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I would like to optimize a design by having an optimizer make changes to a CAD file, which is then analyzed in FEM, and the results fed back into the optimizer to make changes on the design based on the FEM, until the solution converges to an optimum (mass, stiffness, else).
This is what I envision:
create a blueprint of the part in a CAD software (e.g. CATIA).
run an optimizer code (e.g. fmincon) from within a programming language (e.g. Python). The parameters of the optimizer are parameters of the CAD model (angles, lengths, thicknesses, etc.).
the optimizer evaluates a certain design (parameter set). The programming language calls the CAD software and modifies the design accordingly.
the programming language extracts some information (e.g. mass).
then the programming language extracts a STEP file and passes it a FEA solver (e.g. Abaqus) where a predefined analysis is performed.
the programming language reads the results (e.g. max van Mises stress).
the results from CAD and FEM (e.g. mass and stress) are fed to the optimizer, which changes the design accordingly.
until it converges.
I know this exists from within a closed architecture (e.g. isight), but I want to use an open architecture where the optimizer is called from within an open programming language (ideally Python).
So finally, here are my questions:
Can it be done, as I described it or else?
References, tutorials please?
Which softwares do you recommend, for programming, CAD and FEM?
Yes, it can be done. What you're describing is a small parametric structural sizing multidisciplinary optimization (MDO) environment. Before you even begin coding up the tools or environment, I suggest doing some preliminary work on a few areas
Carefully formulate the minimization problem (minimize f(x), where x is a vector containing ... variables, subject to ... constraints, etc.)
Survey and identify individual tools of interest
How would each tool work? Input variables? Output variables?
Outline in a Design Structure Matrix (a.k.a. N^2 diagram) how the tools will feed information (variables) to each other
What optimizer is best suited to your problem (MDF?)
Identify suitable convergence tolerance(s)
Once the above steps are taken, I would then start to think MDO implementation details. Python, while not the fastest language, would be an ideal environment because there are many tools that were built in Python to solve MDO problems like the one you have and the low development time. I suggest going with the following packages
OpenMDAO (http://openmdao.org/): a modern MDO platform written by NASA Glenn Research Center. The tutorials do a good job of getting you started. Note that each "discipline" in the Sellar problem, the 2nd problem in the tutorial, would include a call to your tool(s) instead of a closed-form equation. As long as you follow OpenMDAO's class framework, it does not care what each discipline is and treats it as a black-box; it doesn't care what goes on in-between an input and an output.
Scipy and numpy: two scientific and numerical optimization packages
I don't know what software you have access to, but here are a few tool-related tips to help you in your tool survey and identification:
Abaqus has a Python API (http://www.maths.cam.ac.uk/computing/software/abaqus_docs/docs/v6.12/pdf_books/SCRIPT_USER.pdf)
If you need to use a program that does not have an API, you can automate the GUI using Python's win32com or Pywinauto (GUI automation) package
For FEM/FEA, I used both MSC PATRAN and MSC NASTRAN on previous projects since they have command-line interfaces (read: easy to interface with via Python)
HyperSizer also has a Python API
Install Pythonxy (https://code.google.com/p/pythonxy/) and use the Spyder Python IDE (included)
CATIA can be automated using win32com (quick Google search on how to do it: http://code.activestate.com/recipes/347243-automate-catia-v5-with-python-and-pywin32/)
Note: to give you some sort of development time-frame, what you're asking will probably take at least two weeks to develop.
I hope this helps.
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I am quite new in VHDL, and by using different IP cores (by different providers) can see that sometimes they differ massively as per the space that they occupy or timing constraints.
I was wondering if there are rules of thumb for optimization in VHDL (like there are in C, for example; unroll your loops, etc.).
Is it related to the synthesis tools I am using (like the different compilers are using other methods of optimization in C, so you need to learn to read the feedback asm files they return), or is it dependent on my coding skills?
Is it related to the synthesis tools I am using (like the different compilers are using other methods of optimization in C, so you need to learn to read the feedback asm files they return), or is it dependent on my coding skills?
The answer is "yes." When you are coding in HDL, you are actually describing hardware (go figure). Instead of the code being converted into machine code (like it would with C) it is synthesized to logical functions (AND, NOT, OR, XOR, etc) and memory elements (RAM, ROM, FF...).
VHDL can be used in many different ways. You can use VHDL in a purely structural sense where at the base level you are calling our primitives of the underlying technology that you are targeting. For example, you literally instantiate every AND, OR, NOT, and Flip Flop in your design. While this can give you a lot of control, it is not an efficient use of time in 99% of cases.
You can also implement hardware using behavioral constructs with VHDL. Instead of explicitly calling out each logic element, you describe a function to be implemented. For example, if this, do this, otherwise, do something else. You can describe state machines, math operations, and memories all in a behavioral sense. There are huge advantages to describing hardware in a behavioral sense:
Easier for humans to understand
Easier for humans to maintain
More portable between synthesis tools and target hardware
When using behavioral constructs, knowing your synthesis tool and your target hardware can help in understanding how what you write will actually be implemented. For example, if you describe a memory element with a asynchronous reset the implementation in hardware will be different for architectures with a dedicated asynchronous reset input to the memory element and one without.
Synthesis tools will generally publish in their reference manual or user guide a list of suggested HDL constructs to use in order to obtain some desired implementation result. For basic cases, they will be what you would expect. For more elaborate behavior models (e.g. a dual port RAM) there may be some form that you need to follow for the tool to "recognize" what you are describing.
In summary, for best use of your target device:
Know the device you are targeting. How are the programmable elements laid out? How many inputs and outputs are there from lookup tables? Read the device user manual to find out.
Know your synthesis engine. What types of behavioral constructs will be recognized and how will they be implemented? Read the synthesis tool user guide or reference manual to find out. Additionally, experiment by synthesizing small constructs to see how it gets implemented (via RTL or technology viewer, if available).
Know VHDL. Understand the differences between signals and variables. Be able to recognize statements that will generate many levels of logic in your design.
I was wondering if there are rules of thumb for optimization in VHDL
Now that you know the hardware, synthesis tool, and VHDL... Assuming you want to design for maximum performance, the following concepts should be adhered to:
Pipeline, pipeline, pipeline. The more levels of logic you have between synchronous elements, the more difficulty you are going to have making your timing constraint/goal.
Pipeline some more. Having additional stages of registers can provide additional wiggle-room in the future if you need to add more processing steps to your algorithm without affecting the overall latency/timeline.
Be careful when operating on the boundaries of the normal fabric. For example, if interfacing with an IO pin, dedicated multiplies, or other special hardware, you will take more significant timing hits. Additional memory elements should be placed here to avoid critical paths forming.
Review your synthesis and implementation reports frequently. You can learn a lot from reviewing these frequently. For example, if you add a new feature, and your timing takes a hit, you just introduced a critical path. Why? How can you alleviate this issue?
Take care with your "global" structures -- such as resets. Logic that must be widely distributed in your design deserves special care, since it needs to reach across your whole device. You may need special pipeline stages, or timing constraints on this type of logic. If at all possible, avoid "global" structures, unless truly a requirement.
While synthesis tools have design goals to focus on area, speed or power, the designer's choices and skills is the major contributor for the quality of the output. A designer should have a goal to maximize speed or minimize area and it will greatly influence his choices. A design optimized for speed can be made smaller by asking the tool to reduce the area, but not nearly as much as the same design thought for area in the first place.
However, it is more complicated than that. IP cores often target several FPGA technologies as well as ASIC. This can only be achieved by using general VHDL constructs, (or re-writing the code for each target, which non-critical IP providers don't do). FPGA and ASIC vendor have primitives that will improve speed/area when used, but if you write code to use a primitive for a technology, it doesn't mean that the resulting code will be optimized if you change the technology. Both Xilinx and Altera have DSP blocks to speed multiplication and whatnot, but they don't work exactly the same and writing code that uses the full potential of both is very challenging.
Synthesis tools are notorious for doing exactly what you ask them to, even if a more optimized solution is simple, for example:
a <= (x + y) + z; -- This is a 2 cascaded 2-input adder
b <= x + y + z; -- This is a 3-input adder
Will likely lead a different path from xyz to b/c. In the end, the designer need to know what he wants, and he has to verify that the synthesis tool understands his intent.
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'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.
I was wondering, is it possible to use Artificial Intelligence to make compilers better?
Things I could imagine if it was possible -
More specific error messages
Improving compiler optimizations, so the compiler could actually understand what you're trying to do, and do it better
If it is possible, are there any research projects on this subject?
You should look at MILEPOST GCC -
MILEPOST GCC is the first practical attept to build machine learning enabled open-source self-tuning production (and research) compiler that can adapt to any architecture using iterative feedback-directed compilation, machine learning and collective optimizatio
An optimizing compiler is actually a very complex expert system and Expert systems is one of the oldest branches of artificial intelligence.
Are you refering to something like Genetic Programming?
http://en.wikipedia.org/wiki/Genetic_programming
This is indeed a field being researched. Look at the milepost branch for GCC, which relies on profile-guided optimization and machine learning. The recent scientific literature for compilers is full of papers using a combination of data mining, machine learning (through genetic algorithms or neural networks), and more "classical", pattern-recognition of certain code patterns.