cpu/__init__.py

-from pystencils.cpu.kernelcreation import createKernel, addOpenMP
-from pystencils.cpu.cpujit import makePythonFunction
-from pystencils.backends.cbackend import generateC

cpu/cpujit.py

-import os
-import subprocess
-from ctypes import cdll, c_double, c_float, sizeof
-from tempfile import TemporaryDirectory
-from pystencils.backends.cbackend import generateC
-import numpy as np
-
-
-CONFIG_GCC = {
-    'compiler': 'g++',
-    'flags': '-Ofast -DNDEBUG -fPIC -shared -march=native -fopenmp',
-}
-CONFIG_INTEL = {
-    'compiler': '/software/intel/2017/bin/icpc',
-    'flags': '-Ofast -DNDEBUG -fPIC -shared -march=native -fopenmp -Wl,-rpath=/software/intel/2017/lib/intel64',
-    'env': {
-        'INTEL_LICENSE_FILE': '1713@license4.rrze.uni-erlangen.de',
-        'LM_PROJECT': 'iwia',
-    }
-}
-CONFIG_CLANG = {
-    'compiler': 'clang++',
-    'flags': '-Ofast -DNDEBUG -fPIC -shared -march=native -fopenmp',
-}
-CONFIG = CONFIG_GCC
-
-
-def ctypeFromString(typename, includePointers=True):
-    import ctypes as ct
-
-    typename = typename.replace("*", " * ")
-    typeComponents = typename.split()
-
-    basicTypeMap = {
-        'double': ct.c_double,
-        'float': ct.c_float,
-        'int': ct.c_int,
-        'long': ct.c_long,
-    }
-
-    resultType = None
-    for typeComponent in typeComponents:
-        typeComponent = typeComponent.strip()
-        if typeComponent == "const" or typeComponent == "restrict" or typeComponent == "volatile":
-            continue
-        if typeComponent in basicTypeMap:
-            resultType = basicTypeMap[typeComponent]
-        elif typeComponent == "*" and includePointers:
-            assert resultType is not None
-            resultType = ct.POINTER(resultType)
-
-    return resultType
-
-
-def ctypeFromNumpyType(numpyType):
-    typeMap = {
-        np.dtype('float64'): c_double,
-        np.dtype('float32'): c_float,
-    }
-    return typeMap[numpyType]
-
-
-def compileAndLoad(kernelFunctionNode):
-    with TemporaryDirectory() as tmpDir:
-        srcFile = os.path.join(tmpDir, 'source.cpp')
-        with open(srcFile, 'w') as sourceFile:
-            print('#include <iostream>', file=sourceFile)
-            print("#include <cmath>", file=sourceFile)
-            print('extern "C" { ', file=sourceFile)
-            print(generateC(kernelFunctionNode), file=sourceFile)
-            print('}', file=sourceFile)
-
-        compilerCmd = [CONFIG['compiler']] + CONFIG['flags'].split()
-        libFile = os.path.join(tmpDir, "jit.so")
-        compilerCmd += [srcFile, '-o', libFile]
-        configEnv = CONFIG['env'] if 'env' in CONFIG else {}
-        env = os.environ.copy()
-        env.update(configEnv)
-        subprocess.call(compilerCmd, env=env)
-
-        showAssembly = False
-        if showAssembly:
-            assemblyFile = os.path.join(tmpDir, "assembly.s")
-            compilerCmd = [CONFIG['compiler'], '-S', '-o', assemblyFile, srcFile] + CONFIG['flags'].split()
-            subprocess.call(compilerCmd, env=env)
-            assembly = open(assemblyFile, 'r').read()
-            kernelFunctionNode.assembly = assembly
-        loadedJitLib = cdll.LoadLibrary(libFile)
-
-    return loadedJitLib
-
-
-def buildCTypeArgumentList(kernelFunctionNode, argumentDict):
-    ctArguments = []
-    for arg in kernelFunctionNode.parameters:
-        if arg.isFieldArgument:
-            field = argumentDict[arg.fieldName]
-            if arg.isFieldPtrArgument:
-                ctArguments.append(field.ctypes.data_as(ctypeFromString(arg.dtype)))
-            elif arg.isFieldShapeArgument:
-                dataType = ctypeFromString(arg.dtype, includePointers=False)
-                ctArguments.append(field.ctypes.shape_as(dataType))
-            elif arg.isFieldStrideArgument:
-                dataType = ctypeFromString(arg.dtype, includePointers=False)
-                baseFieldType = ctypeFromNumpyType(field.dtype)
-                strides = field.ctypes.strides_as(dataType)
-                for i in range(len(field.shape)):
-                    assert strides[i] % sizeof(baseFieldType) == 0
-                    strides[i] //= sizeof(baseFieldType)
-                ctArguments.append(strides)
-            else:
-                assert False
-        else:
-            param = argumentDict[arg.name]
-            expectedType = ctypeFromString(arg.dtype)
-            ctArguments.append(expectedType(param))
-    return ctArguments
-
-
-def makePythonFunctionIncompleteParams(kernelFunctionNode, argumentDict):
-    func = compileAndLoad(kernelFunctionNode)[kernelFunctionNode.functionName]
-    func.restype = None
-
-    def wrapper(**kwargs):
-        from copy import copy
-        fullArguments = copy(argumentDict)
-        fullArguments.update(kwargs)
-        args = buildCTypeArgumentList(kernelFunctionNode, fullArguments)
-        func(*args)
-    return wrapper
-
-
-def makePythonFunction(kernelFunctionNode, argumentDict={}):
-    """
-    Creates C code from the abstract syntax tree, compiles it and makes it accessible as Python function
-
-    The parameters of the kernel are:
-        - numpy arrays for each field used in the kernel. The keyword argument name is the name of the field
-        - all symbols which are not defined in the kernel itself are expected as parameters
-
-    :param kernelFunctionNode: the abstract syntax tree
-    :param argumentDict: parameters passed here are already fixed. Remaining parameters have to be passed to the
-                        returned kernel functor.
-    :return: kernel functor
-    """
-    # build up list of CType arguments
-    try:
-        args = buildCTypeArgumentList(kernelFunctionNode, argumentDict)
-    except KeyError:
-        # not all parameters specified yet
-        return makePythonFunctionIncompleteParams(kernelFunctionNode, argumentDict)
-    func = compileAndLoad(kernelFunctionNode)[kernelFunctionNode.functionName]
-    func.restype = None
-    return lambda: func(*args)

cpu/kernelcreation.py

-import sympy as sp
-from pystencils.transformations import resolveFieldAccesses, makeLoopOverDomain, typingFromSympyInspection, \
-    typeAllEquations, getOptimalLoopOrdering, parseBasePointerInfo, moveConstantsBeforeLoop, splitInnerLoop
-from pystencils.typedsymbol import TypedSymbol
-from pystencils.field import Field
-import pystencils.ast as ast
-
-
-def createKernel(listOfEquations, functionName="kernel", typeForSymbol=None, splitGroups=(),
-                 iterationSlice=None, ghostLayers=None):
-    """
-    Creates an abstract syntax tree for a kernel function, by taking a list of update rules.
-
-    Loops are created according to the field accesses in the equations.
-
-    :param listOfEquations: list of sympy equations, containing accesses to :class:`pystencils.field.Field`.
-           Defining the update rules of the kernel
-    :param functionName: name of the generated function - only important if generated code is written out
-    :param typeForSymbol: a map from symbol name to a C type specifier. If not specified all symbols are assumed to
-           be of type 'double' except symbols which occur on the left hand side of equations where the
-           right hand side is a sympy Boolean which are assumed to be 'bool' .
-    :param splitGroups: Specification on how to split up inner loop into multiple loops. For details see
-           transformation :func:`pystencils.transformation.splitInnerLoop`
-    :param iterationSlice: if not None, iteration is done only over this slice of the field
-    :param ghostLayers: a sequence of pairs for each coordinate with lower and upper nr of ghost layers
-                        if None, the number of ghost layers is determined automatically and assumed to be equal for a
-                        all dimensions
-
-    :return: :class:`pystencils.ast.KernelFunction` node
-    """
-    if not typeForSymbol:
-        typeForSymbol = typingFromSympyInspection(listOfEquations, "double")
-
-    def typeSymbol(term):
-        if isinstance(term, Field.Access) or isinstance(term, TypedSymbol):
-            return term
-        elif isinstance(term, sp.Symbol):
-            return TypedSymbol(term.name, typeForSymbol[term.name])
-        else:
-            raise ValueError("Term has to be field access or symbol")
-
-    fieldsRead, fieldsWritten, assignments = typeAllEquations(listOfEquations, typeForSymbol)
-    allFields = fieldsRead.union(fieldsWritten)
-
-    readOnlyFields = set([f.name for f in fieldsRead - fieldsWritten])
-
-    body = ast.Block(assignments)
-    code = makeLoopOverDomain(body, functionName, iterationSlice=iterationSlice, ghostLayers=ghostLayers)
-
-    if splitGroups:
-        typedSplitGroups = [[typeSymbol(s) for s in splitGroup] for splitGroup in splitGroups]
-        splitInnerLoop(code, typedSplitGroups)
-
-    loopOrder = getOptimalLoopOrdering(allFields)
-
-    basePointerInfo = [['spatialInner0'], ['spatialInner1']]
-    basePointerInfos = {field.name: parseBasePointerInfo(basePointerInfo, loopOrder, field) for field in allFields}
-
-    resolveFieldAccesses(code, readOnlyFields, fieldToBasePointerInfo=basePointerInfos)
-    moveConstantsBeforeLoop(code)
-
-    return code
-
-
-def addOpenMP(astNode, schedule="static"):
-    """
-    Parallelizes the outer loop with OpenMP
-
-    :param astNode: abstract syntax tree created e.g. by :func:`createKernel`
-    :param schedule: OpenMP scheduling policy e.g. 'static' or 'dynamic'
-    """
-    assert type(astNode) is ast.KernelFunction
-    body = astNode.body
-    wrapperBlock = ast.PragmaBlock('#pragma omp parallel', body.takeChildNodes())
-    body.append(wrapperBlock)
-
-    outerLoops = [l for l in body.atoms(ast.LoopOverCoordinate) if l.isOutermostLoop]
-    assert outerLoops, "No outer loop found"
-    assert len(outerLoops) <= 1, "More than one outer loop found. Which one should be parallelized?"
-    outerLoops[0].prefixLines.append("#pragma omp for schedule(%s)" % (schedule,))

doc/conf.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+import datetime
+import sphinx_rtd_theme
+import os
+import re
+import sys
+
+sys.path.insert(0, os.path.abspath('.'))
+import pystencils
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.napoleon',
+    'nbsphinx',
+    'sphinxcontrib.bibtex',
+    'sphinx_autodoc_typehints',
+]
+
+add_module_names = False
+templates_path = ['_templates']
+source_suffix = '.rst'
+master_doc = 'index'
+
+copyright = f'{datetime.datetime.now().year}, Martin Bauer, Markus Holzer, Frederik Hennig'
+author = 'Martin Bauer, Markus Holzer, Frederik Hennig'
+# The short X.Y version (including .devXXXX, rcX, b1 suffixes if present)
+version = re.sub(r'(\d+\.\d+)\.\d+(.*)', r'\1\2', pystencils.__version__)
+version = re.sub(r'(\.dev\d+).*?$', r'\1', version)
+# The full version, including alpha/beta/rc tags.
+release = pystencils.__version__
+language = 'en'
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
+default_role = 'any'
+pygments_style = 'sphinx'
+todo_include_todos = False
+
+# Options for HTML output
+
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+html_theme = 'sphinx_rtd_theme'
+htmlhelp_basename = 'pystencilsdoc'
+html_sidebars = {'**': ['globaltoc.html', 'relations.html', 'sourcelink.html', 'searchbox.html']}
+
+# NbSphinx configuration
+nbsphinx_execute = 'never'
+nbsphinx_codecell_lexer = 'python3'
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'python': ('https://docs.python.org/3.8', None),
+                       'numpy': ('https://docs.scipy.org/doc/numpy/', None),
+                       'matplotlib': ('https://matplotlib.org/', None),
+                       'sympy': ('https://docs.sympy.org/latest/', None),
+                       }
+
+autodoc_member_order = 'bysource'
+bibtex_bibfiles = ['sphinx/pystencils.bib']
+
+project = 'pystencils'
+html_logo = 'img/logo.png'

doc/img/logo.svg

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doc/index.rst

+pystencils
+==========
+
+Welcome to the documentation of the pystencils code generation tool for stencil codes.
+pystencils can help you to generate blazingly fast code for image processing, numerical simulations or any other task involving numpy arrays.
+
+
+.. toctree::
+   :maxdepth: 2
+
+   sphinx/tutorials.rst
+   sphinx/api.rst
+
+
+.. image:: /img/pystencils_arch_block_diagram.svg
+    :height: 450px
+    :align: center
+
+