Matrix Solvers#

Cable Equation#

At the heart of the time evolution step in Arbor we find a linear system that must be solved once per time step. This system arises from the cable equation

\[ \begin{align}\begin{aligned}C \partial_t V = \frac{\sigma}{2\pi a}\partial_x(a^2\partial_x V) + I\\I: \mbox{External currents}\\V: \mbox{Membrane potential}\\a: \mbox{cable radius}\\\sigma: \mbox{conductivity}\end{aligned}\end{align} \]

after discretisation into CVs, application of the FVM, and choosing an implicit Euler time step as

\[\left(\frac{\sigma_i C_i}{\Delta\,t} + \sum_{\delta(i, j)} a_{ij}\right)V_i^{k+1} - \sum_{\delta(i, j)} a_ij V_i^{k+1} = \frac{\sigma_i C_i}{\Delta\,t}V_i^k + \sigma_i I_i\]

where \(\delta(i, j)\) indicates whether two CVs are adjacent. It is written in form of a sparse matrix, symmetric by construction.

The currents \(I\) originate from the ion channels on the CVs in question, see the discussion on mechanisms for further details. As \(I\) potentially depends on \(V\), the cable equation is non-linear. We model these dependencies up to first order as \(I = gV + J\) and collect all higher orders into \(J\). This is done to improve accuracy and stability of the solver. Finding \(I\) requires the computation of the symbolic derivative \(g = \partial_V I\) during compilation of the mechanisms. At runtime \(g\) is updated alongside with the currents \(I\) using that symbolic expression.

Each branch in the morphology leads to a tri-diagonal block in the matrix describing the system, since branches do not contain interior branching points. Thus, an interior CV couples to only its neighbours (and itself). However, at branch points, we need to factor in the branch’s parents, which couple blocks via entries outside the tri-diagonal structure. To ensure un-problematic data dependencies for use of a substitution algorithm, ie each row depends only on those of larger indices, we enumerate CVs in breadth-first ordering. This particular form of matrix is called a Hines matrix.



See arbor/backends/multicore/matrix_state.hpp:

  • struct matrix_state * the matrix_state constructor sets up the static parts * the dynamic part is found in assemble * the solver lives in solve.

The matrix solver proceeds in two phases: assembly and the actual solving. Since we are working on cell groups, not individual cells, this is executed for each cell’s matrix.


We store the matrix in compressed form, as its upper and main diagonals. The static parts – foremost the main diagonal – are computed once at construction time and stored. The dynamic parts of the matrix and the right-hand side of the equation are initialised by calling assemble.


The CPU implementation is a straight-forward implemenation of a modified Thomas-algorithm, using an extra input for the parent relationship. If each parent is simply the previous CV, we recover the Thomas algorithm.

void hines(const arb_value_type* diagonal, // main diagonal
           const arb_value_type* upper,    // upper diagonal
                 arb_value_type* rhs,      // rhs / solution
           const arb_index_type* parents,  // CV's parent
           int N) {
  // backward substitution
  for (int i = N-1; i>0; --i) {
    const auto parent  = parents[i];
    const auto factor  = upper[parent] / diagonal[i];
    diagonal[parent]  -= factor * upper[parent];
    rhs[parent]       -= factor * rhs[i];
  // solve root
  b[0] = b[0] / d[0];

  // forward substitution
  for(int i=1; i<N; ++i) {
    const auto parent = parents[i];
    rhs[i] -= upper[i] * rhs[parent];
    rhs[i] /= diagonal[i];



See arbor/backends/gpu/matrix_fine.hpp:

  • struct matrix_state * the matrix_state constructor sets up the static parts * the dynamic part is found in assemble * the solver lives in solve.

There is a simple solver in arbor/backends/gpu/matrix_flat.hpp, which is only used to test/verify the optimised solver described below.

The GPU implementation of the matrix solver is more complex to improve performance and make reasonable use of the hardware’s capabilities. In particular it trades a more complex assembly (and structure) for improved performance.

Looking back at the structure of the Hines matrix, we find that we can solve blocks in parallel, as long as their parents have been processed. Therefore, starting at the root, we parallelise over the children of each branching point and synchronise execution at each such branching point. Each such step is called a level. Execution time is further optimised by packing blocks into threads by size and splitting overly large blocks to minimise divergence.

A detailled description can be found here and the references therein are worthwhile further reading.