Matlab Performance Optimizer Agent Skill

Optimize MATLAB code for better performance through vectorization, memory management, and profiling. Use when user requests optimization, mentions slow code, performance issues, speed improvements, or asks to make code faster or more efficient.

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npx skills add https://github.com/matlab/agent-skills-playground --skill matlab-performance-optimizer

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49 sections, as written by the author

MATLAB Performance Optimizer

Optimize MATLAB code performance with vectorization, memory management, and profiling tools.

When to Use This Skill

Optimizing slow or inefficient MATLAB code
Converting loops to vectorized operations
Reducing memory usage
Improving algorithm performance
When user mentions: slow, performance, optimize, speed up, efficient, memory
Profiling code to find bottlenecks
Parallelizing computations

Core Optimization Principles

1. Vectorization (Most Important)

Replace loops with vectorized operations whenever possible.

SLOW - Using loops:

% Slow approach
n = 1000000;
result = zeros(n, 1);
for i = 1:n
    result(i) = sin(i) * cos(i);
end

FAST - Vectorized:

% Fast approach
n = 1000000;
i = (1:n).';
result = sin(i) .* cos(i);

2. Preallocate Arrays

Always preallocate arrays before loops.

SLOW - Growing arrays:

% Very slow - array grows each iteration
result = [];
for i = 1:10000
    result(end+1) = i^2;
end

FAST - Preallocated:

% Fast - preallocated array
n = 10000;
result = zeros(n, 1);
for i = 1:n
    result(i) = i^2;
end

3. Use Built-in Functions

MATLAB built-in functions are highly optimized.

SLOW - Manual implementation:

% Slow
sum_val = 0;
for i = 1:length(x)
    sum_val = sum_val + x(i);
end

FAST - Built-in function:

% Fast
sum_val = sum(x);

Vectorization Techniques

Element-wise Operations

Use .*, ./, .^ for element-wise operations:

% Instead of this:
for i = 1:length(x)
    y(i) = x(i)^2 + 2*x(i) + 1;
end

% Do this:
y = x.^2 + 2*x + 1;

Logical Indexing

Replace conditional loops with logical indexing:

% Instead of this:
count = 0;
for i = 1:length(data)
    if data(i) > threshold
        count = count + 1;
        filtered(count) = data(i);
    end
end
filtered = filtered(1:count);

% Do this:
filtered = data(data > threshold);

Matrix Operations

Use matrix multiplication instead of nested loops:

% Instead of this:
C = zeros(size(A, 1), size(B, 2));
for i = 1:size(A, 1)
    for j = 1:size(B, 2)
        for k = 1:size(A, 2)
            C(i,j) = C(i,j) + A(i,k) * B(k,j);
        end
    end
end

% Do this:
C = A * B;

Cumulative Operations

Use cumsum, cumprod, cummax, cummin:

% Instead of this:
running_sum = zeros(size(data));
running_sum(1) = data(1);
for i = 2:length(data)
    running_sum(i) = running_sum(i-1) + data(i);
end

% Do this:
running_sum = cumsum(data);

Memory Optimization

Use Appropriate Data Types

% Instead of default double (8 bytes)
data = rand(1000, 1000);  % 8 MB

% Use single precision when appropriate (4 bytes)
data = single(rand(1000, 1000));  % 4 MB

% Use integers when applicable
indices = uint32(1:1000000);  % 4 MB instead of 8 MB

Sparse Matrices

For matrices with mostly zeros:

% Dense matrix (wastes memory)
A = zeros(10000, 10000);
A(1:100, 1:100) = rand(100);  % 800 MB

% Sparse matrix (efficient)
A = sparse(10000, 10000);
A(1:100, 1:100) = rand(100);  % Only stores non-zeros

Clear Unused Variables

% Process large data
largeData = loadData();
processedData = processData(largeData);

% Clear when no longer needed
clear largeData;

% Continue with processed data
results = analyze(processedData);

In-Place Operations

% Instead of creating copies
A = A + 5;  % In-place when possible

% Avoid unnecessary copies
B = A;      % Creates copy if A is modified later
B = A + 0;  % Forces copy

Profiling and Benchmarking

Using the Profiler

% Profile code execution
profile on
myFunction(inputs);
profile viewer
profile off

The profiler shows:

Time spent in each function
Number of calls to each function
Lines that take the most time

Timing Comparisons

% Time single execution
tic;
result = myFunction(data);
elapsedTime = toc;

% Benchmark with timeit (more accurate)
timeit(@() myFunction(data))

% Compare multiple approaches
time1 = timeit(@() approach1(data));
time2 = timeit(@() approach2(data));
fprintf('Approach 1: %.6f s\nApproach 2: %.6f s\n', time1, time2);

Common Optimization Patterns

Pattern 1: Replace find with Logical Indexing

% SLOW
indices = find(x > 5);
y = x(indices);

% FAST
y = x(x > 5);

Pattern 2: Use Implicit Expansion Instead of repmat

% SLOW - repmat to match dimensions
A = rand(1000, 5);
B = rand(1, 5);
C = A - repmat(B, size(A, 1), 1);

% FAST - implicit expansion (R2016b+)
C = A - B;

Pattern 3: Avoid Repeated Calculations

% SLOW - recalculates each iteration
for i = 1:n
    result(i) = data(i) / sqrt(sum(data.^2));
end

% FAST - calculate once
norm_factor = sqrt(sum(data.^2));
for i = 1:n
    result(i) = data(i) / norm_factor;
end

% EVEN FASTER - vectorize
result = data / sqrt(sum(data.^2));

Pattern 4: Efficient String Operations

% SLOW - concatenating in loop
str = '';
for i = 1:1000
    str = [str, sprintf('Line %d\n', i)];
end

% FAST - cell array + join
lines = cell(1000, 1);
for i = 1:1000
    lines{i} = sprintf('Line %d', i);
end
str = strjoin(lines, '\n');

% FASTEST - vectorized sprintf
str = sprintf('Line %d\n', 1:1000);

Pattern 5: Use Table for Mixed Data Types

% Instead of separate arrays
names = cell(1000, 1);
ages = zeros(1000, 1);
scores = zeros(1000, 1);

% Use table
data = table(names, ages, scores);
% Faster access and better organization

Algorithm-Specific Optimizations

Convolution and Filtering

% Use built-in functions
filtered = conv(signal, kernel, 'same');
filtered = filter(b, a, signal);

% For 2D
filtered = conv2(image, kernel, 'same');
filtered = imfilter(image, kernel);

% FFT-based for large kernels (zero-pad for linear convolution)
nfft = length(signal) + length(kernel) - 1;
filtered = ifft(fft(signal, nfft) .* fft(kernel, nfft));

Distance Calculations

% Instead of nested loops for pairwise distances
% SLOW
n = size(points, 1);
distances = zeros(n, n);
for i = 1:n
    for j = 1:n
        distances(i,j) = norm(points(i,:) - points(j,:));
    end
end

% FAST - vectorized
distances = pdist2(points, points);

Sorting and Searching

% Presort for multiple searches
sortedData = sort(data);

% Binary search on sorted data
idx = find(sortedData >= value, 1, 'first');

% Use ismember for set operations
[isPresent, locations] = ismember(searchValues, data);

% Use unique for removing duplicates
uniqueData = unique(data);

Parallel Computing

Simple Parallel Loops (parfor)

% Convert for to parfor for independent iterations
parfor i = 1:n
    results(i) = expensiveFunction(data(i));
end

Requirements for parfor:

Iterations must be independent
Loop variable must be consecutive integers
Variables must be classified as loop, sliced, broadcast, or reduction

Parallel Array Operations

% Create parallel pool
parpool('local', 4);  % 4 workers

% Use parfeval for asynchronous parallel execution
futures = parfeval(@expensiveFunction, 1, data);
result = fetchOutputs(futures);

% GPU arrays for massive parallelization
gpuData = gpuArray(data);
result = arrayfun(@myFunction, gpuData);
result = gather(result);  % Bring back to CPU

Advanced Optimizations

MEX Functions for Critical Sections

Convert performance-critical code to C/C++:

% Create MEX file for bottleneck function
% Write myFunction.c, then compile:
% mex myFunction.c

% Call like regular MATLAB function
result = myFunction(inputs);

Persistent Variables for Cached Results

function result = expensiveComputation(input)
    persistent cachedData cachedInput

    if isequal(input, cachedInput)
        % Return cached result
        result = cachedData;
        return;
    end

    % Compute and cache
    result = computeExpensiveOperation(input);
    cachedData = result;
    cachedInput = input;
end

JIT Acceleration Best Practices

MATLAB's JIT (Just-In-Time) compiler optimizes:

Simple for-loops with scalar operations
Functions without dynamic features

JIT-friendly code:

function result = jitFriendly(n)
    result = 0;
    for i = 1:n
        result = result + i;
    end
end

JIT-unfriendly code (avoid):

function result = jitUnfriendly(n)
    result = 0;
    for i = 1:n
        eval(['x' num2str(i) ' = i;']);  % Dynamic code
    end
end

Performance Checklist

Before finalizing optimized code, verify:

[ ] Loops are vectorized where possible
[ ] Arrays are preallocated before loops
[ ] Built-in functions used instead of manual implementations
[ ] Logical indexing used instead of find + indexing
[ ] Appropriate data types used (single vs double, integers)
[ ] Sparse matrices used for sparse data
[ ] Repeated calculations moved outside loops
[ ] String concatenation uses efficient methods
[ ] Code profiled to identify actual bottlenecks
[ ] Matrix operations used instead of element-wise loops
[ ] Parallel computing considered for independent operations
[ ] Memory-intensive operations optimized
[ ] Caching implemented for repeated expensive calls

Profiling Workflow

Measure First: Profile before optimizing

   profile on
   myScript;
   profile viewer

Identify Bottlenecks: Focus on functions taking most time

Optimize: Apply appropriate techniques

Measure Again: Verify improvement

   % Before
   time_before = timeit(@() myFunction(data));

   % After optimization
   time_after = timeit(@() myFunctionOptimized(data));

   fprintf('Speedup: %.2fx\n', time_before/time_after);

Iterate: Repeat for remaining bottlenecks

Common Performance Pitfalls

Pitfall 1: Premature Optimization

Profile first, optimize second
Focus on actual bottlenecks, not assumptions

Pitfall 2: Over-vectorization

Sometimes loops are clearer and fast enough
Balance readability with performance

Pitfall 3: Ignoring Memory Access Patterns

% SLOW - inner loop over columns (row-major traversal in column-major MATLAB)
for i = 1:rows
    for j = 1:cols
        A(i,j) = process(i, j);
    end
end

% FAST - inner loop over rows (column-major traversal, contiguous memory)
for j = 1:cols
    for i = 1:rows
        A(i,j) = process(i, j);
    end
end

% FASTEST - vectorized
[I, J] = ndgrid(1:rows, 1:cols);
A = process(I, J);

Pitfall 4: Unnecessary Data Type Conversions

% SLOW - repeated conversions
for i = 1:n
    x = double(data(i));
    result(i) = sin(x);
end

% FAST - convert once
x = double(data);
result = sin(x);

Optimization Examples

Example 1: Image Processing

% SLOW
[rows, cols] = size(image);
output = zeros(rows, cols);
for i = 2:rows-1
    for j = 2:cols-1
        output(i,j) = mean(image(i-1:i+1, j-1:j+1), 'all');
    end
end

% FAST
kernel = ones(3,3) / 9;
output = conv2(image, kernel, 'same');

Example 2: Statistical Analysis

% SLOW
n = size(data, 1);
means = zeros(n, 1);
for i = 1:n
    means(i) = mean(data(i, :));
end

% FAST
means = mean(data, 2);

Example 3: Time Series Processing

% SLOW
n = length(signal);
movingAvg = zeros(size(signal));
window = 10;
for i = window:n
    movingAvg(i) = mean(signal(i-window+1:i));
end

% FAST - trailing window: [window-1 past samples, 0 future samples]
movingAvg = movmean(signal, [window-1 0]);

Troubleshooting Performance

Issue: Code still slow after vectorization

Solution: Profile to find new bottlenecks; consider algorithm complexity

Issue: Out of memory errors

Solution: Use smaller data types, process in chunks, use sparse matrices

Issue: parfor slower than for loop

Solution: Check if overhead outweighs benefits; ensure iterations are expensive enough

Issue: GPU computation slower than CPU

Solution: Data transfer overhead may exceed computation time; use for large arrays

Additional Resources

Use profile viewer to analyze performance
Use memory to check memory usage
Use doc with: timeit, tic/toc, parfor, gpuArray, sparse
Check MATLAB Performance and Memory documentation

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