I realize that this might not be the best platform to ask this, but I think this would be best unbiased one to put my question in.
How would you compare OpenMDAO v/s modeFrontier with regards to there optimization capabilities and application scaling and overall software development? Which one would you pick and why?
If you know of any resources or link do provide.
The most fundamental technical difference is OpenMDAO can pass data + derivative information between components. This means that if you want to use gradient based optimization and have access to at least some tools that provide derivative information, OpenMDAO will have far more effective overall capabilities. This is especially important when doing optimization with high-cost analysis tools (e.g. partial differential equation solvers --- CFD, FEA). In those situations making use of derivatives offers between a 100x and 10000x speedup.
One other difference is that OpenMDAO is designed to run natively on a distributed memory compute cluster. Industrial frameworks can submit jobs to remote clusters and query for the results, but OpenMDAO itself can run on the cluster and has a direct and internal MPI based distributed memory capability. This is critical to it being able to efficiently handle derivatives of those expensive PDE solvers. To the best of my knowledge, OpenMDAO is unique in this regard. This is a low level technical detail that most users never need to directly understand, but the consequence is that if you want to do any kind of high fidelity coupled optimziations (aero-structural, aero-propulsive, aero-thermal) with more than one PDE solver in the loop then OpenMDAO's architecture is going to be by far the most effective.
However, OpenMDAO does not offer a GUI. It does not have the same level of data tracking and visualization tools. Also, I know that mode-frontier offers the ability to split a single model up across multiple computers distributed across an organization. Mode Frontier, along with other tools like ModelCenter and Isight, all offer this kind of smooth user experience and code-free interaction that many find valuable.
Honestly, I'm not sure a direct comparison is really warranted. I think if you have an organization that invests in a commercial integration tool like Mode Fronteir, then you can still use OpenMDAO to create tightly coupled integrated optimizations which you can then include as boxes inside your overall integration framework.
You certainly can use OpenMDAO as a complete integration framework, and it has some advantages in that area related to derivatives and execution in distributed memory environments. But you don't have to, and it certainly does not have to be an exclusive decision.
I have been playing around with building some deep learning models in Python and now I have a couple of outcomes I would like to be able to show friends and family.
Unfortunately(?), most of my friends and family aren't really up to the task of installing any of the advanced frameworks that are more or less necessary to have when creating these networks, so I can't just send them my scripts in the present state and hope to have them run.
But then again, I have already created the nets, and just using the finished product is considerably less demanding than making it. We don't need advanced graph compilers or GPU compute powers for the show and tell. We just need the ability to make a few matrix multiplications.
"Just" being a weasel word, regrettably. What I would like to do is convert the the whole model (connectivity,functions and parameters) to a model expressed in e.g. regular Numpy (which, though not part of standard library, is both much easier to install and easier to bundle reliably with a script)
I fail to find any ready solutions to do this. (I find it difficult to pick specific keywords on it for a search engine). But it seems to me that I can't be the first guy who wants to use a ready-made deep learning model on a lower-spec machine operated by people who aren't necessarily inclined to spend months learning how to set the parameters in an artificial neural network.
Are there established ways of transferring a model from e.g. Theano to Numpy?
I'm not necessarily requesting those specific libraries. The main point is I want to go from a GPU-capable framework in the creation phase to one that is trivial to install or bundle in the usage phase, to alleviate or eliminate the threshold the dependencies create for users without extensive technical experience.
An interesting option for you would be to deploy your project to heroku, like explained on this page:
https://github.com/sugyan/tensorflow-mnist
To test the correctness and performance of a mathematical system like Sage, do people use a standard test data set of math problems?
If so I'd appreciate a link or reference to the data set.
NOTE:
I have taken a look at some of the documents related to testing of Sage like Running Sage’s doctests
I cannot answer regarding Mathematica or Macsyma (or Maple or ...), but both Sage and Maxima have unit tests that are indeed run with each micro-release; however, they are usually not a 'standard' set of problems in either case, though both have some subset thereof. Depending on the area, some may be part of a standard set - Sage tries to test as many of Wester's problems in calculus, and Maxima does them in all sorts of areas. Some papers and books have full doctests built into Sage, e.g. the k-Schur function primer. But otherwise it just is a set of representative tests in both cases, e.g. Maxima Lambert W or Sage normal form games.
If any such data sets exist, it would be a very worthwhile contribution to turn them into a testing file for any given system - Sympy comes to mind, for instance, as another worthy target.
I'd like to write algorithms, that prepare results for big data sets. Than, when each dataset changes, incrementally update all affected outputs.
It's called : Incremental computing.
Are there programming tools, libraries, compiler, program analysis etc supporting this approach ?
P.S. I know Incremental computing can be easily achieved by implementing it "by-hand" with proper construction of algorithm. I just wonder if there are tools (like program analysers, compilers, libraries) supporting such approach, to make data-flow dependencies more automatic.
Annie Liu has been pursuing these ideas under the term "finite differencing". See http://ecommons.library.cornell.edu/handle/1813/7208
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.