I am facing the following problem: I have a system of 160000 linear equations with 160000 variables. I am going to write two programs on conjugate gradient method and steepest descent method to solve it. The matrix is block tridiagonal with only 5 non zero diagonals, thus it's not necessary to create and store the matrix. But I am having the following problem: when I go to the iterarion stepe, there must be dot product of vectors involved. I have tried the following commands: dot(u,v), u'*v, which are commonly used. But when I run the program, MATLAB told me the data size is too large for the memory.
To resolve this problem, I tried to decompose the huge vector into sparse vectors with small support, then calculate the dot products of small vectors and finally glue them together. But it seems that this method is more complicated and not very efficient, and it is easy (especially for beginners like me) to make mistakes. I wonder if there're any more efficient ways to deal with this problem. Thanks in advance.
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In my code at each time step sparse matrix A is built as follows:
1< DX <120000
A = sparse(i,j,s,DX,DX,6*DX)
b = (1,DX)
The problem that I am dealing is a sort of discretization problem. I have maximum 120000 nodes. Each of these nodes are having special charachters and I choose only the ones that meet my criteria. the number of these chosen ones is DX and is completely dependent on the physical process.
I am using backslash in x = A\b. But as the size of A could become quite big, the computational time rises drastically (more than 10e5 time steps are having (DX > 6e4).
As far as I know, backslash operation is already well optimized in MATLAB but I would like to know:
Would it make sense to use codegen and convert the code to C?
Does any one know an alternative method instead of backslash, so that the computational time decreases (maybe an iterative method)?
While x = A\b works well for many systems, you can run into memory issues causing slowdowns. Alternately, MATLAB has a number of built in functions for iteratively solving Ax=b for sparse matrices, such as pcq(), bigcg(), cgs(), etc. See the MATLAB Documentation on interative methods for solving systems of linear equations
I have a linear program with order N^4 variables and order N^4 constraints. If I want to solve this in AMPL, I define the constraints one by one without having to bother about the exact coefficient matrices. No memory issues arises. When using the standard LP-solver in Matlab however, I need to define the matrices explicitly.
When I have variables with four subscripts, this will lead to a massively sparse matrix of dimension order N^4 x N^4. This matrix won't even fit in memory for non trivial problem sizes.
Is there a way to get around this problem using Matlab, apart from various column generation/cutting plane techniques? Since AMPL manages to solve it, I suppose they're either automating some kind of decomposition, or they somehow solve the LP without explicitly working with this sparse monster matrix.
Apart from sparse mentioned by m.s. you can also use AMPL API for MATLAB. It is especially useful if you already have an AMPL model and want to work with it from MATLAB.
Converting my comment into an answer:
MATLAB supports sparse matrices using the sparse command which allows you to build your constraint matrix without exceeding memory limits.
In my implementation of an image processing algorithm, I have to solve a large linear system of the form A*x=b, where:
Matrix A=L+D is the sum of a Laplacian matrix L and a diagonal matrix D
Laplacian matrix L is sparse, with about 25 non-zeros per row
The system is large, with as many unknowns as there are pixels in the input image (typically > 1 million).
The Laplacian matrix L does not change between successive runs of the algorithm; I can construct this matrix in preprocessing, and possibly compute its factorization. The diagonal matrix D and right-side vector b change at each run of the algorithm.
I am trying to find out what would be the fastest method to solve the system at runtime; I do not mind spending time on preprocessing (for computing a factorization of L, for example).
My initial idea was to pre-compute a Cholesky factorization of L, then update the factorization at runtime with values from D (rank-1 update with cholupdate), and solve quickly the problem with back-substitution. Unfortunately, the Cholesky factorization is not as sparse as the original L matrix, and just loading it from disk already takes 5.48s; as a comparison, it takes 8.30s to directly solve the system with backslash.
Given the shape of my matrices, is there any other method that you would recommend to speedup the solving at runtime, no matter how long it takes at preprocessing time?
Assuming that you are working on a grid (since you mention images - although this is not guaranteed), that you are more interested in speed than precision (since 5s seems already too slow for 1 million unknowns), I see several options.
First, forget about exact methods such as Cholesky (+reordering). Even if they allow to store the factorization and reuse it for multiple rhs, you'll likely need to store gigantic matrices that appear to be intractable in your case (I hope you're re-ordering rows/columns with reverse Cuthill McKee or anything else though - that sparsifies the factorization a lot).
Depending on your boundary conditions, I would first try a Matlab poisolv that solves a Poisson problem using an FFT, and possible reprojections if you want Dirichlet boundary conditions instead of periodic ones. It's very fast, but might not be appropriate for your problem (you mention having 25 nnz for a Laplacian matrix+identity : why ? is-it a high order Laplace matrix, in which case you may be more interested in precision than what I assume ? or is-it in fact a different problem than the one you describe ?).
Then, you can try multigrid solvers that are very fast for images and smooth problems. You can use a simple relaxation method for each iteration and each level of the multigrid, or use fancier methods (for instance, a preconditioned conjugate gradient par level).
Alternatively, you can do a simpler preconditioned conjugate gradient (or even SSOR) without multigrid, and if you're only interested in an approximate solution, you can stop the iterations before full convergence.
My arguments for iterative solvers are:
you can stop before convergence if you want an approximate problem
you can still re-use other results to initialize your solution (for instance, if your different runs correspond to different frames of a video, then using the solution of the previous frame as an initialization of the next would make some sense).
Of course, a direct solver for which you can precompute, store and keep the factorization also makes sense (although I don't understand your argument for a rank-1 update if your matrix is constant) since only the backsubstitution remains to be done at runtime. But given this ignores the structure of the problem (a regular grid, a possible interest in limited precision results etc.), I'd opt for methods which have been designed for these cases such as Fourier-like methods or multigrids. Both methods can be implemented on the GPU for faster results (recall that GPUs are rather tailored for dealing with images/textures!).
Finally, you can get interesting answers from scicomp.stackexchange which is more targeted to numerical analysis.
I have this problem which requires solving for X in AX=B. A is of the order 15000 x 15000 and is sparse and symmetric. B is 15000 X 7500 and is NOT sparse. What is the fastest way to solve for X?
I can think of 2 ways.
Simplest possible way, X = A\B
Using for loop,
invA = A\speye(size(A))
for i = 1:size(B,2)
X(:,i) = invA*B(:,i);
end
Is there a better way than the above two? If not, which one is best between the two I mentioned?
First things first - never, ever compute inverse of A. That is never sparse except when A is a diagonal matrix. Try it for a simple tridiagonal matrix. That line on its own kills your code - memory-wise and performance-wise. And computing the inverse is numerically less accurate than other methods.
Generally, \ should work for you fine. MATLAB does recognize that your matrix is sparse and executes sparse factorization. If you give a matrix B as the right-hand side, the performance is much better than if you only solve one system of equations with a b vector. So you do that correctly. The only other technical thing you could try here is to explicitly call lu, chol, or ldl, depending on the matrix you have, and perform backward/forward substitution yourself. Maybe you save some time there.
The fact is that the methods to solve linear systems of equations, especially sparse systems, strongly depend on the problem. But in almost any (sparse) case I imagine, factorization of a 15k system should only take a fraction of a second. That is not a large system nowadays. If your code is slow, this probably means that your factor is not that sparse sparse anymore. You need to make sure that your matrix is properly reordered to minimize the fill (added non-zero entries) during sparse factorization. That is the crucial step. Have a look at this page for some tests and explanations on how to reorder your system. And have a brief look at example reorderings at this SO thread.
Since you can answer yourself which of the two is faster, I'll try yo suggest the next options.
Solve it using a GPU. Plenty of details can be found online, including this SO post, a matlab benchmarking of A/b, etc.
Additionally, there's the MATLAB add-on of LAMG (Lean Algebraic Multigrid). LAMG is a fast graph Laplacian solver. It can solve Ax=b in O(m) time and storage.
If your matrix A is symmetric positive definite, then here's what you can do to solve the system efficiently and stably:
First, compute the cholesky decomposition, A=L*L'. Since you have a sparse matrix, and you want to exploit it to accelerate the inversion, you should not apply chol directly, which would destroy the sparsity pattern. Instead, use one of the reordering method described here.
Then, solve the system by X = L'\(L\B)
Finally, if are not dealing with potential complex values, then you can replace all the L' by L.', which gives a bit further acceleration because it's just trying to transpose instead of computing the complex conjugate.
Another alternative would be the preconditioned conjugate gradient method, pcg in Matlab. This one is very popular in practice, because you can trade off speed for accuracy, i.e. give it less number of iterations, and it will give you a (usually pretty good) approximate solution. You also never need to store the matrix A explicitly, but just be able to compute matrix-vector product with A, if your matrix doesn't fit into memory.
If this takes forever to solve in your tests, you are probably going into virtual memory for the solve. A 15k square (full) matrix will require 1.8 gigabytes of RAM to store in memory.
>> 15000^2*8
ans =
1.8e+09
You will need some serious RAM to solve this, as well as the 64 bit version of MATLAB. NO factorization will help you unless you have enough RAM to solve the problem.
If your matrix is truly sparse, then are you using MATLAB's sparse form to store it? If not, then MATLAB does NOT know the matrix is sparse, and does not use a sparse factorization.
How sparse is A? Many people think that a matrix that is half full of zeros is "sparse". That would be a waste of time. On a matrix that size, you need something that is well over 99% zeros to truly gain from a sparse factorization of the matrix. This is because of fill-in. The resulting factorized matrix is almost always nearly full otherwise.
If you CANNOT get more RAM (RAM is cheeeeeeeeep you know, certainly once you consider the time you have wasted trying to solve this) then you will need to try an iterative solver. Since these tools do not factorize your matrix, if it is truly sparse, then they will not go into virtual memory. This is a HUGE savings.
Since iterative tools often require a preconditioner to work as well as possible, it can take some study to find the best preconditioner.
I have this problem which requires solving for X in AX=B. A is of the order 15000 x 15000 and is sparse and symmetric. B is 15000 X 7500 and is NOT sparse. What is the fastest way to solve for X?
I can think of 2 ways.
Simplest possible way, X = A\B
Using for loop,
invA = A\speye(size(A))
for i = 1:size(B,2)
X(:,i) = invA*B(:,i);
end
Is there a better way than the above two? If not, which one is best between the two I mentioned?
First things first - never, ever compute inverse of A. That is never sparse except when A is a diagonal matrix. Try it for a simple tridiagonal matrix. That line on its own kills your code - memory-wise and performance-wise. And computing the inverse is numerically less accurate than other methods.
Generally, \ should work for you fine. MATLAB does recognize that your matrix is sparse and executes sparse factorization. If you give a matrix B as the right-hand side, the performance is much better than if you only solve one system of equations with a b vector. So you do that correctly. The only other technical thing you could try here is to explicitly call lu, chol, or ldl, depending on the matrix you have, and perform backward/forward substitution yourself. Maybe you save some time there.
The fact is that the methods to solve linear systems of equations, especially sparse systems, strongly depend on the problem. But in almost any (sparse) case I imagine, factorization of a 15k system should only take a fraction of a second. That is not a large system nowadays. If your code is slow, this probably means that your factor is not that sparse sparse anymore. You need to make sure that your matrix is properly reordered to minimize the fill (added non-zero entries) during sparse factorization. That is the crucial step. Have a look at this page for some tests and explanations on how to reorder your system. And have a brief look at example reorderings at this SO thread.
Since you can answer yourself which of the two is faster, I'll try yo suggest the next options.
Solve it using a GPU. Plenty of details can be found online, including this SO post, a matlab benchmarking of A/b, etc.
Additionally, there's the MATLAB add-on of LAMG (Lean Algebraic Multigrid). LAMG is a fast graph Laplacian solver. It can solve Ax=b in O(m) time and storage.
If your matrix A is symmetric positive definite, then here's what you can do to solve the system efficiently and stably:
First, compute the cholesky decomposition, A=L*L'. Since you have a sparse matrix, and you want to exploit it to accelerate the inversion, you should not apply chol directly, which would destroy the sparsity pattern. Instead, use one of the reordering method described here.
Then, solve the system by X = L'\(L\B)
Finally, if are not dealing with potential complex values, then you can replace all the L' by L.', which gives a bit further acceleration because it's just trying to transpose instead of computing the complex conjugate.
Another alternative would be the preconditioned conjugate gradient method, pcg in Matlab. This one is very popular in practice, because you can trade off speed for accuracy, i.e. give it less number of iterations, and it will give you a (usually pretty good) approximate solution. You also never need to store the matrix A explicitly, but just be able to compute matrix-vector product with A, if your matrix doesn't fit into memory.
If this takes forever to solve in your tests, you are probably going into virtual memory for the solve. A 15k square (full) matrix will require 1.8 gigabytes of RAM to store in memory.
>> 15000^2*8
ans =
1.8e+09
You will need some serious RAM to solve this, as well as the 64 bit version of MATLAB. NO factorization will help you unless you have enough RAM to solve the problem.
If your matrix is truly sparse, then are you using MATLAB's sparse form to store it? If not, then MATLAB does NOT know the matrix is sparse, and does not use a sparse factorization.
How sparse is A? Many people think that a matrix that is half full of zeros is "sparse". That would be a waste of time. On a matrix that size, you need something that is well over 99% zeros to truly gain from a sparse factorization of the matrix. This is because of fill-in. The resulting factorized matrix is almost always nearly full otherwise.
If you CANNOT get more RAM (RAM is cheeeeeeeeep you know, certainly once you consider the time you have wasted trying to solve this) then you will need to try an iterative solver. Since these tools do not factorize your matrix, if it is truly sparse, then they will not go into virtual memory. This is a HUGE savings.
Since iterative tools often require a preconditioner to work as well as possible, it can take some study to find the best preconditioner.