HPCG benchmark

.github/workflows/ci.yml

@@ -3,48 +3,73 @@ on:
   push:
     branches:
       - master
-    tags: '*'
+    tags: "*"
   pull_request:
 concurrency:
   # Skip intermediate builds: always.
   # Cancel intermediate builds: only if it is a pull request build.
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
 jobs:
-  test:
-    name: PartitionedArrays / Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+  # test:
+  #   name: PartitionedArrays / Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+  #   runs-on: ${{ matrix.os }}
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       version:
+  #         - "1.6"
+  #         - "1"
+  #       os:
+  #         - ubuntu-latest
+  #       arch:
+  #         - x64
+  #   steps:
+  #     - uses: actions/checkout@v2
+  #     - uses: julia-actions/setup-julia@v1
+  #       with:
+  #         version: ${{ matrix.version }}
+  #         arch: ${{ matrix.arch }}
+  #     - uses: julia-actions/cache@v1
+  #     - uses: julia-actions/julia-buildpkg@v1
+  #     - uses: julia-actions/julia-runtest@v1
+  #     - uses: julia-actions/julia-processcoverage@v1
+  #     - uses: codecov/codecov-action@v2
+  #       with:
+  #         files: lcov.info
+  # PartitionedSolvers:
+  #   name: PartitionedSolvers / Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+  #   runs-on: ${{ matrix.os }}
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       version:
+  #         - "1"
+  #       os:
+  #         - ubuntu-latest
+  #       arch:
+  #         - x64
+  #   steps:
+  #     - uses: actions/checkout@v2
+  #     - uses: julia-actions/setup-julia@v1
+  #       with:
+  #         version: ${{ matrix.version }}
+  #         arch: ${{ matrix.arch }}
+  #     - uses: julia-actions/cache@v1
+  #     - uses: julia-actions/julia-buildpkg@v1
+  #     - run: |
+  #         julia --project=PartitionedSolvers -e '
+  #           using Pkg
+  #           Pkg.develop(path=".")
+  #           Pkg.test("PartitionedSolvers")'
+  HPCG:
+    name: HPCG / Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
-          - '1'
-        os:
-          - ubuntu-latest
-        arch:
-          - x64
-    steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
-      - uses: julia-actions/cache@v1
-      - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
-      - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v2
-        with:
-          files: lcov.info
-  PartitionedSolvers:
-    name: PartitionedSolvers / Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        version:
-          - '1'
+          - "1"
         os:
           - ubuntu-latest
         arch:
@@ -58,31 +83,31 @@ jobs:
       - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
       - run: |
-          julia --project=PartitionedSolvers -e '
+          julia --project=HPCG -e '
             using Pkg
             Pkg.develop(path=".")
-            Pkg.test("PartitionedSolvers")'
-  docs:
-    name: Documentation
-    runs-on: ubuntu-latest
-    permissions:
-      contents: write
-    steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: '1'
-      - uses: julia-actions/julia-buildpkg@v1
-      - run: |
-          julia --project=docs -e '
-            using Pkg
-            Pkg.develop(path="PartitionedSolvers")'
-      - uses: julia-actions/julia-docdeploy@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - run: |
-          julia --project=docs -e '
-            using Documenter: DocMeta, doctest
-            using PartitionedArrays
-            DocMeta.setdocmeta!(PartitionedArrays, :DocTestSetup, :(using PartitionedArrays); recursive=true)
-            doctest(PartitionedArrays)'
+            Pkg.test("HPCG")'
+  # docs:
+  #   name: Documentation
+  #   runs-on: ubuntu-latest
+  #   permissions:
+  #     contents: write
+  #   steps:
+  #     - uses: actions/checkout@v2
+  #     - uses: julia-actions/setup-julia@v1
+  #       with:
+  #         version: "1"
+  #     - uses: julia-actions/julia-buildpkg@v1
+  #     - run: |
+  #         julia --project=docs -e '
+  #           using Pkg
+  #           Pkg.develop(path="PartitionedSolvers")'
+  #     - uses: julia-actions/julia-docdeploy@v1
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  #     - run: |
+  #         julia --project=docs -e '
+  #           using Documenter: DocMeta, doctest
+  #           using PartitionedArrays
+  #           DocMeta.setdocmeta!(PartitionedArrays, :DocTestSetup, :(using PartitionedArrays); recursive=true)
+  #           doctest(PartitionedArrays)'

.gitignore

@@ -8,3 +8,7 @@ Manifest.toml
 docs/build/
 tmp/
 docs/src/examples.md
+
+HPCG/src/results/
+
+HPCG/results/

HPCG/Project.toml

@@ -0,0 +1,19 @@
+name = "HPCG"
+uuid = "f200b046-3a0e-49a8-9a9e-044aa3bf7874"
+authors = ["Reinier van Elderen <[email protected]>"]
+version = "0.1.0"
+
+[deps]
+DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
+PartitionedArrays = "5a9dfac6-5c52-46f7-8278-5e2210713be9"
+PartitionedSolvers = "11b65f7f-80ac-401b-9ef2-3db765482d62"
+Primes = "27ebfcd6-29c5-5fa9-bf4b-fb8fc14df3ae"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+SparseMatricesCSR = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

HPCG/src/HPCG.jl

@@ -0,0 +1,32 @@
+module HPCG
+
+using PartitionedArrays
+using PartitionedSolvers
+using LinearAlgebra
+using DelimitedFiles
+using Dates
+using Statistics
+using Primes
+using DataStructures
+using JSON
+using SparseMatricesCSR
+import Base: iterate
+
+export hpcg_benchmark_mpi
+export hpcg_benchmark_debug
+export hpcg_benchmark
+include("hpcg_benchmark.jl")
+
+export build_matrix
+export build_p_matrix
+export ref_cg!
+export pc_setup
+export pc_solve!
+include("hpcg_utils.jl")
+include("compute_optimal_xyz.jl")
+include("sparse_matrix.jl")
+include("ref_cg.jl")
+include("opt_cg.jl")
+include("report_results.jl")
+include("mg_preconditioner.jl")
+end # module HPCG

HPCG/src/compute_optimal_xyz.jl

@@ -0,0 +1,64 @@
+include("mixed_base_counter.jl")
+
+"""
+	compute_optimal_shape_XYZ(np)
+
+	Calculate the optimal way to partition a 3D shape over np processors.
+"""
+function compute_optimal_shape_XYZ(np)
+
+	if np == 1
+		return 1, 1, 1
+	end
+
+	factors = Primes.factor(DataStructures.SortedDict, np)
+	primes = collect(keys(factors))
+	z = 0
+	x = primes[1]
+
+	if (length(primes) > 1)
+		y = primes[2]
+	end
+
+	if length(primes) == 1
+		z = x^(floor(Int, factors[x] / 3))
+		y = x^(floor(Int, factors[x] / 3 + ((factors[x] % 3) >= 2 ? 1 : 0)))
+		x = x^(floor(Int, factors[x] / 3 + ((factors[x] % 3) >= 1 ? 1 : 0)))
+	elseif length(primes) == 2 && factors[x] == 1 && factors[y] == 1 # two distinct prime factors
+		z = 1
+	elseif length(primes) == 2 && factors[x] + factors[y] == 3 # three prime factors one repeated
+		z = factors[x] == 2 ? x : y
+	elseif length(primes) == 3 && factors[x] == 1 && factors[y] == 1 && factors[primes[3]] == 1 # three distinct and single prime factors
+		z = primes[3]
+	else # 3 or more prime factors so try all possible 3-subsets
+
+		powers = collect(values(factors))
+		l, m, c = mixedbasecounter(powers, length(primes))
+		c_main = Mixed_base_counter(l, m, c)
+		c1 = Mixed_base_counter(l, m, c)
+
+		min_area = 2.0 * np + 1.0
+
+		c1 = next(c1)
+		while is_zero(c1)
+			c2 = mixedbasecounter1(c_main, c1)
+			c2 = next(c2)
+			while is_zero(c2)
+				tf1 = product(c1, primes)
+				tf2 = product(c2, primes)
+				tf3 = np / tf1 / tf2 # we derive the third dimension, we don't keep track of the factors it has
+
+				area = tf1 * tf2 + tf2 * tf3 + tf1 * tf3
+				if (area < min_area)
+					min_area = area
+					x = tf1
+					y = tf2
+					z = tf3
+				end
+				c2 = next(c2)
+			end
+			c1 = next(c1)
+		end
+	end
+	return x, y, floor(Int, z)
+end