[feature] add data layout support

Add new building block describing how data
is organized in memory.

.gitlab-ci.yml

@@ -28,7 +28,7 @@ make:generic:
     - /^wip.*/
     - /^WIP.*/
   variables:
-    CFLAGS: "-std=c99 -pedantic -Wall -Wextra -Werror -Wno-unused-but-set-parameter"
+    CFLAGS: "-std=c99 -pedantic -Wall -Wextra -Werror -Wno-pointer-arith -Wno-unused-but-set-parameter"
   script:
     - ./autogen.sh
     - mkdir build
@@ -48,7 +48,7 @@ make:out-of-tree:
     - /^wip.*/
     - /^WIP.*/
   variables:
-    CFLAGS: "-std=c99 -pedantic -Wall -Wextra -Werror -Wno-unused-but-set-parameter"
+    CFLAGS: "-std=c99 -pedantic -Wall -Wextra -Werror -Wno-pointer-arith -Wno-unused-but-set-parameter"
   script:
     - ./autogen.sh
     - mkdir out

AUTHORS

@@ -4,3 +4,4 @@ Brian Suchy <briansuchy2022@u.northwestern.edu>
 Valentin Reis <fre@freux.fr>
 Nicolas Denoyelle <ndenoyelle@anl.gov>
 Clement Foyer <cfoyer@cray.com>
+Brice Videau <bvideau@anl.gov>

doc/aml.doxy

@@ -792,6 +792,7 @@ WARN_LOGFILE           =
 
 INPUT                  = ../include \
                          ../include/aml/area \
+                         ../include/aml/layout \			 
 			 ../include/aml/tiling \
 			 ../include/aml/dma \
 			 ../include/aml/scratch \

doc/index.rst

@@ -34,7 +34,8 @@ As of now, AML implements the following abstractions:
    :align: right
 
 * :doc:`Areas <pages/areas>`, a set of addressable physical memories,
-* :doc:`Tilings <pages/tilings>`, a description of tiling data structures,
+* :doc:`Layout <pages/layout>`, a description of data structures organization,
+* :doc:`Tilings <pages/tilings>`, (soon to be replaced),
 * :doc:`DMAs <pages/dmas>`, an engine to asynchronously move data structures between areas,
 * :doc:`Scratchpads <pages/scratchs>`, a stage-in, stage-out abstraction for prefetching.
 
@@ -132,5 +133,6 @@ for more info.
 
    pages/areas
    pages/tilings
+   pages/layout
    pages/dmas
    pages/scratchs

doc/pages/layout.rst

+Layout: Description of Data Organization
+========================================
+
+.. doxygengroup:: aml_layout
+
+Implementations
+---------------
+
+   .. toctree::
+
+      layout_dense
+      layout_native
+      

doc/pages/layout_dense.rst

+AML Dense Layouts
+=================
+
+.. doxygengroup:: aml_layout_dense

doc/pages/layout_native.rst

+AML Layouts Native Ops
+======================
+
+.. doxygengroup:: aml_layout_native

include/Makefile.am

@@ -4,6 +4,12 @@ include_aml_areadir=$(includedir)/aml/area
 include_aml_area_HEADERS = \
 			      aml/area/linux.h
 
+include_aml_layoutdir=$(includedir)/aml/layout
+include_aml_layout_HEADERS = \
+			      aml/layout/native.h \
+			      aml/layout/dense.h \
+			      aml/layout/reshape.h
+
 include_aml_dmadir=$(includedir)/aml/dma
 include_aml_dma_HEADERS = \
 			      aml/dma/linux-seq.h \

include/aml.h

@@ -6,7 +6,7 @@
  * For more info, see https://xgitlab.cels.anl.gov/argo/aml
  *
  * SPDX-License-Identifier: BSD-3-Clause
-*******************************************************************************/
+ ******************************************************************************/
 
 /**
  * \file aml.h
@@ -393,7 +393,7 @@ int aml_tiling_create_iterator(struct aml_tiling *tiling,
  * @return 0 if successful; an error code otherwise.
  **/
 void aml_tiling_destroy_iterator(struct aml_tiling *tiling,
-				struct aml_tiling_iterator **iterator);
+				 struct aml_tiling_iterator **iterator);
 
 
 /**
@@ -474,17 +474,17 @@ struct aml_dma_request;
 struct aml_dma_data;
 
 /**
- aml_dma_ops is a structure containing operations for a specific
- * aml_dma implementation.
- * These operation are operation are detailed in the structure.
- * They are specific in:
- * - the type of aml_area source and destination,
- * - the progress engine performing the operation,
- * - the type of of source and destination data structures.
- *
- * Each different combination of these three points may require a different
- * set of dma operations.
- **/
+   aml_dma_ops is a structure containing operations for a specific
+   * aml_dma implementation.
+   * These operation are operation are detailed in the structure.
+   * They are specific in:
+   * - the type of aml_area source and destination,
+   * - the progress engine performing the operation,
+   * - the type of of source and destination data structures.
+   *
+   * Each different combination of these three points may require a different
+   * set of dma operations.
+   **/
 struct aml_dma_ops {
 	/**
 	 * Initiate a data movement, from a source pointer to a destination
@@ -585,6 +585,365 @@ int aml_dma_cancel(struct aml_dma *dma, struct aml_dma_request *req);
 
 ////////////////////////////////////////////////////////////////////////////////
 
+/**
+ * @}
+ * @defgroup aml_layout "AML Layout"
+ * @brief Low level description of data orrganization at the byte granularity.
+ *
+ * Layout describes how contiguous element of a flat memory address space are
+ * organized into a multidimensional array of elements of a fixed size.
+ * The abstraction provide functions to build layouts, access elements,
+ * reshape a layout, or subset a layout.
+ *
+ * Layouts are characterized by:
+ * * A pointer to the data it describes
+ * * A set of dimensions on which data spans.
+ * * A stride in between elements of a dimension.
+ * * A pitch indicating the space between contiguous elements of a dimension.
+ *
+ * The figure below describes a 2D layout with a sub-layout
+ * (obtained with aml_layout_slice()) operation. The sub-layout has a stride
+ * of 1 element along the second dimension. The slice has an offset of 1 element
+ * along the same dimension, and its pitch is the pitch of the original
+ * layout. Calling aml_layout_deref() on this sublayout with appropriate
+ * coordinates will return a pointer to elements noted (coor_x, coord_y).
+ * @see aml_layout_slice()
+ *
+ * @image html layout.png "2D layout with a 2D slice." width=400cm
+ *
+ * Access to specific elements of a layout can be done with
+ * the aml_layout_deref() function. Access to an element is always done
+ * relatively to the dimensions order set by at creation time.
+ * However, internally, the library will store dimensions from the last
+ * dimension to the first dimension such that elements along the first dimension
+ * are contiguous in memory. This order is defined called with the value
+ * AML_LAYOUT_ORDER_FORTRAN. Therefore, AML provides access to elements
+ * without the overhead of user order choice through function suffixed
+ * with "native".
+ * @see aml_layout_deref()
+ * @see aml_layout_deref_native()
+ * @see aml_layout_dims_native()
+ * @see aml_layout_slice_native()
+ *
+ * The layout abstraction also provides a function to reshape data
+ * with a different set of dimensions. A reshaped layout will access
+ * the same data but with different coordinates as pictured in the
+ * figure below.
+ * @see aml_layout_reshape()
+ *
+ * @image html reshape.png "2D layout turned into a 3D layout." width=700cm
+ *
+ * @see aml_layout_dense
+ * @see aml_layout_pad
+ * @{
+ **/
+
+////////////////////////////////////////////////////////////////////////////////
+
+struct aml_layout_ops;
+struct aml_layout_data;
+
+/** Structure definition of AML layouts **/
+struct aml_layout {
+	/** Layout functions implementation **/
+	struct aml_layout_ops *ops;
+	/** Implementation specific data of a layout**/
+	struct aml_layout_data *data;
+};
+
+/** List of operators implemented by layouts. **/
+struct aml_layout_ops {
+	/**
+	 * Layout must provide a way to access a specific element
+	 * according to the provided dimensions.
+	 * Coordinates bounds checking is done in the generic API.
+	 * Coordinates provided by the user will match the order
+	 * Of the dimensions provided by the user in the constructor.
+	 * However, dimensions are always stored internally in the
+	 * AML_LAYOUT_ORDER_FORTRAN order.
+	 * @param data[in]: The non-NULL handle to layout internal data.
+	 * @param coords[in]: The non-NULL coordinates on which to access data.
+	 * Coordinates are checked to be valid in aml_layout_deref().
+	 * @return A pointer to the dereferenced element on success.
+	 * @return NULL on failure with aml_errno set to the error reason.
+	 **/
+	void *(*deref)(const struct aml_layout_data *data,
+		       const size_t *coords);
+
+	/**
+	 * Function for derefencing elements of a layout inside the library.
+	 * Layout assumes data is always stored in AML_LAYOUT_ORDER_FORTRAN
+	 * order. Coordinates provided by the library will match the same
+	 * order, i.e last dimension first.
+	 * @param data[in]: The non-NULL handle to layout internal data.
+	 * @param coords[in]: The non-NULL coordinates on which to access data.
+	 * The first coordinate should be the last dimensions and so on to the
+	 * last, coordinate, last dimension.
+	 * @return A pointer to the dereferenced element on success.
+	 * @return NULL on failure with aml_errno set to the error reason.
+	 **/
+	void *(*deref_native)(const struct aml_layout_data *data,
+			      const size_t *coords);
+
+	/**
+	 * Get the order in which dimensions of the layout are
+	 * supposed to be accessed by the user.
+	 * @param data[in]: The non-NULL handle to layout internal data.
+	 * @return Order value. It is a bitmask with order bit set (or not set).
+	 * Output value can be further checked against order AML_LAYOUT_ORDER
+	 * flags by using the macro AML_LAYOUT_ORDER() on output value.
+	 * @see AML_LAYOUT_ORDER()
+	 **/
+	int (*order)(const struct aml_layout_data *data);
+
+	/**
+	 * Return the layout dimensions in the user order.
+	 * @param data[in]: The non-NULL handle to layout internal data.
+	 * @param dims[out]: The non-NULL array of dimensions to fill. It is
+	 * supposed to be large enough to contain ndims() elements.
+	 * @return AML_SUCCESS on success, else an AML error code.
+	 **/
+	int (*dims)(const struct aml_layout_data *data, size_t *dims);
+
+	/**
+	 * Return the layout dimensions in the order they are actually stored
+	 * in the library.
+	 * @param data[in]: The non-NULL handle to layout internal data.
+	 * @param dims[out]: The non-NULL array of dimensions to fill. It is
+	 * supposed to be large enough to contain ndims() elements.
+	 * @return AML_SUCCESS on success, else an AML error code.
+	 **/
+	int (*dims_native)(const struct aml_layout_data *data,
+			   size_t *dims);
+
+	/**
+	 * Return the number of dimensions in a layout.
+	 * @param data[in]: The non-NULL handle to layout internal data.
+	 * @return The number of dimensions in the layout.
+	 **/
+	size_t (*ndims)(const struct aml_layout_data *data);
+
+	/**
+	 * Return the size of layout elements.
+	 * @param data[in]: The non-NULL handle to layout internal data.
+	 * @return The size of elements stored with this layout.
+	 **/
+	size_t (*element_size)(const struct aml_layout_data *data);
+
+	/**
+	 * Reshape the layout with different dimensions.
+	 * Layout dimensions are checked in aml_layout_reshape() to store
+	 * the exact same number of elements.
+	 * @param data[in]: The non-NULL handle to layout internal data.
+	 * @param output[out]: A non NULL pointer to a layout where to allocate
+	 * a new layout resulting from the reshape operation.
+	 * @param ndims[in]: The number of dimensions of the new layout.
+	 * @param dims[in]: The number of elements along each dimension of
+	 * the new layout.
+	 * @return AML_SUCCESS on success, else an AML error code (<0).
+	 **/
+	int (*reshape)(const struct aml_layout_data *data,
+		       struct aml_layout **output,
+		       const size_t ndims,
+		       const size_t *dims);
+
+	/**
+	 * Return a layout that is a subset of another layout.
+	 * Slice arguments compatibility with the original layout are
+	 * checked in aml_layout_slice().
+	 * @param data[in]: The non-NULL handle to layout internal data.
+	 * @param output[out]: A non NULL pointer to a layout where to allocate
+	 * a new layout resulting from the slice operation.
+	 * @param dims[in]: The number of elements of the slice along each
+	 * dimension .
+	 * @param offsets[in]: The index of the first element of the slice
+	 * in each dimension.
+	 * @param strides[in]: The displacement (in number of elements) between
+	 * elements of the slice.
+	 * @return A newly allocated layout with the queried subset of the
+	 * original layout on succes.
+	 * @return NULL on error with aml_errno set to the failure reason.
+	 **/
+	int (*slice)(const struct aml_layout_data *data,
+		     struct aml_layout **output,
+		     const size_t *dims,
+		     const size_t *offsets,
+		     const size_t *strides);
+
+	/**
+	 * Return a layout that is a subset of another layout, assuming
+	 * dimensions are stored with AML_LAYOUT_ORDER_FORTRAN.
+	 * Slice arguments compatibility with the original layout are
+	 * checked in aml_layout_slice().
+	 * @param data[in]: The non-NULL handle to layout internal data.
+	 * @param output[out]: A non NULL pointer to a layout where to allocate
+	 * a new layout resulting from the slice operation.
+	 * @param dims[in]: The number of elements of the slice along each
+	 * dimension .
+	 * @param offsets[in]: The index of the first element of the slice
+	 * in each dimension.
+	 * @param strides[in]: The displacement (in number of elements) between
+	 * elements of the slice.
+	 * @return A newly allocated layout with the queried subset of the
+	 * original layout on succes.
+	 * @return NULL on error with aml_errno set to the failure reason.
+	 **/
+	int (*slice_native)(const struct aml_layout_data *data,
+			    struct aml_layout **output,
+			    const size_t *dims,
+			    const size_t *offsets,
+			    const size_t *strides);
+};
+
+/**
+ * Tag specifying user storage of dimensions inside a layout.
+ * Layout order is the first bit in an integer bitmask.
+ * @see AML_LAYOUT_ORDER()
+ * This tag will store dimensions in the order provided by the user,
+ * i.e elements of the last dimension will be contiguous in memory.
+ **/
+#define AML_LAYOUT_ORDER_C (0<<0)
+
+/**
+ * Tag specifying user storage of dimensions inside a layout.
+ * Layout order is the first bit in an integer bitmask.
+ * @see AML_LAYOUT_ORDER()
+ * This tag will store dimensions in the reversed order provided
+ * by the user, i.e elements of the first dimension will be contiguous
+ * in memory. This storage is the actual storage used by the library
+ * inside the structure.
+ **/
+#define AML_LAYOUT_ORDER_FORTRAN (1<<0)
+
+/**
+ * This is equivalent to AML_LAYOUT_ORDER_C.
+ * @see AML_LAYOUT_ORDER_C
+ **/
+#define AML_LAYOUT_ORDER_COLUMN_MAJOR (0<<0)
+
+/**
+ * This is equivalent to AML_LAYOUT_ORDER_FORTRAN.
+ * @see AML_LAYOUT_ORDER_FORTRAN
+ **/
+#define AML_LAYOUT_ORDER_ROW_MAJOR (1<<0)
+
+/**
+ * Get the order bit of an integer bitmask.
+ * The value can be further checked for equality
+ * with AML_LAYOUT_ORDER_* values.
+ * @param x: An integer with the first bit set
+ * to the order value.
+ * @return An integer containing only the bit order.
+ **/
+#define AML_LAYOUT_ORDER(x) ((x) & (1<<0))
+
+/**
+ * Dereference an element of a layout by its coordinates.
+ * @param layout[in]: An initialized layout.
+ * @param coords[in]: The coordinates on which to access data.
+ * @return A pointer to the dereferenced element on success.
+ * @return NULL on failure with aml_errno set to the error reason:
+ * * AML_EINVAL if coordinate are out of bound
+ * * See specific implementation of layout for further information
+ * on possible error codes.
+ **/
+void *aml_layout_deref(const struct aml_layout *layout,
+		       const size_t *coords);
+
+/**
+ * Equivalent to aml_layout_deref() but with bound checking
+ * on coordinates.
+ * @see aml_layout_deref()
+ **/
+void *aml_layout_deref_safe(const struct aml_layout *layout,
+			    const size_t *coords);
+
+/**
+ * Get the order in which dimensions of the layout are supposed to be
+ * accessed by the user.
+ * @param layout[in]: An initialized layout.
+ * @return The order (>0) on success, an AML error (<0) on failure.
+ * @return On success, a bitmask with order bit set (or not set).
+ * Output value can be further checked against order AML_LAYOUT_ORDER
+ * flags by using the macro AML_LAYOUT_ORDER() on output value.
+ * @see AML_LAYOUT_ORDER()
+ **/
+int aml_layout_order(const struct aml_layout *layout);
+
+/**
+ * Return the layout dimensions in the user order.
+ * @param layout[in]: An initialized layout.
+ * @param dims[out]: The non-NULL array of dimensions to fill. It is
+ * supposed to be large enough to contain ndims() elements.
+ * @return AML_SUCCESS on success, else an AML error code.
+ **/
+int aml_layout_dims(const struct aml_layout *layout, size_t *dims);
+
+/**
+ * Return the number of dimensions in a layout.
+ * @param layout[in]: An initialized layout.
+ * @return The number of dimensions in the layout.
+ **/
+size_t aml_layout_ndims(const struct aml_layout *layout);
+
+/**
+ * @brief Return the size of layout elements.
+ * @param layout[in]: An initialized layout.
+ * @return The size of elements stored with this layout.
+ **/
+size_t aml_layout_element_size(const struct aml_layout *layout);
+
+/**
+ * @brief Reshape the layout with different dimensions.
+ * This function checks that the number of elements of
+ * the reshaped layout matches the number of elements
+ * in the original layout. Additional constraint may apply
+ * depending on the layout implementation.
+ * @param layout[in]: An initialized layout.
+ * @param reshaped_layout[out]: A newly allocated layout
+ * with the queried shape on succes.
+ * @param ndims[in]: The number of dimensions of the new layout.
+ * @param dims[in]: The number of elements along each dimension of
+ * the new layout.
+ * @return AML_SUCCESS on success.
+ * @return AML_EINVAL if reshape dimensions are not compatible
+ * with original layout dimensions.
+ * @return AML_ENOMEM if AML failed to allocate the new structure.
+ * @return Another aml_error code. Refer to the layout
+ * implementation of reshape function.
+ **/
+int aml_layout_reshape(const struct aml_layout *layout,
+		       struct aml_layout **reshaped_layout,
+		       const size_t ndims,
+		       const size_t *dims);
+
+/**
+ * Return a layout that is a subset of another layout.
+ * The number of elements to subset along each dimension
+ * must be compatible with offsets and strides.
+ * This function checks that the amount of elements along
+ * each dimensions of the slice actually fits in the original
+ * layout.
+ * @param layout[in]: An initialized layout.
+ * @param reshaped_layout[out]: a pointer where to store a
+ * newly allocated layout with the queried subset of the
+ * original layout on succes.
+ * @param dims[in]: The number of elements of the slice along each
+ * dimension .
+ * @param offsets[in]: The index of the first element of the slice
+ * in each dimension. If NULL, offset is set to 0.
+ * @param strides[in]: The displacement (in number of elements) between
+ * elements of the slice. If NULL, stride is set to 1.
+ * @return AML_SUCCESS on success, else an AML error code (<0).
+ **/
+int aml_layout_slice(const struct aml_layout *layout,
+		     struct aml_layout **reshaped_layout,
+		     const size_t *dims,
+		     const size_t *offsets,
+		     const size_t *strides);
+
+////////////////////////////////////////////////////////////////////////////////
+
 /**
  * @}
  * @defgroup aml_scratch "AML Scratchpad"

include/aml/layout/dense.h

+/*******************************************************************************
+ * Copyright 2019 UChicago Argonne, LLC.
+ * (c.f. AUTHORS, LICENSE)
+ *
+ * This file is part of the AML project.
+ * For more info, see https://xgitlab.cels.anl.gov/argo/aml
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+*******************************************************************************/
+
+#ifndef AML_AREA_LAYOUT_DENSE_H
+#define AML_AREA_LAYOUT_DENSE_H
+
+/**
+ * @defgroup aml_layout_dense "AML Layout Dense"
+ * @brief Default aml layout.
+ *
+ * Dense layouts describe how a multi-dimensional dense data structure
+ * is collapsed into a linear (and contiguous) virtual address range.
+ * Dimensions of a layout may contain a stride (space between elements)
+ * on the virtual address space, and a pitch (distance between contiguous
+ * elements of the same dimension).
+ *
+ * #include <aml/layout/dense.h>
+ * @see aml_layout
+ * @{
+ **/
+
+/**
+ * Structure of a dense layout.
+ **/
+struct aml_layout_dense {
+	/**
+	 * dimensions, in element size, of the data structure,
+	 * by order of appearance in memory.
+	 **/
+	size_t *dims;
+	/**
+	 * Offset between elements of the same dimension.
+	 * Offset in number of elements.
+	 **/
+	size_t *stride;
+	/**
+	 * distances between two elements of the next dimension
+	 * (or total dimension of the layout in this dimension).
+	 **/
+	size_t *pitch;
+	/**
+	 * cumulative distances between two elements in the same
+	 * dimension (pitch[0] is the element size in bytes).
+	 **/
+	size_t *cpitch;
+	/** base pointer of the address range **/
+	void *ptr;
+	/** number of dimensions **/
+	size_t ndims;
+};
+
+/**
+ * Dense layout constructor.
+ * @param layout[out]: A pointer where to store a newly allocated layout.
+ * @param ptr[in]: The pointer to the data structure described by this layout.
+ * @param order[in]: The order in which dimensions are organized.
+ * Can be AML_LAYOUT_ORDER_COLUMN_MAJOR or AML_LAYOUT_ORDER_ROW_MAJOR.
+ * @param element_size[in]: The size of each element in layout.
+ * @param ndims[in]: The number of dimensions of the layout.
+ * @param dims[in]: The number of elements along each dimension of the layout.
+ * @param stride[in]: The space between elements (in number of elements),
+ * along each dimension. If NULL then the stride is set to one for each
+ * dimension.
+ * @param pitch[in]: The space between consecutive elements of the same
+ * dimension. If NULL, pitch is set to the number of elements in each dimension.
+ * @return -AML_ENOMEM if layout allocation failed.
+ * @return -AML_EINVAL if layout is NULL.
+ * @return AML_SUCCESS if creation succeeded.
+ * @see aml_layout_dense
+ **/
+int aml_layout_dense_create(struct aml_layout **layout,
+			    void *ptr,
+			    const int order,
+			    const size_t element_size,
+			    const size_t ndims,
+			    const size_t *dims,
+			    const size_t *stride,
+			    const size_t *pitch);
+
+/**
+ * Function to free a dense layout.
+ * @param layout[inout]: The layout to deallocate. NULL on return.
+ **/
+void aml_layout_dense_destroy(struct aml_layout **layout);
+
+/**
+ * Deref operator for dense layout in AML_ORDER_COLUMN_MAJOR.
+ * Also used as the deref operator for this type of layout.
+ * Does not check its argument. If data is NULL, or coords are out
+ * of bounds, the behaviour of aml_layout_column_deref() is undefined.
+ * @see aml_layout_deref()
+ * @see aml_layout_deref_native()
+ **/
+void *aml_layout_column_deref(const struct aml_layout_data *data,
+			      const size_t *coords);
+
+/**
+ * Layout operator for retrieving order of dimension storage.
+ * This function shall not fail.
+ * @see aml_layout_order()
+ **/
+int aml_layout_column_order(const struct aml_layout_data *data);
+
+/**
+ * Operator for retrieving the number of dimensions in the layout.
+ * Does not check data is not NULL. If data is NULL or not the good
+ * pointer type, the behaviour is undefined.
+ * @see aml_layout_ndims()
+ **/
+size_t aml_layout_dense_ndims(const struct aml_layout_data *data);
+
+/**
+ * Layout operator for retrieving layout elements size.
+ * Does not check data is not NULL. If data is NULL or not the good
+ * @see aml_layout_element_size()
+ **/
+size_t aml_layout_dense_element_size(const struct aml_layout_data *data);
+
+/**
+ * Operator for reshaping dense layouts with column major order.
+ * Does not check if the number of elements match.
+ * This should be done in aml_layout_reshape().
+ * @return -AML_EINVAL if merge then split of dimensions
+ * cannot be done appropriatly.
+ * @return -AML_ENOMEM if the resulting layout cannot be allocated.
+ * @return AML_SUCCESS on successful reshape.