User:RaymondJoseph - Revision history

Ksenija: A bit of formatting

2015-09-08T01:37:22Z

A bit of formatting

← Older revision		Revision as of 01:37, 8 September 2015
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	~~'''~~Final Report on the Project~~'''~~		==Final Report on the Project==

	About the Project		===About the Project===

	----		----
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	d) An overall goal was to make the code handling the solvers/ida moule compact.		d) An overall goal was to make the code handling the solvers/ida moule compact.

	The Hows		===The Hows===

	----		----
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	13. Once all the timesteps have been completed, the integration is complete, and the solution is returned.		13. Once all the timesteps have been completed, the integration is complete, and the solution is returned.

	To dos in the Project		===To dos in the Project===

	----		----
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	~~'''~~Timeline~~'''~~		==Timeline==

	'''Week 13''' (17th July to 21st August)		'''Week 13''' (17th July to 21st August)
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	~~'''~~GSoC 2015 Proposal~~'''~~		==GSoC 2015 Proposal==

	Organization: ASCEND		Organization: ASCEND

	~~'''~~Abstract:~~'''~~ The IDA solver requires more refinements both in the numerical as well as user-facing aspects is desirable. One important issue is to do with EVENT syntax - which helps to model whole range of systems, in which parametric constants themselves change values with triggered events, or even more sophisticated systems in which constraint equations are added or deleted when a given event is triggered. This project attempts to strengthen the functionalities of the IDA solver.		===Abstract:=== The IDA solver requires more refinements both in the numerical as well as user-facing aspects is desirable. One important issue is to do with EVENT syntax - which helps to model whole range of systems, in which parametric constants themselves change values with triggered events, or even more sophisticated systems in which constraint equations are added or deleted when a given event is triggered. This project attempts to strengthen the functionalities of the IDA solver.
	(* I'm using the proposal format, obtained from Carlos' GSoC 2012 proposal *)		(* I'm using the proposal format, obtained from Carlos' GSoC 2012 proposal *)

	~~'''~~About:~~'''~~		===About:===
	Master's student at TUM Germany/IITM India. Specializing in the numerical aspects in EECS, such as machine learning and probabilistic methods. Research enthusiast, few publications. Amateur poet and writer.		Master's student at TUM Germany/IITM India. Specializing in the numerical aspects in EECS, such as machine learning and probabilistic methods. Research enthusiast, few publications. Amateur poet and writer.

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	~~'''What are~~ the ~~goals of your~~ project~~? How is your success with these goals measurable?'''~~		===Goals of the project===

	The main goal (Deliverable 1, D1) is to fully integrate IDA into ASCEND by providing and refining EVENT support syntax elements, especially ensuring that the integrator restarts efficiently after events are triggered with modified constraint equations.		The main goal (Deliverable 1, D1) is to fully integrate IDA into ASCEND by providing and refining EVENT support syntax elements, especially ensuring that the integrator restarts efficiently after events are triggered with modified constraint equations.
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	- Make the documentation of migration and faq for users with applications. (D7)		- Make the documentation of migration and faq for users with applications. (D7)

	~~'''What is your planning schedule for completing these goals? '''~~		===Schedule===

	Week 1: Read up and understand IDA integration issues. Great sources and discussions have been documented on the integration issues.		Week 1: Read up and understand IDA integration issues. Great sources and discussions have been documented on the integration issues.
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	Coding experience		===Coding experience===
	Programming languages you have learnt, and how many lines of code, approximately, you have written in each.		Programming languages you have learnt, and how many lines of code, approximately, you have written in each.
	C++ >1500 LoC (Lots of numerical methods experience. Monte-carlo methods, Newton-Raphson method, ODE simulation, etc.)		C++ >1500 LoC (Lots of numerical methods experience. Monte-carlo methods, Newton-Raphson method, ODE simulation, etc.)

RaymondJoseph at 19:35, 24 August 2015

2015-08-24T19:35:02Z

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	I'm Harry Raymond Joseph, a master's student in EECS at IIT Madras, India. This page is intended to serve as a journal to keep track of my development work at Ascend as part of GSoC 2015. Updates and some relevant aspects of the GSoC proposal I submitted to Ascend are made available below.		I'm Harry Raymond Joseph, a master's student in EECS at IIT Madras, India. This page is intended to serve as a journal to keep track of my development work at Ascend as part of GSoC 2015. Updates and some relevant aspects of the GSoC proposal I submitted to Ascend are made available below.


			'''Final Report on the Project'''

			About the Project

			----

			The project was to better organize the entire ida solver module in Ascend. Specific sub-tasks included:

			a) Writing a separate function to pre-process the integrator. Before the project this was packaged as part of the ida.c file.
			b) Work on ida.c and make it a lot more readable and understandable.
			c) Handle the events syntax, with particular requirements and constraints on time-steps after roots.
			d) An overall goal was to make the code handling the solvers/ida moule compact.

			The Hows

			----
			Created process_integrator.c

			1. Initially, as already mentioned preparing the integrator and allocating memory to it was actually part of the ida.c module. This made it slightly more complicated and difficult to understand the main module. The separate prepare_integrator that was created has the following functionality:

			2. Allocate ida_mem : This is done by use of IDA_MALLOC.

			3. Pass the integrator configuration settings: several integration configuration settings (eg. Pass tolerance settings, type of solver, etc) need to be obtained from the user and passed as input to the IDA, these are accomplished by using a variety of functions, as listed in the IDA manula.

			4. Analyse the equations - An initial analysis of the equations is completed – for instance checking solvability, etc.

			5. configure IDA (set up the sufficient memory for y, y_d etc vectors)

			Created Process_events_and_whens.c

			1. Process_events_and_whens.c is actually the main module that handles all the event processing and boundary checking.

			2. It returns a flag peaw (process_events_and_whens) – to the ida.c main function. Based on the value of the flag, the integrator makes several choices on the size of time-steps and direction of roots, etc.

			3. In this module, the lrslv solver is called to check for roots.

			4. Another important role of this function is that it returns root directions, so that if a boundary is crossed from one side, lrslv need not check that side for boundary crossings again. This is done by passing the array pointer by reference to the Process_events_and_whens.c function.

			Made changes to ida.c

			1. The complete configuration of the ida.c was changed. The following is a brief outline of how the new ida.c is organized:

			2. From within ida.c, the solver calls first prepare_integrator.c to make necessary memory allocations and to load integrator preferences.

			3. Once this has been done, the main solver routine calls process_events_and_whnens to solve initial conditions as well as to check for crossed boundaries.

			4. An important point to note is that this solving of initial condition happens only once within the loop – this is highly efficient, as this enabled combining together two functions – solve_initial_conditions_and_whens and process_events_and_whens.c into one single file.

			5. This was accomplished by means of the flag ‘first_run’ which is initialized to TRUE, but is set to FALSE as soon as the process_events_and_whens function is called for the first time.

			6. Now, during the subsequent calls, process_events_and_whens returns ‘peaw’, which is a flag, to ascertain the status if roots were found, and smaller integration time-steps need to be taken by the main solver routine calling process_events_and_whens.

			7. Peaw is 143 if roots have been found, if roots have been found it also reconfigures ida, before proceeding to next integration SMALLER timestep.

			8. The two cases (normal timestep and short after_root timestep) are handled in the if statements on peaw.

			9. subpeaw, is for auxiliary shorter timesteps, if there are further roots closer to the roots first found (indicated by peaw==143)

			10. Once peaw is set to 143 (root found), shorter timesteps are being taken. So integration now happens from t0 to t0+tmin instead of from t0 to tout.

			11. Now further shorter timesteps need to be taken, to check for changes - at this point we also take into account rootdir.

			12. Say, after the first root, we increment time by tmin, and we find another root - satisfying rootdir conditions, so within the loop, the integration now changes from t0+tmin(auxcount-1) to t0+tmin(auxcount).

			13. Once all the timesteps have been completed, the integration is complete, and the solution is returned.

			To dos in the Project

			----

			1. More testing is required to see if time-steps and changing happen properly;

			2. Process_events_and_whens needs t be properly debugged.

			3. At least the main ida.c and prepare_integrator seem to be working fine, but it might be better to add more comments within the code and perhaps search for places to make it more efficient.

RaymondJoseph at 00:59, 19 August 2015

2015-08-19T00:59:35Z

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	'''Timeline'''		'''Timeline'''

			'''Week 13''' (17th July to 21st August)

			-Fixed all errors Ksenija pointed out on prepare_integrator earlier.

			-Finishing a final report for end-term review;

			-Successful in compiling working code with new main function and new prepare_integrator

			-Succeesful in building new process_events_and_whens, although with the older ida.c

			-Loaded some models but a syntax error was returned issue to be investigated.



			'''Week 12''' (10th August to 16th August)



			-Completed debugging prepare_integrator.

			-Several errors found when I started debugging process_events_and_whens with the new ida.c

			-Errors ranged from complex linking and type incompatibility errors to simple and trivial but difficult t fix beacket_unbalanced errors.

			-Also was a good time to revisit process_events_and_whens and see if the logic underlying the code was appropriate




			'''Week 11''' (3rd August to 9th August)

			-Received detailed feedback from Ksenija on particularly the process_events_and_whens function. In particular
			Ksenija pointed out the following issues:
			"1. At the beginning you initialize the boundary state variables. But this function will do that every time
			you call it regardless of whether it is the first call or not. I suggest putting it into an 'if (first_run \|\| all_bnds_set == 0)'. And I think that this
			boundary evaluation can be moved to a separate function - this will just be more readable.

			2. setup_lrslv is called each time when process_events_and_whens
			is called, while it should be called only at the first run.

			3. The way you check if a boundary has been crossed is incorrect. IDA_ROOT_RETURN is a constant,
			the actual status is returned by IDASolve and it should be compared to IDA_ROOT_RETURN.

			4. If
			no boundary is crossed (so we are making a small step after a root), you call ida_cross_boundary and then check that it does not change the structure o
			f a model. But ida_log_solve can change some logical variables, and some events might be triggered, but most likely only false events, which should not really
			be called. So you don't need to call the whole ida_cross_boundary function, but only the logical solver.

			5. If a root has been found, you don't need to evaluate
			the boundary states here."

			-Looked into each of these issues, but was unable to attend to them then, since I was still debugging prepare_intgerator

			-There was also an
			issue with linking new files on scons. The error detailed an unusual filename. This was because of a string concatenation mistake in the SConscripts file.

			-Further
			re-analysed if steps being done in prepare_integrator are right;

RaymondJoseph at 20:30, 2 August 2015

2015-08-02T20:30:27Z

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	-Fixed previous errors but got stuck at an 'unrecognized symbol' error. The error seems to be very common, but many of the fixes suggested didn't seem to work. Have requested Ksenija for help on this error.		-Fixed previous errors but got stuck at an 'unrecognized symbol' error. The error seems to be very common, but many of the fixes suggested didn't seem to work. Have requested Ksenija for help on this error.

	-Fixed many corrections suggested by Ksenija regarding process_events_..		-Fixed many corrections suggested by Ksenija regarding process_events_..

			-Some errors fixed include: 'load_rellist' not defined - on running the main solver. There was a problem in linking the files.

RaymondJoseph at 20:29, 2 August 2015

2015-08-02T20:29:13Z

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	'''Week 10''' (27th July to 2nd August)		'''Week 10''' (27th July to 2nd August)

	-Fixed previous errors but got stuck at an 'unrecognized symbol' error. The error seems to be very common, but many of the fixes suggested didn't seem to work. Have requested Ksenija for help on this error.		-Fixed previous errors but got stuck at an 'unrecognized symbol' error. The error seems to be very common, but many of the fixes suggested didn't seem to work. Have requested Ksenija for help on this error.

RaymondJoseph at 20:28, 2 August 2015

2015-08-02T20:28:57Z

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	'''Timeline'''		'''Timeline'''

	'''Week 10'''
			'''Week 10''' (27th July to 2nd August)
	-Fixed previous errors but got stuck at an 'unrecognized symbol' error. The error seems to be very common, but many of the fixes suggested didn't seem to work. Have requested Ksenija for help on this error.		-Fixed previous errors but got stuck at an 'unrecognized symbol' error. The error seems to be very common, but many of the fixes suggested didn't seem to work. Have requested Ksenija for help on this error.

RaymondJoseph at 20:28, 2 August 2015

2015-08-02T20:28:07Z

← Older revision		Revision as of 20:28, 2 August 2015
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	'''Timeline'''		'''Timeline'''

			'''Week 10'''
			-Fixed previous errors but got stuck at an 'unrecognized symbol' error. The error seems to be very common, but many of the fixes suggested didn't seem to work. Have requested Ksenija for help on this error.

			-Fixed many corrections suggested by Ksenija regarding process_events_..

RaymondJoseph at 03:53, 29 July 2015

2015-07-29T03:53:36Z

← Older revision		Revision as of 03:53, 29 July 2015
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	'''Timeline'''		'''Timeline'''


	'''Week 9''' (20th July to 26th July)		'''Week 9''' (20th July to 26th July)
	-Faced ida registration problem - Ascend GUI returns the following erroor - 'cannot register ida solver'. Solved the problem - it was due to a wrongly commented command in the prepare_integrator.		-Faced ida registration problem - Ascend GUI returns the following erroor - 'cannot register ida solver'. Solved the problem - it was due to a wrongly commented command in the prepare_integrator.

RaymondJoseph at 03:53, 29 July 2015

2015-07-29T03:53:17Z

← Older revision		Revision as of 03:53, 29 July 2015
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	'''Timeline'''		'''Timeline'''
			'''Week 9''' (20th July to 26th July)
			-Faced ida registration problem - Ascend GUI returns the following erroor - 'cannot register ida solver'. Solved the problem - it was due to a wrongly commented command in the prepare_integrator.

			-Spoke at length with Ksenija, and shared most of the debugging details and progress by sharing screens on Skype.

			-Ksenija suggested I use plots to make sure that everything is alright. Plotting in Ascend requires matplotlib, faced problems getting that sorted out.

			-Continued making changes to ida.c, Ksenija pointed out a flaw in testing - was not using ida to solve the models.

			-Ran tests integrtor_idaevent and integrator_ida both returned errors so far, and I'm rectifying the same.


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	-Continued running tests and mostly making changes to the main solver file.		-Continued running tests and mostly making changes to the main solver file.


	'''Week 7''' (6th to 12th July)		'''Week 7''' (6th to 12th July)

RaymondJoseph at 03:38, 29 July 2015

2015-07-29T03:38:02Z

← Older revision		Revision as of 03:38, 29 July 2015
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	'''Timeline'''		'''Timeline'''


			'''Week 8''' (13th to 19th July)
			-Made further changes to process_event_and_whens.

			-Tested both prepare_integrator as well as process_events_and_whens by calling these from the previous versions of the ida.c.

			-For this, I commented out several lines of code in both ida.c as well as idaboundary.c to see if it worked well - the returned values for models in the Ksenija branch were correct.

			-Continued running tests and mostly making changes to the main solver file.

	'''Week 7''' (6th to 12th July)		'''Week 7''' (6th to 12th July)
	-Continued debugging and running all tests to fully complete the integration of the codes I wrote into the Ascend framework.		-Continued debugging and running all tests to fully complete the integration of the codes I wrote into the Ascend framework.

	-Faced difficulties debugging. The problem was mainly due to the en bloc approach followed. Instead of debugging small pieces of code, as Ksenija advised, I ended up integrating ~~assive~~ code chunks (eg: ida.c) in one shot. Better code architecture planning could have helped minimize debugging trouble.		-Faced difficulties debugging. The problem was mainly due to the en bloc approach followed. Instead of debugging small pieces of code, like Ksenija advised, I ended up integrating massive code chunks (eg: ida.c) in one shot. Better code architecture planning could have helped minimize debugging trouble.

	-Completed the integration of prepare_integrator.		-Completed the integration of prepare_integrator.