a Schur-Parlett algorithm)
 
''Milestone 1'': general purpose funm based on a Schur-Parlett algorithm.


'''weeks 8-9'''
'''weeks 8-9'''


expm and logm
expm[7] and logm


'''weeks 10-11'''
'''weeks 10-11'''


sqrtm
sqrtm
p-th roots (p = integer) algorithm [?]
p-th roots (p = integer) algorithm [?]
''Milestone 2'': logm, sqrtm, funm
''Milestone 2'': logm, sqrtm, funm


'''weeks 12'''
'''week 12'''


implement trigonometric functions (I submitted  a snippet of cosm [http://octave.1599824.n4.nabble.com/GSoC-2015-improving-matrix-funtcions-td4669227.html to the mailing list], [http://agora.octave.org/snippet/tqUQ/ updated])
implement trigonometric functions (I submitted  a snippet of cosm [http://octave.1599824.n4.nabble.com/GSoC-2015-improving-matrix-funtcions-td4669227.html to the mailing list], [http://agora.octave.org/snippet/tqUQ/ updated])
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Pencils down. Run tests on the Matrix Functions and write/review their documentation.
Pencils down. Run tests on the Matrix Functions and write/review their documentation.
''' ''Firm Pencils Down'' on the 21st of August '''
''' ''Final Evaluation'' on the 28th of August '''




<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
'''TENTATIVE TIMELINE'''(previous)
'''TENTATIVE TIME LINE'''(previous)
<div class="mw-collapsible-content">'''Introduction'''
<div class="mw-collapsible-content">'''Introduction'''
It appears to me that the natural task division for this project is to first improve and test funm (this should be ready by the mid-term), and then get to the rest, picking logm first.
It appears to me that the natural task division for this project is to first improve and test funm (this should be ready by the mid-term), and then get to the rest, picking logm first.
'''weeks 1-2'''
'''weeks 1-2'''


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</div>
</div>


 
<!-- references
these feel like I have just one source, and I am citing it over and over again...
--->
[1] N.J. Higham. A New sqrtm for MATLAB.  Numerical Analysis Report No. 336, Manchester Centre for Computational Mathematics, Manchester, England, January 1999.
[1] N.J. Higham. A New sqrtm for MATLAB.  Numerical Analysis Report No. 336, Manchester Centre for Computational Mathematics, Manchester, England, January 1999.


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[5] N. J. Higham. The Matrix Computation Toolbox. http://www.ma.man.ac.uk/~higham/mctoolbox
[5] N. J. Higham. The Matrix Computation Toolbox. http://www.ma.man.ac.uk/~higham/mctoolbox
-------


This section is being reworked in a sandbox, [[User:Antonio_Pino:anotherwiki|the other wiki]]. Will add it here when done. Note that the previous is still going though changes.
[6]  M. I. Smith (2003). [http://www.maths.manchester.ac.uk/~higham/narep/narep392.ps.gz A Schur Algorithm For Computing Matrix Pth Roots], SIAM J. MATRIX ANAL. APPL. 24, 4, 971-989.
 
[7] A.H. Al-Mohy and N.J. Higham (2009). "A New Scaling and Squaring Algorithm for the Matrix Exponential," SIAM J. Matrix Anal. Applic. 31, 970-989 <http://eprints.ma.man.ac.uk/1217/01/covered/MIMS_ep2009_9.pdf>


==Z: submitted proposal==
==Z: submitted proposal==
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'''Organization''': GNU Project
'''Organization''': GNU Project


'''Abstract''': Matrix Functions are widely used to describe dynamical systems, this project aims at implementing those based on algorithms developed at the University of Manchester by Dr. Philip Davies and Matthew Smith, led by Prof. Nick Higham. Upon completion Gnu Octave should have a reliable working funm based on the Schur-Parlett algorithms by Higham et al., that calls to specific matrix functions if these have an instance of their own.
'''Abstract''': Matrix Functions are widely used to describe dynamical systems, this project aims at implementing those based on algorithms developed at the University of Manchester by Dr. Philip Davies and Matthew Smith, led by Prof. Nick Higham. Upon completion Gnu Octave should have no problem (extending compatibility with Matlab) when running the toolboxes by Higham, and should also have a reliable working funm based on the Schur-Parlett algorithms, that calls to specific matrix functions if these have an instance of their own.


Additional info: http://wiki.octave.org/User:Antonio_Pino
Additional info: http://wiki.octave.org/User:Antonio_Pino
<div class="mw-collapsible-content">'''Introduction'''
<div class="mw-collapsible-content">'''Introduction'''


I am Antonio Pino Robles, and if selected I will be working on the project for about 6-8 hours a day (8:00-16:00 UTC+0), with the exception of the first two weeks when I will be taking my final exams.  Therefore, mine will be a soft start.  As for IRC, I may be contacted anytime during the day at AntonioPino in the #octave channel at freenode, via a mobile connection. That work plan shall not be altered, as I don't plan to travel this summer.
I am Antonio Pino Robles, and if selected I will be working on the project for about 6-8 hours a day (8:00-16:00 UTC+0), with the exception of the first two weeks when I will be taking my final exams.  Therefore, mine will be a soft start.  As for IRC, I may be contacted any time during the day at AntonioPino in the #octave channel at freenode, via a mobile connection. That work plan shall not be altered, as I don't plan to travel this summer.


On the other hand, I am a fluent English speaker, hold a Cambridge CAE certificate and have taken several university courses taught entirely in the English language. Besides, I am an avid reader, with a passion for the English literature.  What I mean is that I do not expect any problem communicating with the mentors or organizers, either in a written fashion or orally.
On the other hand, I am a fluent English speaker, hold a Cambridge CAE certificate and have taken several university courses taught entirely in the English language. Besides, I am an avid reader, with a passion for the English literature.  What I mean is that I do not expect any problem communicating with the mentors or organizers, either in a written fashion or orally.
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'''Benefit-Deliverables'''
'''Benefit-Deliverables'''


The project's aim is to improve the existing implementations of Matrix Functions in Gnu Octave based on the algorithms developed by a team lead by Prof. Higham at the University of Manchester. At this point in time, in Gnu Octave there are the following: expm makes use of Padé approximant, logm uses a Schur-Parlett algorithm, and sqrtm using a variant of the algorithm in A New sqrtm for MATLAB[1]. On the other hand, in Octave-Forge there are funm and trigonometric and hyperbolic matrix functions.
The project's aim is to improve the existing implementations of Matrix Functions in Gnu Octave based on the algorithms developed by a team lead by Prof. Higham at the University of Manchester. At this point in time, in Gnu Octave there are the following: expm makes use of Padé approximant, logm uses a Schur-Parlett algorithm, and sqrtm using a variant of the algorithm in A New sqrtm for MATLAB[0]. On the other hand, in Octave-Forge there are funm and trigonometric and hyperbolic matrix functions.
 
I believe this is of interest to Gnu Octave first, due to the goal of overall MATLAB compatibility and second, because more and more systems are being described by a matrix equation lately.  


I believe this is of interest to Gnu Octave first, due to the goal of overall MATLAB compatibility and second, because more and more systems are being described by a matrix equation lately.
Part of the work is already done by Prof. N.J. Higham and is available under a GPLv3+ license: The Matrix Function Toolbox[1] which is closely related to the book by the same author[4], The Matrix Computation Toolbox[2] is also provided by the same author, under the same license. That is the project offers a twofold benefit: renewed Matrix Functions as well as further Matlab compatibility.


funm should be ready by the mid-term. The rest will follow. The tentative time line can be read in the "Additional Info URL".
Hence, the first part of the project is to focus on Octave-Matlab compatibility by making the toolboxes --originally intended to work with Matlab-- work smoothly as they are under Octave. Then recent algorithms will be used to replace existing implementations.


funm should be ready by the mid-term.  The tentative time line can be read in the "Additional Info URL".


'''Qualification'''
'''Qualification'''
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Finally, I have been writing m-scripts for two years now, to solve specific engineering problems, a strong python background. I order to fulfil it I will have to refresh my C++ knowledge by becoming familiar with the source tree, and get used to mercurial (hg), the version control system used to manage Gnu Octave.
Finally, I have been writing m-scripts for two years now, to solve specific engineering problems, a strong python background. I order to fulfil it I will have to refresh my C++ knowledge by becoming familiar with the source tree, and get used to mercurial (hg), the version control system used to manage Gnu Octave.


[1] N.J. Higham. A New sqrtm for MATLAB. Numerical Analysis Report No. 336, Manchester Centre for Computational Mathematics, Manchester, England, January 1999.
[0] N.J. Higham. A New sqrtm for MATLAB. Numerical Analysis Report No. 336, Manchester Centre for Computational Mathematics, Manchester, England, January 1999.
 
[1] N. J. Higham. The Matrix Function Toolbox. http://www.ma.man.ac.uk/~higham/mftoolbox
 
[2] N. J. Higham. The Matrix Computation Toolbox. http://www.ma.man.ac.uk/~higham/mctoolbox


</div>
</div>
Antonio Pino
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