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Matrix multiplication for tatami

Unit tests Documentation Codecov

Overview

This library contains functions for multiplying a tatami matrix with a vector or matrix. It provides specialized code paths depending on the properties of the tatami::Matrix - namely, sparsity or row-based iteration. Parallelization is achieved via the usual tatami::parallelize() function.

Quick start

Matrix-vector multiplication is pretty straightforward:

#include "tatami_mult/tatami_mult.hpp"

std::shared_ptr<tatami::NumericMatrix> mat(
    new tatami::DenseRowMatrix<double, int>(nrows, ncols, vals)
);

// Create an RHS vector.
std::vector<double> rhs(mat.ncol());

// Store the matrix-vector product in 'output'.
std::vector<double> output(mat.nrow());
tatami_mult::Options opt;
tatami_mult::multiply(*mat, rhs.data(), output.data(), opt);

If multiple vectors are present, we can handle it in a single pass through our matrix:

// Create multiple LHS vectors.
std::vector<std::vector<double> > lhs(10, std::vector<double>(mat.nrow()));
std::vector<const double*> lhs_ptrs(10);
for (size_t l = 0; l < lhs.size(); ++l) {
    lhs_ptrs[l] = lhs[l].data()
}

// Vector-matrix product for each vector.
std::vector<std::vector<double> > output(10, std::vector<double>(mat.ncol()));
std::vector<double*> out_ptrs(10);
for (size_t l = 0; l < output.size(); ++l) {
    out_ptrs[l] = output[l].data()
}

tatami_mult::Options opt;
tatami_mult::multiply(lhs_ptrs, *mat, out_ptrs, opt);

With two tatami::Matrix objects, multiply() will prefer a single pass through the larger matrix, and will save the product as a column-major array. Both of these behaviors can be modified by changing the settings in Options.

std::shared_ptr<tatami::NumericMatrix> mat2(
    new tatami::DenseRowMatrix<double, int>(ncols, 100, vals)
);

std::vector<double> output(nrow, 100);
tatami_mult::multiply(mat, mat2, output.data(), opt);

Check out the reference documentation for more details.

Building projects

CMake with FetchContent

If you're using CMake, you just need to add something like this to your CMakeLists.txt:

include(FetchContent)

FetchContent_Declare(
  tatami_mult
  GIT_REPOSITORY https://github.com/tatami-inc/tatami_mult
  GIT_TAG master # or any version of interest 
)

FetchContent_MakeAvailable(tatami_mult)

Then you can link to tatami_mult to make the headers available during compilation:

# For executables:
target_link_libraries(myexe tatami_mult)

# For libaries
target_link_libraries(mylib INTERFACE tatami_mult)

CMake with find_package()

You can install the library by cloning a suitable version of this repository and running the following commands:

mkdir build && cd build
cmake .. -DTATAMI_MULT_TESTS=OFF
cmake --build . --target install

Then you can use find_package() as usual:

find_package(tatami_tatami_mult CONFIG REQUIRED)
target_link_libraries(mylib INTERFACE tatami::tatami_mult)

By default, this will use FetchContent to fetch all external dependencies. If you want to install them manually, use -DTATAMI_MULT_FETCH_EXTERN=OFF. See extern/CMakeLists.txt to find compatible versions of each dependency.

Manual

If you're not using CMake, the simple approach is to just copy the files the include/ subdirectory - either directly or with Git submodules - and include their path during compilation with, e.g., GCC's -I. You'll need to include the transitive dependencies yourself, check out extern/CMakeLists.txt for a list.