I'm using the ORTOOLS library for solving a VRP problem. I give it an initial feasible solution to my problem, satisfying all the constraints of my problem but sub-optimal. Then ORTOOLS performs a GUIDED_LOCAL_SEARCH heuristic, continuously perturbing parts of my solution (possibly making it infeasible at times) until it hopefully reaches a better solution than my initial solution.
Why is it using a constraint programming solver? My understanding is that classic constraint programming starts with an infeasible (possibly empty) solution, propagates the constraints to narrow the domains of my variables until reaching a stationary state, and then makes a decision. Then it iterates again until solving the problem or backtracks if reaching a dead-end (think SUDOKU).
In what way are these capabilities (propagation, backtracking) needed when making the small perturbations?
There are two reasons.
1) The initial solution heuristics is a combination of fast LS heuristic search and standard constraint programming search.
2) The whole local search implementation is build on top of a traditional constraint programming solver and uses constraints and propagators to validate solution, and complete them.
See: https://github.com/google/or-tools/issues/920
There are a lot of programs that do parameter learning for Bayes nets. I am having a hard time finding libraries or tools that do (or try to do) structure learning. Specifically, one that uses an information theoretic approach, by looking at the information gain from adding an edge, or analyzing the cross entropy across Random Variables to determine if they have any relationships or are independent. This is not the core problem I am trying to work on, but learning structure is an important part of it. So finding an existing tool/library would help immensely.
Try the bnlearn library. It contains structure learning, parameter learning, inference and various well-known example datasets such as Sprinkler, Asia, Alarm.
Github documentation pages
Examples can be found here
Blog about detecting causal relationships can be found here.
Hypothetically speaking, if my scientific work was leading toward the development of functions/modules/subroutines (on a desktop), what would I need to know to incorporate it into a large-scale simulation to be run on a supercomputer (which might simulate molecules, fluids, reactions, and so on)?
My impression is that it has to do with taking advantage of certain libraries (e.g., BLAS, LAPLACK) where possible, revising algorithms (reducing iteration), profiling, parallelizing, considering memory-hard disk-processor use/access... I am aware of the adage, "want to optimize your code? don't do it", but if one were interested in learning about writing efficient code, what references might be available?
I think this question is language agnostic, but since many number-crunching packages for biomolecular simulation, climate modeling, etc. are written in some version of Fortran, this language would probably be my target of interest (and I have programmed rather extensively in Fortran 77).
Profiling is a must at any level of machinery. In common usage, I've found that scaling to larger and larger grids requires a better understanding of the grid software and the topology of the grid. In that sense, everything you learn about optimizing for one machine is still applicable, but understanding the grid software gets you additional mileage. Hadoop is one of the most popular and widespread grid systems, so learning about the scheduler options, interfaces (APIs and web interfaces), and other aspects of usage will help. Although you may not use Hadoop for a given supercomputer, it is one of the less painful methods for learning about distributed computing. For parallel computing, you may pursue MPI and other systems.
Additionally, learning to parallelize code on a single machine, across multiple cores or processors, is something you can begin learning on a desktop machine.
Recommendations:
Learn to optimize code on a single machine:
Learn profiling
Learn to use optimized libraries (after profiling: so that you see the speedup)
Be sure you know algorithms and data structures very well (*)
Learn to do embarrassingly parallel programming on multiple core machines.
Later: consider multithreaded programming. It's harder and may not pay off for your problem.
Learn about basic grid software for distributed processing
Learn about tools for parallel processing on a grid
Learn to program for alternative hardware, e.g. GPUs, various specialized computing systems.
This is language agnostic. I have had to learn the same sequence in multiple languages and multiple HPC systems. At each step, take a simpler route to learn some of the infrastructure and tools; e.g. learn multicore before multithreaded, distributed before parallel, so that you can see what fits for the hardware and problem, and what doesn't.
Some of the steps may be reordered depending on local computing practices, established codebases, and mentors. If you have a large GPU or MPI library in place, then, by all means, learn that rather than foist Hadoop onto your collaborators.
(*) The reason to know algorithms very well is that as soon as your code is running on a grid, others will see it. When it is hogging up the system, they will want to know what you're doing. If you are running a process that is polynomial and should be constant, you may find yourself mocked. Others with more domain expertise may help you find good approximations for NP-hard problems, but you should know that the concept exists.
Parallelization would be the key.
Since the problems you cited (e.g. CFD, multiphysics, mass transfer) are generally expressed as large-scale linear algebra problems, you need matrix routines that parallelize well. MPI is a standard for those types of problems.
Physics can influence as well. For example, it's possible to solve some elliptical problems efficiently using explicit dynamics and artificial mass and damping matricies.
3D multiphysics means coupled differential equations with varying time scales. You'll want a fine mesh to resolve details in both space and time, so the number of degrees of freedom will rise rapidly; time steps will be governed by the stability requirements of your problem.
If someone ever figures out how to run linear algebra as a map-reduce problem they'll have it knocked.
Hypothetically speaking, if my scientific work was leading toward the development of functions/modules/subroutines (on a desktop), what would I need to know to incorporate it into a large-scale simulation to be run on a supercomputer (which might simulate molecules, fluids, reactions, and so on)?
First, you would need to understand the problem. Not all problems can be solved in parallel (and I'm using the term parallel in as wide meaning as it can get). So, see how the problem is now solved. Can it be solved with some other method quicker. Can it be divided in independent parts ... and so on ...
Fortran is the language specialized for scientific computing, and during the recent years, along with the development of new language features, there has also been some very interesting development in terms of features that are aiming for this "market". The term "co-arrays" could be an interesting read.
But for now, I would suggest reading first into a book like Using OpenMP - OpenMP is a simpler model but the book (fortran examples inside) explains nicely the fundamentals. Message parsing interface (for friends, MPI :) is a larger model, and one of often used. Your next step from OpenMP should probably go in this direction. Books on the MPI programming are not rare.
You mentioned also libraries - yes, some of those you mentioned are widely used. Others are also available. A person who does not know exactly where the problem in performance lies should IMHO never try to undertake the task of trying to rewrite library routines.
Also there are books on parallel algorithms, you might want to check out.
I think this question is language agnostic, but since many number-crunching packages for biomolecular simulation, climate modeling, etc. are written in some version of Fortran, this language would probably be my target of interest (and I have programmed rather extensively in Fortran 77).
In short it comes down to understanding the problem, learning where the problem in performance is, re-solving the whole problem again with a different approach, iterating a few times, and by that time you'll already know what you're doing and where you're stuck.
We're in a position similar to yours.
I'm most in agreement with #Iterator's answer, but I think there's more to say.
First of all, I believe in "profiling" by the random-pausing method, because I'm not really interested in measuring things (It's easy enough to do that) but in pinpointing code that is causing time waste, so I can fix it. It's like the difference between a floodlight and a laser.
For one example, we use LAPACK and BLAS. Now, in taking my stack samples, I saw a lot of the samples were in the routine that compares characters. This was called from a general routine that multiplies and scales matrices, and that was called from our code. The matrix-manipulating routine, in order to be flexible, has character arguments that tell it things like, if a matrix is lower-triangular or whatever. In fact, if the matrices are not very large, the routine can spend more than 50% of its time just classifying the problem. Of course, the next time it is called from the same place, it does the same thing all over again. In a case like that, a special routine should be written. When it is optimized by the compiler, it will be as fast as it reasonably can be, and will save all that classifying time.
For another example, we use a variety of ODE solvers. These are optimized to the nth degree of course. They work by calling user-provided routines to calculate derivatives and possibly a jacobian matrix. If those user-provided routines don't actually do much, samples will indeed show the program counter in the ODE solver itself. However, if the user-provided routines do much more, samples will find the lower end of the stack in those routines mostly, because they take longer, while the ODE code takes roughly the same time. So, optimization should be concentrated in the user-provided routines, not the ODE code.
Once you've done several of the kind of optimization that is pinpointed by stack sampling, which can speed things up by 1-2 orders of magnitude, then by all means exploit parallelism, MPI, etc. if the problem allows it.
I am looking for practical problem (or implementations, applications) examples which are effectively algoritmized using swarm intelligence. I found that multicriteria optimization is one example. Are there any others?
IMHO swarm-intelligence should be added to the tags
Are you looking for toy problems or more for real-world applications?
In the latter category I know variants on swarm intelligence algorithms are used in Hollywood for CGI animations such as large (animated) armies riding the fields of battle.
Related but more towards the toy-problem end of the spectrum you can model large crowds with similar algorithms, and use it for example to simulate disaster-scenarios. AFAIK the Dutch institute TNO has research groups on this topic, though I couldn't find an English link just by googling.
One suggestion for a place to start further investigation would be this PDF book:
http://www.cs.vu.nl/~schut/dbldot/collectivae/sci/sci.pdf
That book also has an appendix (B) with some sample projects you could try and work on.
If you want to get a head start there are several frameworks (scientific use) for multi-agent systems such as swarming intelligence (most of 'em are written with Java I think). Some of them include sample apps too. For example have a look at these:
Repast:
http://repast.sourceforge.net/repast_3/
Swarm.org:
http://swarm.org/
Netlogo:
http://ccl.northwestern.edu/netlogo
Post edited, added more info.
I will take your question like: what kind of real-world problems SI can solve?
There are alot. Swarm intelligence is based on the complex behaviour of swarms, where agents in the swarm coordinate and cooperate by executing very simple rules to generate an emergent complex auto organized behaviour. Also, the agents often make a deliberation process to make efficient decisions, and also, the emergent behaviour of the swarms allows them to find patterns, learn and adapt to their environment. Therefore, real-world applications based on SI are those that often required coordination and cooperation techniques, optimization process, exploratory analysis, dynamical poblems, etc. Some of these are:
Optimization techniques (mathematical functions for example)
Coordination of a swarm of robots (to organize inventory for example)
Routing in communication networks. (This is also dynamical combinatorial optimization)
Data analysis (usually exploratory, like clustering). SI has alot of applications in data mining and machine learning. This allows SI algorithms to find interesting patterns in big sets of data.
Np problems in general
I'm sure there are alot more. You should check the book:
"Swarm Intelligence: from natural to artificial systems". This is the basic book.
Take care.
I was recently talking with someone in Resource Management and we discussed the problem of assigning developers to projects when there are many variables to consider (of possibly different weights), e.g.:
The developer's skills & the technology/domain of the project
The developer's travel preferences & the location of the project
The developer's interests and the nature of the project
The basic problem the RM person had to deal with on a regular basis was this: given X developers where each developers has a unique set of attributes/preferences, assign them to Y projects where each project has its own set of unique attributes/requirements.
It seems clear to me that this is a very mathematical problem; it reminds me of old optimization problems from algebra and/or calculus (I don't remember which) back in high school: you know, find the optimal dimensions for a container to hold the maximum volume given this amount of material—that sort of thing.
My question isn't about the math, but rather whether there are any software projects/libraries out there designed to address this kind of problem. Does anyone know of any?
My question isn't about the math, but rather whether there are any software projects/libraries out there designed to address this kind of problem. Does anyone know of any?
In my humble opinion, I think that this is putting the cart before the horse. You first need to figure out what problem you want to solve. Then, you can look for solutions.
For example, if you formulate the problem by assigning some kind of numerical compatibility score to every developer/project pair with the goal of maximizing the total sum of compatibility scores, then you have a maximum-weight matching problem which can be solved with the Hungarian algorithm. Conveniently, this algorithm is implemented as part of Google's or-tools library.
On the other hand, let's say that you find that computing compatibility scores to be infeasible or unreasonable. Instead, let's say that each developer ranks all the projects from best to worst (e.g.: in terms of preference) and, similarly, each project ranks each developer from best to worst (e.g.: in terms of suitability to the project). In this case, you have an instance of the Stable Marriage problem, which is solved by the Gale-Shapley algorithm. I don't have a pointer to an established library for G-S, but it's simple enough that it seems that lots of people just code their own.
Yes, there are mathematical methods for solving a type of problem which this problem can be shoehorned into. It is the natural consequence of thinking of developers as "resources", like machine parts, largely interchangeable, their individuality easily reduced to simple numerical parameters. You can make up rules such as
The fitness value is equal to the subject skill parameter multiplied by the square root of the reliability index.
and never worry about them again. The same rules can be applied to different developers, different subjects, different scales of projects (with a SLOC scaling factor of, say, 1.5). No insight or real leadership is needed, the equations make everything precise and "assured". The best thing about this approach is that when the resources fail to perform the way your equations say they should, you can just reduce their performance scores to make them fit. And if someone has already written the tool, then you don't even have to worry about the math.
(It is interesting to note that Resource Management people always seem to impose such metrics on others in an organization -- thereby making their own jobs easier-- and never on themselves...)