Merge pull request #3 from yungyuc/feature/nsd

Feature/nsd

.github/workflows/nsd.yml

@@ -0,0 +1,197 @@
+name: nsd
+
+on:
+  push:
+    branches:
+      - '**/nsd**'
+  pull_request:
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+
+    env:
+      CPPROOT: nsd/03cpp/code
+      MATRIXROOT: nsd/04matrix/code
+      CACHEROOT: nsd/05cache/code
+      SIMDROOT: nsd/06simd/code
+      MEMROOT: nsd/07mem/code
+      SMARTROOT: nsd/08smart/code
+      MODERNCPPROOT: nsd/09moderncpp/code
+      ARRAYDESIGNROOT: nsd/11arraydesign/code
+
+    strategy:
+        matrix:
+          os: [ubuntu-20.04, macos-10.15]
+
+        fail-fast: false
+
+    steps:
+
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 1
+
+    - name: apt (ubuntu)
+      if: startsWith(matrix.os, 'ubuntu')
+      run: |
+        sudo apt-get -q update
+        sudo apt-get -qy install \
+            curl build-essential make cmake libc6-dev \
+            gcc g++ clang clang-tidy \
+            gfortran intel-mkl-full \
+            python3 python3-pip python3-pytest \
+            python3-numpy python3-scipy python3-pandas
+
+    - name: brew (macos)
+      if: startsWith(matrix.os, 'macos')
+      run: |
+        brew install make cmake llvm libomp python3 radare2
+
+    - name: pip (ubuntu)
+      if: startsWith(matrix.os, 'ubuntu')
+      run: |
+        sudo pip3 install -U flake8
+        sudo pip3 install -U https://github.com/aldanor/ipybind/tarball/master
+
+    - name: pip (macos)
+      if: startsWith(matrix.os, 'macos')
+      run: |
+        pip3 install -U pip
+        pip3 install -U setuptools
+        pip3 install -U pytest numpy scipy pandas
+        pip3 install -U flake8
+        pip3 install -U https://github.com/aldanor/ipybind/tarball/master
+
+    - name: INSTALL_PREFIX (ubuntu)
+      if: startsWith(matrix.os, 'ubuntu')
+      run: |
+        echo "INSTALL_PREFIX=/usr" >> ${GITHUB_ENV}
+
+    - name: INSTALL_PREFIX (macos)
+      if: startsWith(matrix.os, 'macos')
+      run: |
+        echo "INSTALL_PREFIX=/usr/local" >> ${GITHUB_ENV}
+
+    - name: custom
+      run: |
+        INSTALL_PREFIX=${{ env.INSTALL_PREFIX }}
+        echo "INSTALL_PREFIX=${INSTALL_PREFIX}"
+        #nsd/contrib/install.sh radare2 # skip to save time, for now
+        nsd/contrib/install.sh pybind11
+        nsd/contrib/install.sh xtl
+        nsd/contrib/install.sh xsimd
+        nsd/contrib/install.sh xtensor
+        nsd/contrib/install.sh xtensor_blas
+        nsd/contrib/install.sh xtensor_python
+
+    - name: show dependency
+      run: |
+        echo "radare2 path: $(which radare2)"
+        echo "radare2 version: $(radare2 -v)"
+        echo "gcc path: $(which gcc)"
+        echo "gcc version: $(gcc --version)"
+        echo "cmake path: $(which cmake)"
+        echo "cmake version: $(cmake --version)"
+        echo "python3 path: $(which python3)"
+        echo "python3 version: $(python3 --version)"
+        python3 -c 'import numpy ; print("numpy.__version__:", numpy.__version__)'
+        echo "pytest path: $(which pytest)"
+        echo "pytest version: $(pytest --version)"
+        echo "clang-tidy path: $(which clang-tidy)"
+        echo "clang-tidy version: $(clang-tidy -version)"
+        echo "flake8 path: $(which flake8)"
+        echo "flake8 version: $(flake8 --version)"
+
+    - name: 03cpp
+      run: |
+        make -C ${{ env.CPPROOT }} clean
+        make -C ${{ env.CPPROOT }} runall
+
+    - name: 04matrix_pod
+      run: |
+        make -C ${{ env.MATRIXROOT }} clean
+        make -C ${{ env.MATRIXROOT }} runpod
+
+    - name: 04matrix_ma
+      run: |
+        make -C ${{ env.MATRIXROOT }} clean
+        make -C ${{ env.MATRIXROOT }} runma
+
+    - name: 04matrix_la
+      # macos does not have MKL.
+      if: startsWith(matrix.os, 'ubuntu')
+      run: |
+        make -C ${{ env.MATRIXROOT }} clean
+        make -C ${{ env.MATRIXROOT }} runla
+
+    - name: 05cache_skip_access
+      run: |
+        make -C ${{ env.CACHEROOT }} clean
+        make -C ${{ env.CACHEROOT }} run_01_skip_access
+
+    - name: 05cache_locality
+      run: |
+        make -C ${{ env.CACHEROOT }} clean
+        make -C ${{ env.CACHEROOT }} run_02_locality
+
+    - name: 05cache_matrix_matrix
+      # macos does not have MKL.
+      if: startsWith(matrix.os, 'ubuntu')
+      run: |
+        make -C ${{ env.CACHEROOT }} clean
+        make -C ${{ env.CACHEROOT }} run_03_matrix_matrix
+
+    - name: 06simd_mul
+      run: |
+        make -C ${{ env.SIMDROOT }} hardware
+        make -C ${{ env.SIMDROOT }} clean
+        make -C ${{ env.SIMDROOT }}/01_mul run
+        #make -C ${{ env.SIMDROOT }}/02_fma run # server not supporting FMA
+
+    - name: 06simd_mul_r2
+      # ubuntu does not have a working r2.
+      if: startsWith(matrix.os, 'macos')
+      run: |
+        make -C ${{ env.SIMDROOT }}/01_mul r2all
+
+    - name: 06simd_omp
+      run: |
+        make -C ${{ env.SIMDROOT }}/03_omp
+        make -C ${{ env.SIMDROOT }}/03_omp run
+        [ "$(env OMP_NUM_THREADS=5 make -C ${{ env.SIMDROOT }}/03_omp run | grep 'Hello from thread' | wc -l | xargs)" = "5" ]
+
+    - name: 07mem
+      run: |
+        make -C ${{ env.MEMROOT }} clean
+        make -C ${{ env.MEMROOT }} runall
+
+    - name: 08smart_pointer
+      run: |
+        make -C ${{ env.SMARTROOT }}/01_pointer clean
+        make -C ${{ env.SMARTROOT }}/01_pointer runall
+
+    - name: 08smart_shared
+      run: |
+        make -C ${{ env.SMARTROOT }}/02_shared clean
+        make -C ${{ env.SMARTROOT }}/02_shared runall
+
+    - name: 09moderncpp
+      run: |
+        make -C ${{ env.MODERNCPPROOT }}/03_elision clean
+        make -C ${{ env.MODERNCPPROOT }}/03_elision runall
+        make -C ${{ env.MODERNCPPROOT }}/04_template clean
+        make -C ${{ env.MODERNCPPROOT }}/04_template runall
+        make -C ${{ env.MODERNCPPROOT }}/05_lambda clean
+        make -C ${{ env.MODERNCPPROOT }}/05_lambda runall
+
+    - name: 11arraydesign_solve_cpp
+      run: |
+        make -C ${{ env.ARRAYDESIGNROOT }} solve_cpp.so
+
+    - name: 11arraydesign_data_prep
+      # macos does not have MKL.
+      if: startsWith(matrix.os, 'ubuntu')
+      run: |
+        make -C ${{ env.ARRAYDESIGNROOT }} data_prep.so

conf.py

@@ -31,6 +31,7 @@
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = [
+    'sphinx.ext.intersphinx',
     'sphinx.ext.mathjax',
     'pstake',
 ]
@@ -261,3 +262,9 @@
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
 #texinfo_show_urls = 'footnote'
 blog_top_name = 'everydaywork'
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
+    'numpy': ('https://numpy.org/doc/stable/', None),
+    'pybind11': ('https://pybind11.readthedocs.io/en/stable/', None),
+}

nsd/00intro.rst

@@ -1,6 +1,6 @@
-============
-Introduction
-============
+========
+Overview
+========
 
 What Is Numerical Software
 ==========================

nsd/01engineering/code/.gitignore

@@ -0,0 +1,4 @@
+nsd/
+repo1/
+gtest/
+line*.log

nsd/01engineering/code/Makefile

@@ -0,0 +1,7 @@
+.PHONY: default
+default:
+	@echo "do nothing"
+
+.PHONY: clean
+clean:
+	rm -rf repo1/ nsd/ gtest/ *.log

nsd/01engineering/code/bashfunction.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+runcmd () {
+  echo "run command: ${@:2}"
+  { time "${@:2}" ; } > $1 2>&1
+  echo "done; log file: $(cd "$(dirname $1)" && pwd)/$1"
+}
+runcmd line1.log echo "first command"
+runcmd line2.log echo "second command"

nsd/01engineering/code/bind1/.gitignore

@@ -0,0 +1,2 @@
+build/
+*.so

nsd/01engineering/code/bind1/CMakeLists.txt

@@ -0,0 +1,11 @@
+cmake_minimum_required(VERSION 3.9)
+project(vector)
+
+find_package(pybind11 REQUIRED)
+
+pybind11_add_module(
+    _vector
+    vector.cpp
+)
+
+install(TARGETS _vector DESTINATION .)

nsd/01engineering/code/bind1/vector.cpp

@@ -0,0 +1,30 @@
+#include <pybind11/pybind11.h>
+
+#include <cmath>
+#include <tuple>
+
+std::tuple<double, double> rotate(
+    std::tuple<double, double> const & vec
+  , double rad
+)
+{
+
+    const double cth = cos(rad);
+    const double sth = sin(rad);
+
+    return std::tuple<double, double>(
+        std::get<0>(vec) * cth - std::get<1>(vec) * sth
+      , std::get<0>(vec) * sth + std::get<1>(vec) * cth);
+
+}
+
+PYBIND11_MODULE(_vector, mod)
+{
+
+    mod.doc() = "example C extension module";
+
+    mod.def("rotate", &rotate, "vector rotation");
+
+}
+
+/* vim: set et ts=4 sw=4: */

nsd/01engineering/code/dosomething.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+export MYENVVAR="MYENVVAR is set to what I want"
+echo "do something"

nsd/01engineering/code/make1/.gitignore

@@ -0,0 +1,2 @@
+hello
+*.o

nsd/01engineering/code/make1/Makefile

@@ -0,0 +1,12 @@
+CXX = g++
+
+hello: hello.o hellomain.o
+	$(CXX) hello.o hellomain.o -o hello
+
+hello.o: hello.cpp hello.hpp
+	$(CXX) -c hello.cpp -o hello.o
+
+hellomain.o: hellomain.cpp hello.hpp
+	$(CXX) -c hellomain.cpp -o hellomain.o
+
+# vim: set noet nobomb fenc=utf8 ff=unix:

nsd/01engineering/code/make1/hello.cpp

@@ -0,0 +1,7 @@
+#include <iostream>
+#include "hello.hpp"
+void hello()
+{
+    std::cout << "hello with standalone compiling unit" << std::endl;
+}
+// vim: set sw=4 ts=4 sts=4 et:

nsd/01engineering/code/make1/hello.hpp

@@ -0,0 +1,3 @@
+#pragma once
+void hello();
+// vim: set sw=4 ts=4 sts=4 et:

nsd/01engineering/code/make1/hellomain.cpp

@@ -0,0 +1,7 @@
+#include "hello.hpp"
+int main(int argc, char ** argv)
+{
+    hello();
+    return 0;
+}
+// vim: set sw=4 ts=4 sts=4 et:

nsd/01engineering/code/make2/.gitignore

@@ -0,0 +1,2 @@
+hello
+*.o

nsd/01engineering/code/make2/Makefile

@@ -0,0 +1,12 @@
+CXX = g++
+
+hello: hello.o hellomain.o
+	$(CXX) $^ -o $@
+
+hello.o: hello.cpp hello.hpp
+	$(CXX) -c $< -o $@
+
+hellomain.o: hellomain.cpp hello.hpp
+	$(CXX) -c $< -o $@
+
+# vim: set noet nobomb fenc=utf8 ff=unix:

nsd/01engineering/code/make2/hello.cpp

@@ -0,0 +1,7 @@
+#include <iostream>
+#include "hello.hpp"
+void hello()
+{
+    std::cout << "hello with standalone compiling unit" << std::endl;
+}
+// vim: set sw=4 ts=4 sts=4 et:

nsd/01engineering/code/make2/hello.hpp

@@ -0,0 +1,3 @@
+#pragma once
+void hello();
+// vim: set sw=4 ts=4 sts=4 et:

nsd/01engineering/code/make2/hellomain.cpp

@@ -0,0 +1,6 @@
+#include "hello.hpp"
+int main(int argc, char ** argv)
+{
+    hello();
+}
+// vim: set sw=4 ts=4 sts=4 et:

nsd/01engineering/code/make3/.gitignore

@@ -0,0 +1,2 @@
+hello
+*.o

nsd/01engineering/code/make3/Makefile

@@ -0,0 +1,9 @@
+CXX = g++
+
+hello: hello.o hellomain.o
+	$(CXX) $^ -o $@
+
+%.o: %.cpp hello.hpp
+	$(CXX) -c $< -o $@
+
+# vim: set noet nobomb fenc=utf8 ff=unix:

nsd/01engineering/code/make3/hello.cpp

@@ -0,0 +1,7 @@
+#include <iostream>
+#include "hello.hpp"
+void hello()
+{
+    std::cout << "hello with standalone compiling unit" << std::endl;
+}
+// vim: set sw=4 ts=4 sts=4 et:

nsd/01engineering/code/make3/hello.hpp

@@ -0,0 +1,3 @@
+#pragma once
+void hello();
+// vim: set sw=4 ts=4 sts=4 et: