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Merge branch 'splines-docs4' of github.com:Maison-de-la-Simulation/dd…
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@blegouix
blegouix committed May 17, 2024
2 parents 0a07f15 + d3fdeb0 commit 5a42d35
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6 changes: 3 additions & 3 deletions docker/doxygen/Dockerfile
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Expand Up @@ -19,9 +19,9 @@ RUN chmod +x /bin/bash_run \
apt-utils \
ca-certificates \
wget \
&& echo "deb [ arch=amd64 ] https://raw.githubusercontent.com/pdidev/repo/ubuntu lunar main" > /etc/apt/sources.list.d/pdi.list \
&& wget -q -O /etc/apt/trusted.gpg.d/pdidev-archive-keyring.gpg https://raw.githubusercontent.com/pdidev/repo/ubuntu/pdidev-archive-keyring.gpg \
&& chmod -R a+r /etc/apt/trusted.gpg.d/ \
&& mkdir --parents --mode=0755 /etc/apt/keyrings \
&& echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/pdidev-archive-keyring.gpg] https://raw.githubusercontent.com/pdidev/repo/ubuntu lunar main" > /etc/apt/sources.list.d/pdi.list \
&& wget -q -O /etc/apt/keyrings/pdidev-archive-keyring.gpg https://raw.githubusercontent.com/pdidev/repo/ubuntu/pdidev-archive-keyring.gpg \
&& apt-get update -y \
&& apt-get install -y --no-install-recommends \
build-essential \
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15 changes: 8 additions & 7 deletions docker/latest/Dockerfile
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Expand Up @@ -23,16 +23,17 @@ RUN chmod +x /bin/bash_run \
apt-transport-https \
apt-utils \
ca-certificates \
gpg \
wget \
&& mkdir --parents --mode=0755 /etc/apt/keyrings \
&& if [ "xhip" = "x${BACKEND}" ] \
; then echo 'deb [arch=amd64] https://repo.radeon.com/amdgpu/latest/ubuntu jammy main' > /etc/apt/sources.list.d/amdgpu.list \
&& echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/5.7.3 jammy main' > /etc/apt/sources.list.d/rocm.list \
&& wget -q -O /etc/apt/trusted.gpg.d/rocm.asc https://repo.radeon.com/rocm/rocm.gpg.key \
&& echo -e 'Package: *\nPin: release o=repo.radeon.com\nPin-Priority: 600' > /etc/apt/preferences.d/rocm-pin-600 \
; then echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/rocm.gpg] https://repo.radeon.com/amdgpu/5.7.3/ubuntu jammy main" > /etc/apt/sources.list.d/amdgpu.list \
&& echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/rocm.gpg] https://repo.radeon.com/rocm/apt/5.7.3 jammy main" > /etc/apt/sources.list.d/rocm.list \
&& wget -q -O - https://repo.radeon.com/rocm/rocm.gpg.key | gpg --dearmor --output /etc/apt/keyrings/rocm.gpg \
&& echo -e "Package: *\nPin: release o=repo.radeon.com\nPin-Priority: 600" > /etc/apt/preferences.d/rocm-pin-600 \
; fi \
&& echo "deb [arch=amd64] https://raw.githubusercontent.com/pdidev/repo/ubuntu jammy main" > /etc/apt/sources.list.d/pdi.list \
&& wget -q -O /etc/apt/trusted.gpg.d/pdidev-archive-keyring.gpg https://raw.githubusercontent.com/pdidev/repo/ubuntu/pdidev-archive-keyring.gpg \
&& chmod -R a+r /etc/apt/trusted.gpg.d/ \
&& echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/pdidev-archive-keyring.gpg] https://raw.githubusercontent.com/pdidev/repo/ubuntu jammy main" > /etc/apt/sources.list.d/pdi.list \
&& wget -q -O /etc/apt/keyrings/pdidev-archive-keyring.gpg https://raw.githubusercontent.com/pdidev/repo/ubuntu/pdidev-archive-keyring.gpg \
&& apt-get update -y \
&& apt-get install -y --no-install-recommends \
build-essential \
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15 changes: 8 additions & 7 deletions docker/oldest/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -23,16 +23,17 @@ RUN chmod +x /bin/bash_run \
apt-transport-https \
apt-utils \
ca-certificates \
gpg \
wget \
&& mkdir --parents --mode=0755 /etc/apt/keyrings \
&& if [ "xhip" = "x${BACKEND}" ] \
; then echo 'deb [arch=amd64] https://repo.radeon.com/amdgpu/latest/ubuntu focal main' > /etc/apt/sources.list.d/amdgpu.list \
&& echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/5.7.3 focal main' > /etc/apt/sources.list.d/rocm.list \
&& wget -q -O /etc/apt/trusted.gpg.d/rocm.asc https://repo.radeon.com/rocm/rocm.gpg.key \
&& echo -e 'Package: *\nPin: release o=repo.radeon.com\nPin-Priority: 600' > /etc/apt/preferences.d/rocm-pin-600 \
; then echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/rocm.gpg] https://repo.radeon.com/amdgpu/5.7.3/ubuntu focal main" > /etc/apt/sources.list.d/amdgpu.list \
&& echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/rocm.gpg] https://repo.radeon.com/rocm/apt/5.7.3 focal main" > /etc/apt/sources.list.d/rocm.list \
&& wget -q -O - https://repo.radeon.com/rocm/rocm.gpg.key | gpg --dearmor --output /etc/apt/keyrings/rocm.gpg \
&& echo -e "Package: *\nPin: release o=repo.radeon.com\nPin-Priority: 600" > /etc/apt/preferences.d/rocm-pin-600 \
; fi \
&& echo "deb [arch=amd64] https://raw.githubusercontent.com/pdidev/repo/ubuntu focal main" > /etc/apt/sources.list.d/pdi.list \
&& wget -q -O /etc/apt/trusted.gpg.d/pdidev-archive-keyring.gpg https://raw.githubusercontent.com/pdidev/repo/ubuntu/pdidev-archive-keyring.gpg \
&& chmod -R a+r /etc/apt/trusted.gpg.d/ \
&& echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/pdidev-archive-keyring.gpg] https://raw.githubusercontent.com/pdidev/repo/ubuntu focal main" > /etc/apt/sources.list.d/pdi.list \
&& wget -q -O /etc/apt/keyrings/pdidev-archive-keyring.gpg https://raw.githubusercontent.com/pdidev/repo/ubuntu/pdidev-archive-keyring.gpg \
&& apt-get update -y \
&& apt-get install -y --no-install-recommends \
build-essential \
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91 changes: 91 additions & 0 deletions include/ddc/kernels/splines/matrix.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -14,19 +14,46 @@

namespace ddc::detail {

/**
* @brief The parent class for matrices.
*
* It represents a square Matrix. Implementations may have different storage formats, filling methods and multiple right-hand sides linear solvers.
*/
class Matrix
{
int m_n;

public:
explicit Matrix(const int mat_size) : m_n(mat_size) {}

/// @brief Destruct
virtual ~Matrix() = default;

/**
* @brief Get an element of the matrix at indexes i, j. It must not be called after `factorize`.
*
* @param i The row index of the desired element.
* @param j The column index of the desired element.
*
* @return The value of the element of the matrix.
*/
virtual double get_element(int i, int j) const = 0;

/**
* @brief Set an element of the matrix at indexes i, j. It must not be called after `factorize`.
*
* @param i The row index of the setted element.
* @param j The column index of the setted element.
* @param aij The value to set in the element of the matrix.
*/
virtual void set_element(int i, int j, double aij) = 0;

/**
* @brief Performs a pre-process operation on the Matrix.
*
* Note: this function should be renamed in the future because the pre-
* process operation is not necessarily a factorization.
*/
virtual void factorize()
{
int const info = factorize_method();
Expand All @@ -45,6 +72,11 @@ class Matrix
}
}

/**
* @brief Solve the linear problem Ax=b inplace.
*
* @param[in, out] b A 1D mdpsan storing a right-hand side of the problem and receiving the corresponding solution.
*/
virtual ddc::DSpan1D solve_inplace(ddc::DSpan1D const b) const
{
assert(int(b.extent(0)) == m_n);
Expand All @@ -57,6 +89,13 @@ class Matrix
return b;
}

/**
* @brief Solve the transposed linear problem A^tx=b inplace.
*
* @param[in, out] b A 1D mdpsan storing a right-hand side of the problem and receiving the corresponding solution.
*
* @return b
*/
virtual ddc::DSpan1D solve_transpose_inplace(ddc::DSpan1D const b) const
{
assert(int(b.extent(0)) == m_n);
Expand All @@ -69,6 +108,15 @@ class Matrix
return b;
}

/**
* @brief Solve the multiple right-hand sides linear problem Ax=b inplace.
*
* @param[in, out] bx A 2D mdpsan storing the multiple right-hand sides of the problem and receiving the corresponding solution.
* Important note: the convention is the reverse of the common matrix one, row number is second index and column number
* the first one. This means when solving `A x_i = b_i`, element `(b_i)_j` is stored in `b(j, i)`.
*
* @return bx
*/
virtual ddc::DSpan2D solve_multiple_inplace(ddc::DSpan2D const bx) const
{
assert(int(bx.extent(1)) == m_n);
Expand All @@ -81,6 +129,15 @@ class Matrix
return bx;
}

/**
* @brief Solve the transposed multiple right-hand sides linear problem A^tx=b inplace.
*
* @param[in, out] bx A 2D mdspan storing the multiple right-hand sides of the problem and receiving the corresponding solution.
* Important note: the convention is the reverse of the common matrix one, row number is second index and column number
* the first one. It should be changed in the future.
*
* @return bx
*/
virtual ddc::DSpan2D solve_multiple_transpose_inplace(ddc::DSpan2D const bx) const
{
assert(int(bx.extent(1)) == m_n);
Expand All @@ -93,6 +150,15 @@ class Matrix
return bx;
}

/**
* @brief Solve the multiple-right-hand sides linear problem Ax=b inplace.
*
* @param[in, out] bx A 2D Kokkos::View storing the multiple right-hand sides of the problem and receiving the corresponding solution.
* Important note: the convention is the reverse of the common matrix one, row number is second index and column number
* the first one. It should be changed in the future.
*
* @return bx
*/
template <class... Args>
Kokkos::View<double**, Args...> solve_batch_inplace(
Kokkos::View<double**, Args...> const bx) const
Expand All @@ -107,11 +173,23 @@ class Matrix
return bx;
}

/**
* @brief Get the size of the square matrix in one of its dimensions.
*
* @return The size of the matrix in one of its dimensions.
*/
int get_size() const
{
return m_n;
}

/**
* @brief Prints a Matrix in a std::ostream. It must not be called after `factorize`.
*
* @param out The stream in which the matrix is printed.
*
* @return The stream in which the matrix is printed.
**/
std::ostream& operator<<(std::ostream& os)
{
int const n = get_size();
Expand All @@ -125,8 +203,21 @@ class Matrix
}

protected:
/**
* @brief A function called by factorize() to actually perform the pre-process operation.
*
* @return The error code of the function.
*/
virtual int factorize_method() = 0;

/**
* @brief A function called by solve_inplace() and similar functions to actually perform the linear solve operation.
*
* @param b A double* to a contiguous array containing the (eventually multiple) right-hand-sides. The memory layout is right.
* @param transpose A character identifying if the normal ('N') or transposed ('T') linear system is solved.
* @param n_equations The number of multiple-right-hand-sides (number of columns of b).
* @return The error code of the function.
*/
virtual int solve_inplace_method(double* b, char transpose, int n_equations) const = 0;
};

Expand Down
19 changes: 19 additions & 0 deletions include/ddc/kernels/splines/matrix_maker.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,28 @@

namespace ddc::detail {

/**
* @brief A static factory for Matrix classes.
*/
class MatrixMaker
{
public:
/**
* @brief Construct a sparse matrix
*
* @tparam the Kokkos::ExecutionSpace on which matrix-related operation will be performed.
* @param n The size of one of the dimensions of the square matrix.
* @param cols_per_chunk A parameter used by the slicer (internal to the solver) to define the size
* of a chunk of right-hand sides of the linear problem to be computed in parallel (chunks are treated
* by the linear solver one-after-the-other).
* This value is optional. If no value is provided then the default value is chosen by the requested solver.
*
* @param preconditionner_max_block_size A parameter used by the slicer (internal to the solver) to
* define the size of a block used by the Block-Jacobi preconditioner.
* This value is optional. If no value is provided then the default value is chosen by the requested solver.
*
* @return The Matrix instance.
*/
template <typename ExecSpace>
static std::unique_ptr<Matrix> make_new_sparse(
int const n,
Expand Down
60 changes: 58 additions & 2 deletions include/ddc/kernels/splines/matrix_sparse.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,8 @@
namespace ddc::detail {

/**
* @brief Convert KokkosView to Ginkgo Dense matrix.
*
* @param gko_exec[in] A Ginkgo executor that has access to the Kokkos::View memory space
* @param view[in] A 2-D Kokkos::View with unit stride in the second dimension
* @return A Ginkgo Dense matrix view over the Kokkos::View data
Expand All @@ -41,6 +43,15 @@ auto to_gko_dense(std::shared_ptr<const gko::Executor> const& gko_exec, KokkosVi
view.stride_0());
}

/**
* @brief Return the default value of the parameter cols_per_chunk for a given Kokkos::ExecutionSpace.
*
* The values are hardware-specific (but they can be overriden in the constructor of MatrixSparse).
* They have been tuned on the basis of ddc/benchmarks/splines.cpp results on 4xIntel 6230 + Nvidia V100.
*
* @tparam ExecSpace The Kokkos::ExecutionSpace type.
* @return The default value for the parameter cols_per_chunk.
*/
template <class ExecSpace>
int default_cols_per_chunk() noexcept
{
Expand All @@ -67,6 +78,15 @@ int default_cols_per_chunk() noexcept
return 1;
}

/**
* @brief Return the default value of the parameter preconditionner_max_block_size for a given Kokkos::ExecutionSpace.
*
* The values are hardware-specific (but they can be overriden in the constructor of MatrixSparse).
* They have been tuned on the basis of ddc/benchmarks/splines.cpp results on 4xIntel 6230 + Nvidia V100.
*
* @tparam ExecSpace The Kokkos::ExecutionSpace type.
* @return The default value for the parameter preconditionner_max_block_size.
*/
template <class ExecSpace>
unsigned int default_preconditionner_max_block_size() noexcept
{
Expand All @@ -93,7 +113,13 @@ unsigned int default_preconditionner_max_block_size() noexcept
return 1u;
}

// Matrix class for sparse storage and iterative solve
/**
* @brief A sparse Matrix.
*
* The storage format is CSR. Ginkgo is used to perform every matrix and linear solver-related operations.
*
* @tparam ExecSpace The Kokkos::ExecutionSpace on which operations related to the matrix are performed.
*/
template <class ExecSpace>
class Matrix_Sparse : public Matrix
{
Expand Down Expand Up @@ -121,7 +147,15 @@ class Matrix_Sparse : public Matrix
unsigned int m_preconditionner_max_block_size; // Maximum size of Jacobi-block preconditionner

public:
// Constructor
/**
* @brief Matrix_Sparse constructor.
*
* @param mat_size The size of one of the dimensions of the square matrix.
* @param cols_per_chunk An optional parameter used to define the number of right-hand sides to pass to
* Ginkgo solver calls. see default_cols_per_chunk.
* @param preconditionner_max_block_size An optional parameter used to define the maximum size of a block
* used by the block-Jacobi preconditionner. see default_preconditionner_max_block_size.
*/
explicit Matrix_Sparse(
const int mat_size,
std::optional<int> cols_per_chunk = std::nullopt,
Expand Down Expand Up @@ -149,6 +183,15 @@ class Matrix_Sparse : public Matrix
m_matrix_dense->at(i, j) = aij;
}

/**
* @brief A function called by factorize() to perform the pre-process operation.
*
* Removes the zeros from the CSR object and instantiate a Ginkgo solver. It also constructs a transposed version of the solver.
*
* The stopping criterion is a reduction factor ||x||/||b||<1e-15 with 1000 maximum iterations.
*
* @return The error code of the function.
*/
int factorize_method() override
{
// Remove zeros
Expand Down Expand Up @@ -185,6 +228,19 @@ class Matrix_Sparse : public Matrix
return 0;
}

/**
* @brief A function called by solve_inplace() and similar functions to actually perform the linear solve operation.
*
* The solver method is currently Bicgstab on CPU Serial and GPU and Gmres on OMP (because of Ginkgo issue #1563).
*
* Multiple right-hand sides are sliced in chunks of size cols_per_chunk which are passed one-after-the-other to Ginkgo.
*
* @param b A double* to a contiguous array containing the (eventually multiple) right-hand sides.
* @param transpose A character identifying if the normal ('N') or transposed ('T') linear system is solved.
* @param n_equations The number of multiple right-hand sides (number of columns in b).
*
* @return The error code of the function.
*/
virtual int solve_inplace_method(double* b, char transpose, int n_equations) const override
{
std::shared_ptr const gko_exec = m_solver->get_executor();
Expand Down

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