I've been out of the modeling biz, so to speak, for a while now. When I was in college, most of the models I worked with were written in FORTRAN, which I never liked. I'm looking to get back into science, so I'm wondering if there are modern languages with feature sets suited for this kind of application. What would you consider to be an optimal language for simulating complex physics systems?
While certainly Fortran was the absolute ruler for this, Python is being used more and more exactly for this purpose. While it is very hard to say which is the BEST program for this, I've found python pretty useful for physics simulations and physics education.
It depends on the task
C++ is good at complicated data structures, but it is bad at slicing and multiply matrices. (This task equires you to spend a lot of time writing for loops.)
FORTRAN has a nice notation for slicing and multiplying matrices, but it is clumsy for creating complicated data structure such as graphs and linked lists.
Python/scipy has a nice notation for everything, but python is an interepreted language, so it is slow at certain tasks.
Some people are interested in languages like CUDA that allow you to use your GPU to speed up your simulations.
In the molecular dynamics community c++ seems to be popular, because you need somewhat complicated data structures to represent the shapes of the molecules.
I think it's arguable that FORTRAN is still dominant when it comes to solving large-scale problems in physics, as long as we're talking about serial calculations.
I know that parallelization is changing the game. I'm less certain about whether or not parallelized versions of LINPACK and other linear algebra packages are still written in FORTRAN.
A lot of engineers are using MATLAB and Mathematica these days, because they combine numerical and graphics capabilities.
I'd also point out that there's a difference between calculation and display engines. The former might still be written in FORTRAN, but the latter may be using more modern languages and OpenGL.
I'm also unsure about how much modeling has crept into biology. Physical chemistry might be a very different animal altogether.
If you write a terrific parallel linear algebra package in Scala or F# or Haskell that performs well, the world will beat a path to your door.
Python + Matplotlib + NumPy + α
The nuclear/particle/high energy physics community has moved heavily toward c++ (in part due to ROOT and Geant4), with some interest in Python (because it has ROOT bindings).
But you'll note that this is sub-discipline dependent..."physics" and "modeling" are big, broad topics, so there is no one answer.
Modelica is a specialized language for modeling (and simulating) physical systems. OpenModelica is an open source implementation of Modelica.
Python is very popular among science-oriented people, as is Matlab. The issue with these is that they are both VERY slow (to run). If you want to do large simulations that may take minutes/hours/days, you're going to have to pick another language.
As long as you are picking a language for speed, suck it up and use C/C++, maybe with CUDA depending on your needs.
Final thought though: if it takes you two days longer to write and debug your model in C than in python, and the resulting code takes 10 minutes to run instead of an hour, have your really saved any time?
There's also a lot of capability with MATLAB. Especially when interfacing your simulations with hardware, or if you need your results visualised.
I'll chime in with Python but you should also look to R for any statistical work you may need to do. You should really be asking more about what packages for which languages to use rather than the language itself.
Related
Which of the following optimisation methods can't be done in an optimisation software such as CPLEX? Why not?
Dynamic programming
Integer programming
Combinatorial optimisation
Nonlinear programming
Graph theory
Precedence diagram method
Simulation
Queueing theory
Can anyone point me in the right direction? I didn't find too much information regarding the limitations of CPLEX on the IBM website.
Thank you!
That's kind-of a big shopping list, and most of the things on it are not optimisation methods.
For sure CPLEX does integer programming, non-linear programming (just quadratic, SOCP, and similar but not general non-linear) and combinatoric optimisation out of the box.
It is usually possible to re-cast things like DP as MILP models, but will obviously require a bit of work. Lots of MILP models are also based on graphs, so yes it is certainly possible to solve a lot of graph problems using a MILP solver such as CPLEX.
Looking wider at topics like simulation, then that is quite a different approach. Simulation really is NOT an optimisation method, but it can be used alongside optimisation to get extra insights which may be useful in a business context. Might be used for example to discover some empirical relationships that could be used in an optimisation model by CPLEX.
The same can probably also be said for things like queuing theory, precedence, etc. Basically, use CPLEX as an optimisation tool to solve part or all of your problem once you have structured and analysed it via one of these other approaches.
Hope that helps.
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 have been working lately on a number of iterative algorithms in MATLAB, and been getting hit hard by MATLAB's performance (or lack thereof) when it comes to loops. I'm aware of the benefit of vectorizing code when possible, but are there any tools for optimization when you need the loop for your algorithm?
I am aware of the MEX-file option to write small subroutines in C/C++, although given my algorithms, this can be a very painful option given the data structures required. I mainly use MATLAB for the simplicity and speed of prototyping, so a syntactically complex, statically typed language is not ideal for my situation.
Are there any other suggestions? Even other languages (python?) which have relatively painless matrix tools are an option.
It was once true that vectorization would improve the speed of your MATLAB code. However, that is largely no longer true with the JIT-accelerator
This video demonstrating the MATLAB profiler might help.
PROFILER is very useful tool to find bottlenecks in Matlab code. it does not change your code of course, but helps to find which functions/lines to optimize with vectorization or mex.
http://www.mathworks.com/access/helpdesk/help/techdoc/ref/profile.html
http://www.mathworks.com/access/helpdesk/help/techdoc/matlab_env/f9-17018.html
If you have a choice, be sure to set up your loops so you scan the data column-wise which is how the data in MATLAB are arranged. In addition, be sure to preallocate any output arrays before the loop and index into them instead of growing the array inside the for-loop.
If you can cast your code so your operations are called on the whole matrix then you will see great improvement in the speed of your code. Many functions are much quicker when operating on the whole matrix rather than in an element-wise fashion with loops.
You might want to investigate MATLAB's Parallel Computing Toolbox which can make a big difference if you have the right hardware. I re-wrote about 12 lines of code and got 4 - 6 times speedup for one of our loop-intensive programs on and eight core PC.
Today I read this blog entry by Roger Alsing about how to paint a replica of the Mona Lisa using only 50 semi transparent polygons.
I'm fascinated with the results for that particular case, so I was wondering (and this is my question): how does genetic programming work and what other problems could be solved by genetic programming?
There is some debate as to whether Roger's Mona Lisa program is Genetic Programming at all. It seems to be closer to a (1 + 1) Evolution Strategy. Both techniques are examples of the broader field of Evolutionary Computation, which also includes Genetic Algorithms.
Genetic Programming (GP) is the process of evolving computer programs (usually in the form of trees - often Lisp programs). If you are asking specifically about GP, John Koza is widely regarded as the leading expert. His website includes lots of links to more information. GP is typically very computationally intensive (for non-trivial problems it often involves a large grid of machines).
If you are asking more generally, evolutionary algorithms (EAs) are typically used to provide good approximate solutions to problems that cannot be solved easily using other techniques (such as NP-hard problems). Many optimisation problems fall into this category. It may be too computationally-intensive to find an exact solution but sometimes a near-optimal solution is sufficient. In these situations evolutionary techniques can be effective. Due to their random nature, evolutionary algorithms are never guaranteed to find an optimal solution for any problem, but they will often find a good solution if one exists.
Evolutionary algorithms can also be used to tackle problems that humans don't really know how to solve. An EA, free of any human preconceptions or biases, can generate surprising solutions that are comparable to, or better than, the best human-generated efforts. It is merely necessary that we can recognise a good solution if it were presented to us, even if we don't know how to create a good solution. In other words, we need to be able to formulate an effective fitness function.
Some Examples
Travelling Salesman
Sudoku
EDIT: The freely-available book, A Field Guide to Genetic Programming, contains examples of where GP has produced human-competitive results.
Interestingly enough, the company behind the dynamic character animation used in games like Grand Theft Auto IV and the latest Star Wars game (The Force Unleashed) used genetic programming to develop movement algorithms. The company's website is here and the videos are very impressive:
http://www.naturalmotion.com/euphoria.htm
I believe they simulated the nervous system of the character, then randomised the connections to some extent. They then combined the 'genes' of the models that walked furthest to create more and more able 'children' in successive generations. Really fascinating simulation work.
I've also seen genetic algorithms used in path finding automata, with food-seeking ants being the classic example.
Genetic algorithms can be used to solve most any optimization problem. However, in a lot of cases, there are better, more direct methods to solve them. It is in the class of meta-programming algorithms, which means that it is able to adapt to pretty much anything you can throw at it, given that you can generate a method of encoding a potential solution, combining/mutating solutions, and deciding which solutions are better than others. GA has an advantage over other meta-programming algorithms in that it can handle local maxima better than a pure hill-climbing algorithm, like simulated annealing.
I used genetic programming in my thesis to simulate evolution of species based on terrain, but that is of course the A-life application of genetic algorithms.
The problems GA are good at are hill-climbing problems. Problem is that normally it's easier to solve most of these problems by hand, unless the factors that define the problem are unknown, in other words you can't achieve that knowledge somehow else, say things related with societies and communities, or in situations where you have a good algorithm but you need to fine tune the parameters, here GA are very useful.
A situation of fine tuning I've done was to fine tune several Othello AI players based on the same algorithms, giving each different play styles, thus making each opponent unique and with its own quirks, then I had them compete to cull out the top 16 AI's that I used in my game. The advantage was they were all very good players of more or less equal skill, so it was interesting for the human opponent because they couldn't guess the AI as easily.
http://en.wikipedia.org/wiki/Genetic_algorithm#Problem_domains
You should ask yourself : "Can I (a priori) define a function to determine how good a particular solution is relative to other solutions?"
In the mona lisa example, you can easily determine if the new painting looks more like the source image than the previous painting, so Genetic Programming can be "easily" applied.
I have some projects using Genetic Algorithms. GA are ideal for optimization problems, when you cannot develop a fully sequential, exact algorithm do solve a problem. For example: what's the best combination of a car characteristcs to make it faster and at the same time more economic?
At the moment I'm developing a simple GA to elaborate playlists. My GA has to find the better combinations of albums/songs that are similar (this similarity will be "calculated" with the help of last.fm) and suggests playlists for me.
There's an emerging field in robotics called Evolutionary Robotics (w:Evolutionary Robotics), which uses genetic algorithms (GA) heavily.
See w:Genetic Algorithm:
Simple generational genetic algorithm pseudocode
Choose initial population
Evaluate the fitness of each individual in the population
Repeat until termination: (time limit or sufficient fitness achieved)
Select best-ranking individuals to reproduce
Breed new generation through crossover and/or mutation (genetic
operations) and give birth to
offspring
Evaluate the individual fitnesses of the offspring
Replace worst ranked part of population with offspring
The key is the reproduction part, which could happen sexually or asexually, using genetic operators Crossover and Mutation.
In my independent study of various compiler books and web sites, I am learning about many different ways that a compiler can optimize the code that is being compiled, but I am having trouble figuring out how much of a benefit each optimization will tend to give.
How do most compiler writers go about deciding which optimizations to implement first? Or which optimizations are worth the effort or not worth the effort? I realize that this will vary between types of code and even individual programs, but I'm hoping that there is enough similarity between most programs to say, for instance, that one given technique will usually give you a better performance gain than another technique.
I found when implementing textbook compiler optimizations that some of them tended to reverse the improvements made by other optimizations. This entailed a lot of work trying to find the right balance between them.
So there really isn't a good answer to your question. Everything is a tradeoff. Many optimizations work well on one type of code, but are pessimizations for other types. It's like designing a house - if you make the kitchen bigger, the pantry gets smaller.
The real work in building an optimizer is trying out the various combinations, benchmarking the results, and, like a master chef, picking the right mix of ingredients.
Tongue in cheek:
Hubris
Benchmarks
Embarrassment
More seriously, it depends on your compiler's architecture and goals. Here's one person's experience...
Go for the "big payoffs":
native code generation
register allocation
instruction scheduling
Go for the remaining "low hanging fruit":
strength reduction
constant propagation
copy propagation
Keep bennchmarking.
Look at the output; fix anything that looks stupid.
It is usually the case that combining optimizations, or even repeating optimization passes, is more effective than you might expect. The benefit is more than the sum of the parts.
You may find that introduction of one optimization may necessitate another. For example, SSA with Briggs-Chaitin register allocation really benefits from copy propagation.
Historically, there are "algorithmical" optimizations from which the code should benefit in most of the cases, like loop unrolling (and compiler writers should implement those "documented" and "tested" optimizations first).
Then there are types of optimizations that could benefit from the type of processor used (like using SIMD instructions on modern CPUs).
See Compiler Optimizations on Wikipedia for a reference.
Finally, various type of optimizations could be tested profiling the code or doing accurate timing of repeated executions.
I'm not a compiler writer, but why not just incrementally optimize portions of your code, profiling all the while?
My optimization scheme usually goes:
1) make sure the program is working
2) find something to optimize
3) optimize it
4) compare the test results with what came out from 1; if they are different, then the optimization is actually a breaking change.
5) compare the timing difference
Incrementally, I'll get it faster.
I choose which portions to focus on by using a profiler. I'm not sure what extra information you'll garner by asking the compiler writers.
This really depends on what you are compiling. There is was a reasonably good discussion about this on the LLVM mailing list recently, it is of course somewhat specific to the optimizers they have available. They use abbreviations for a lot of their optimization passes, if you not familiar with any of acronyms they are tossing around you can look at their passes page for documentation. Ultimately you can spend years reading academic papers on this subject.
This is one of those topics where academic papers (ACM perhaps?) may be one of the better sources of up-to-date information. The best thing to do if you really want to know could be to create some code in unoptimized form and some in the form that the optimization would take (loops unrolled, etc) and actually figure out where the gains are likely to be using a compiler with optimizations turned off.
It is worth noting that in many cases, compiler writers will NOT spend much time, if any, on ensuring that their libraries are optimized. Benchmarks tend to de-emphasize or even ignore library differences, presumably because you can just use different libraries. For example, the permutation algorithms in GCC are asymptotically* less efficient than they could be when trying to permute complex data. This relates to incorrectly making deep copies during calls to swap functions. This will likely be corrected in most compilers with the introduction of rvalue references (part of the C++0x standard). Rewriting the STL to be much faster is surprisingly easy.
*This assumes the size of the class being permuted is variable. E.g. permutting a vector of vectors of ints would slow down if the vectors of ints were larger.
One that can give big speedups but is rarely done is to insert memory prefetch instructions. The trick is to figure out what memory the program will be wanting far enough in advance, never ask for the wrong memory and never overflow the D-cache.