I'm working on a mathematical model written in VB6. The amount of CPU time this model is consuming is becoming a concern to some of our customers and the notion has been floated that porting it to VB.NET will improve its performance.
The model is performing a lot of single-precision arithmetic (a finite-difference scheme over a large grid) with small bursts of database access every five seconds or so (not enough to be important). Only basic arithmetic functions with occasional use of the ^ 4 operator are involved.
Does anyone think porting to VB.NET is likely to improve matters (or not)? Does anyone know any reliable articles or papers I can check over to help with this decision?
My opinion is that VB.Net won't improve performance by far. The improvement is given by your ability to make an optimized algorith.
Probably the best performance boost you can get is eliminating the DB access (even if it doesnt look important I/O usually is the bottleneck, not the language itself). If possible get the data upfront and save it at the end instead of accesing every 5 secs.
Also as other pointed out, change the algorithm if possible since porting the code to .NET probably will only get you small performance benefits.
But if you change it to .NET 4.0 maybe you can use the parallel extensions and really get a boost by using multiple cores. http://msdn.microsoft.com/en-us/library/dd460693.aspx , but that also means, changing the algorithm
Hope it helps. ;-)
I think that improvements in memory management improve performance in VB.NET
To provide you with a correct answer we should check your code...
But certainly VB.NET in theory should be more performant:
possibility to compile on 64 bit machines (without too much effort)
VB6 was interpreted, VB.NET is almost compiled
You can use threads (depends on your algorithm) and other "tricks", so you can use more CPUs to make calculations in parallel
Best thing to try: port the most CPU consuming part of your application to VB.NET and compare.
The same algorithm will perform faster in VB6, because it is compiled in native language.
If the program has extensive memory allocation, it may perform faster in a .NET when running in a 64 bit environment though.
Related
I have a complex recursive algorithm that in it's php implementation runs about 15 minutes in the CLI to complete. I was thinking about porting it to objective-c and wanted to know who I can make use of the the GPU for the calculations. Is there a way to designate threads to be executed by the GPU?
Thanks
Yes, it's possible to use the GPU for calculations, although depending on the task it may not be advantageous. Without posting code it's anyone's guess what the most efficient means for your implementation might be. I would recommend reading the "Concurrency Programming Guide", for it's an excellent starting point in terms understanding the appropriate ways one might want to handle concurrent threading within Objective-C.
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 need to write software that will do a lot of math. Mostly it will be matrix multiplication with integers to compute DCT. How much faster should I expect the code to run in native c as compared to VB .Net? Factor of 2, factor of 10, factor of 1000...? Has someone tried and collected statistics on this?
.Net code is JIT-compiled to native code before execution, so it should not be slower than native code in general. I'd expect a factor < 10.
Moreover, adaptive optimization techniques profile the code as it runs, gaining more information than a typical static compiler. So, the JIT can make more informed decisions for further optimizations
The .NET code is compiled into native code by the JIT compiler, so you get native code in both cases.
The difference is that the C code has somewhat less overhead around the calculations, so you should perhaps expect a performace difference of factor 2.
VB is 93.7% as fast as C. If you pick the right scenario.
Actually, if your 'native C' includes regular calls to malloc() and free(), any kind of Gargage Collected language like VB.Net is going to literally run circles around it. GC can be 10x faster than mallocs in your inner loops.
If you break down and use C, try to reuse structures that you declared just once instead of making new ones, to avoid this problem. This may be of benefit even in VB if your solution lends itself to it. However it will be harder to program and GC is very fast.
As far as bounds/overflow checks, if speed is important and testing has revealed they don't happen, and you're not risking life or millions from an error or abend, they are a waste of time. But if you can't get rid of them, your time is likely still more valuable in a language with which you can program more quickly.
If you expect serious size and usage, it pays to split the task with a controlling program and store the allocated 'task definitions' into a shared directory with a file per task solver, or a database. Then you can run a solver per processor (2 per HT CPU), or network computers. Be weary of queue structures - it's tough to atomicly 'Mark-Taken-And-Get-Data-If-Not-Taken'. You know how many task solvers you're going to start. I did this with an imaging utility I develop, it was much easier than expected, and it creamed the previous version. Plus if you use multiple processes with a properly dividable problem domain, you avoid the slight-to-significant programming burden of multithreading. Or convincing your coworkers that your culrly braces are in the right place. Peace.
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.
A two parter:
1) Say you're designing a new type of application and you're in the process of coming up with new algorithms to express the concepts and content -- does it make sense to attempt to actively not consider optimisation techniques at that stage, even if in the back of your mind you fear it might end up as O(N!) over millions of elements?
2) If so, say to avoid limiting cool functionality which you might be able to optimise once the proof-of-concept is running -- how do you stop yourself from this programmers habit of a lifetime? I've been trying mental exercises, paper notes, but I grew up essentially counting clock cycles in assembler and I continually find myself vetoing potential solutions for being too wasteful before fully considering the functional value.
Edit: This is about designing something which hasn't been done before (the unknown), when you're not even sure if it can be done in theory, never mind with unlimited computing power at hand. So answers along the line of "of course you have to optimise before you have a prototype because it's an established computing principle," aren't particularly useful.
I say all the following not because I think you don't already know it, but to provide moral support while you suppress your inner critic :-)
The key is to retain sanity.
If you find yourself writing a Theta(N!) algorithm which is expected to scale, then you're crazy. You'll have to throw it away, so you might as well start now finding a better algorithm that you might actually use.
If you find yourself worrying about whether a bit of Pentium code, that executes precisely once per user keypress, will take 10 cycles or 10K cycles, then you're crazy. The CPU is 95% idle. Give it ten thousand measly cycles. Raise an enhancement ticket if you must, but step slowly away from the assembler.
Once thing to decide is whether the project is "write a research prototype and then evolve it into a real product", or "write a research prototype". With obviously an expectation that if the research succeeds, there will be another related project down the line.
In the latter case (which from comments sounds like what you have), you can afford to write something that only works for N<=7 and even then causes brownouts from here to Cincinnati. That's still something you weren't sure you could do. Once you have a feel for the problem, then you'll have a better idea what the performance issues are.
What you're doing, is striking a balance between wasting time now (on considerations that your research proves irrelevant) with wasting time later (because you didn't consider something now that turns out to be important). The more risky your research is, the more you should be happy just to do something, and worry about what you've done later.
My big answer is Test Driven Development. By writing all your tests up front then you force yourself to only write enough code to implement the behavior you are looking for. If timing and clock cycles becomes a requirement then you can write tests to cover that scenario and then refactor your code to meet those requirements.
Like security and usability, performance is something that has to be considered from the beginning of the project. As such, you should definitely be designing with good performance in mind.
The old Knuth line is "We should forget about small efficiencies, say about 97% of the time: premature optimization is the root of all evil." O(N!) to O(poly(N)) is not a "small efficiency"!
The best way to handle type 1 is to start with the simplest thing that could possibly work (O(N!) cannot possibly work unless you're not scaling past a couple dozen elements!) and encapsulate it from the rest of the application so you could rewrite it to a better approach assuming that there is going to be a performance issue.
Optimization isn't exactly a danger; its good to think about speed to some extent when writing code, because it stops you from implementing slow and messy solutions when something simpler and faster would do. It also gives you a check in your mind on whether something is going to be practical or not.
The worst thing that can happen is you design a large program explicitly ignoring optimization, only to go back and find that your entire design is completely useless because it cannot be optimized without completely rewriting it. This never happens if you consider everything when writing it--and part of that "everything" is potential performance issues.
"Premature optimization is the root of all evil" is the root of all evil. I've seen projects crippled by overuse of this concept. At my company we have a software program that broadcasts transport streams from disk on the network. It was originally created for testing purposes (so we would just need a few streams at once), but it was always in the program's spec requirements that it work for larger numbers of streams so it could later be used for video on demand.
Because it was written completely ignoring speed, it was a mess; it had tons of memcpys despite the fact that they should never be necessary, its TS processing code was absurdly slow (it actually parsed every single TS packet multiple times), and so forth. It handled a mere 40 streams at a time instead of the thousands it was supposed to, and when it actually came time to use it for VOD, we had to go back and spend a huge amount of time cleaning it up and rewriting large parts of it.
"First, make it run. Then make it run fast."
or
"To finish first, first you have to finish."
Slow existing app is usually better than ultra-fast non-existing app.
First of all peopleclaim that finishign is only thing that matters (or almost).
But if you finish a product that has O(N!) complexity on its main algorithm, as a rule of thumb you did not finished it! You have an incomplete and unacceptable product for 99% of the cases.
A reasonable performance is part of a working product. A perfect performance might not be. If you finish a text editor that needs 6 GB of memory to write a short note, then you have not finished a product at all, you have only a waste of time at your hands.. You must remember always that is not only delivering code that makes a product complete, is making it achieve capability of supplying the costumer/users needs. If you fail at that it matters nothing that you have finished the code writing in the schedule.
So all optimizations that avoid a resulting useless product are due to be considered and applied as soon as they do not compromise the rest of design and implementation proccess.
"actively not consider optimisation" sounds really weird to me. Usually 80/20 rule works quite good. If you spend 80% of your time to optimize program for less than 20% of use cases, it might be better to not waste time unless those 20% of use-cases really matter.
As for perfectionism, there is nothing wrong with it unless it starts to slow you down and makes you miss time-frames. Art of computer programming is an act of balancing between beauty and functionality of your applications. To help yourself consider learning time-management. When you learn how to split and measure your work, it would be easy to decide whether to optimize it right now, or create working version.
I think it is quite reasonable to forget about O(N!) worst case for an algorithm. First you need to determine that a given process is possible at all. Keep in mind that Moore's law is still in effect, so even bad algorithms will take less time in 10 or 20 years!
First optimize for Design -- e.g. get it to work first :-) Then optimize for performance. This is the kind of tradeoff python programmers do inherently. By programming in a language that is typically slower at run-time, but is higher level (e.g. compared to C/C++) and thus faster to develop, python programmers are able to accomplish quite a bit. Then they focus on optimization.
One caveat, if the time it takes to finish is so long that you can't determine if your algorithm is right, then it is a very good time to worry about optimization earlier up stream. I've encountered this scenario only a few times -- but good to be aware of it.
Following on from onebyone's answer there's a big difference between optimising the code and optimising the algorithm.
Yes, at this stage optimising the code is going to be of questionable benefit. You don't know where the real bottlenecks are, you don't know if there is going to be a speed problem in the first place.
But being mindful of scaling issues even at this stage of the development of your algorithm/data structures etc. is not only reasonable but I suspect essential. After all there's not going to be a lot of point continuing if your back-of-the-envelope analysis says that you won't be able to run your shiny new application once to completion before the heat death of the universe happens. ;-)
I like this question, so I'm giving an answer, even though others have already answered it.
When I was in grad school, in the MIT AI Lab, we faced this situation all the time, where we were trying to write programs to gain understanding into language, vision, learning, reasoning, etc.
My impression was that those who made progress were more interested in writing programs that would do something interesting than do something fast. In fact, time spent worrying about performance was basically subtracted from time spent conceiving interesting behavior.
Now I work on more prosaic stuff, but the same principle applies. If I get something working I can always make it work faster.
I would caution however that the way software engineering is now taught strongly encourages making mountains out of molehills. Rather than just getting it done, folks are taught to create a class hierarchy, with as many layers of abstraction as they can make, with services, interface specifications, plugins, and everything under the sun. They are not taught to use these things as sparingly as possible.
The result is monstrously overcomplicated software that is much harder to optimize because it is much more complicated to change.
I think the only way to avoid this is to get a lot of experience doing performance tuning and in that way come to recognize the design approaches that lead to this overcomplication. (Such as: an over-emphasis on classes and data structure.)
Here is an example of tuning an application that has been written in the way that is generally taught.
I will give a little story about something that happened to me, but not really an answer.
I am developing a project for a client where one part of it is processing very large scans (images) on the server. When i wrote it i was looking for functionality, but i thought of several ways to optimize the code so it was faster and used less memory.
Now an issue has arisen. During Demos to potential clients for this software and beta testing, on the demo unit (self contained laptop) it fails due to too much memory being used. It also fails on the dev server with really large files.
So was it an optimization, or was it a known future bug. Do i fix it or oprtimize it now? well, that is to be determined as their are other priorities as well.
It just makes me wish I did spend the time to reoptimize the code earlier on.
Think about the operational scenarios. ( use cases)
Say that we're making a pizza-shop finder gizmo.
The user turns on the machine. It has to show him the nearest Pizza shop in meaningful time. It Turns out our users want to know fast: in under 15 seconds.
So now, any idea you have, you think: is this going to ever, realistically run in some time less than 15 seconds, less all other time spend doing important stuff..
Or you're a trading system: accurate sums. Less than a millisecond per trade if you can, please. (They'd probably accept 10ms), so , agian: you look at every idea from the relevant scenarios point of view.
Say it's a phone app: has to start in under (how many seconds)
Demonstrations to customers fomr laptops are ALWAYS a scenario. We've got to sell the product.
Maintenance, where some person upgrades the thing are ALWAYS a scenario.
So now, as an example: all the hard, AI heavy, lisp-customized approaches are not suitable.
Or for different strokes, the XML server configuration file is not user friendly enough.
See how that helps.
If I'm concerned about the codes ability to handle data growth, before I get too far along I try to set up sample data sets in large chunk increments to test it with like:
1000 records
10000 records
100000 records
1000000 records
and see where it breaks or becomes un-usable. Then you can decide based on real data if you need to optimize or re-design the core algorithms.