Merge branch 'master' into master

.github/workflows/bench.yml

@@ -0,0 +1,49 @@
+name: 'Benchmark'
+
+on:
+  pull_request:
+
+jobs:
+  self:
+    name: Georgia Tech | Phoenix (NVHPC)
+    if: github.repository == 'MFlowCode/MFC'
+    strategy:
+      matrix:
+        device: ['cpu', 'gpu']
+    runs-on:
+      group:  phoenix
+      labels: gt
+    steps:
+      - name: Clone - PR
+        uses: actions/checkout@v3
+        with:
+          path: pr
+
+      - name: Clone - Master
+        uses: actions/checkout@v3
+        with:
+          repository: MFlowCode/MFC
+          ref: master
+          path: master
+
+      - name: Bench (Master v. PR)
+        run: |
+          (cd pr     && bash .github/workflows/phoenix/submit.sh .github/workflows/phoenix/bench.sh ${{ matrix.device }}) &
+          (cd master && bash .github/workflows/phoenix/submit.sh .github/workflows/phoenix/bench.sh ${{ matrix.device }}) &
+          wait %1 && wait %2
+
+      - name: Generate & Post Comment
+        run: |
+          . ./mfc.sh load -c p -m g
+          ./mfc.sh bench_diff master/bench-${{ matrix.device }}.yaml pr/bench-${{ matrix.device }}.yaml
+
+      - name: Archive Logs
+        uses: actions/upload-artifact@v3
+        if:   always()
+        with:
+          name: logs-${{ matrix.device }}
+          path: |
+            pr/bench-${{ matrix.device }}.*
+            pr/build/benchmarks/*
+            master/bench-${{ matrix.device }}.*
+            master/build/benchmarks/*

.github/workflows/count.yml

@@ -0,0 +1,40 @@
+name: Check Line Counts
+on:
+  push:
+
+  pull_request:
+
+  workflow_dispatch:
+
+jobs:
+  sz:
+    name: Core MFC Line Difference
+    permissions:
+      contents: read
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code from PR branch
+        uses: actions/checkout@v4
+        with:
+          path: pr
+
+      - name: Checkout code from MFC master
+        uses: actions/checkout@v4
+        with:
+          repository: ${{ github.event.pull_request.repository }}
+          ref:        ${{ github.event.pull_request.base.ref }}
+          path:       base
+          # repository: MFlowCode/MFC
+          # ref:        master
+          # path:       base
+
+      - name: Get Line Diff
+        run: |
+          BASE="$GITHUB_WORKSPACE/base"
+          PR="$GITHUB_WORKSPACE/pr"
+          cd $BASE
+          export MFC_PR=$PR
+          pwd
+          ./mfc.sh count_diff
+

.github/workflows/docker.yml

@@ -27,4 +27,3 @@ jobs:
         file: toolchain/Dockerfile
         push: true
         tags: ${{ secrets.DOCKER_USERNAME }}/mfc:latest
-

.github/workflows/docs.yml

@@ -11,7 +11,12 @@ jobs:
   docs:
     name:    Build & Publish
     runs-on: ubuntu-latest
-
+
+    if: github.repository == 'MFlowCode/MFC'
+    concurrency:
+      group: docs-publish
+      cancel-in-progress: true
+
     steps:
     - uses: actions/checkout@v3
 

.github/workflows/links.yml

@@ -0,0 +1,13 @@
+name: LinkChecker
+
+on: push
+
+jobs:
+  markdown-link-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1
+      with:
+        config-file: '.link_config.json'
+        use-verbose-mode: 'yes'

.github/workflows/lint.yml

@@ -0,0 +1,19 @@
+name: Lint
+
+on:
+  push:
+
+  pull_request:
+
+  workflow_dispatch:
+
+jobs:
+  docs:
+    name:    Lint Toolchain
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Lint the toolchain
+      run: ./mfc.sh lint

.github/workflows/phoenix/bench.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+n_ranks=4
+
+if [ "$job_device" == "gpu" ]; then
+    n_ranks=$(nvidia-smi -L | wc -l)        # number of GPUs on node
+    gpu_ids=$(seq -s ' ' 0 $(($n_ranks-1))) # 0,1,2,...,gpu_count-1
+    device_opts="--gpu -g $gpu_ids"
+fi
+
+./mfc.sh bench -j $(nproc) -o "$job_slug.yaml" -- -c phoenix $device_opts -n $n_ranks

.github/workflows/phoenix/submit.sh

@@ -0,0 +1,63 @@
+#!/bin/bash
+
+set -e
+
+usage() {
+    echo "Usage: $0 [script.sh] [cpu|gpu]"
+}
+
+if [ ! -z "$1" ]; then
+    sbatch_script_contents=`cat $1`
+else
+    usage
+    exit 1
+fi
+
+sbatch_cpu_opts="\
+#SBATCH -p cpu-small               # partition
+#SBATCH --ntasks-per-node=24       # Number of cores per node required
+#SBATCH --mem-per-cpu=2G           # Memory per core\
+"
+
+sbatch_gpu_opts="\
+#SBATCH -CV100-16GB
+#SBATCH -G2\
+"
+
+if [ "$2" == "cpu" ]; then
+    sbatch_device_opts="$sbatch_cpu_opts"
+elif [ "$2" == "gpu" ]; then
+    sbatch_device_opts="$sbatch_gpu_opts"
+else
+    usage
+    exit 1
+fi
+
+job_slug="`basename "$1" | sed 's/\.sh$//' | sed 's/[^a-zA-Z0-9]/-/g'`-$2"
+
+sbatch <<EOT
+#!/bin/bash
+#SBATCH -Jshb-$job_slug            # Job name
+#SBATCH --account=gts-sbryngelson3 # charge account
+#SBATCH -N1                        # Number of nodes required
+$sbatch_device_opts
+#SBATCH -t 04:00:00                # Duration of the job (Ex: 15 mins)
+#SBATCH -q embers                  # QOS Name
+#SBATCH -o$job_slug.out            # Combined output and error messages file
+#SBATCH -W                         # Do not exit until the submitted job terminates.
+
+set -e
+set -x
+
+cd "\$SLURM_SUBMIT_DIR"
+echo "Running in $(pwd):"
+
+job_slug="$job_slug"
+job_device="$2"
+
+. ./mfc.sh load -c p -m $2
+
+$sbatch_script_contents
+
+EOT
+

.github/workflows/phoenix/test.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+build_opts=""
+if [ "$job_device" == "gpu" ]; then
+    build_opts="--gpu"
+fi
+
+./mfc.sh build -j 8 $build_opts
+
+n_test_threads=8
+
+if [ "$job_device" == "gpu" ]; then
+    gpu_count=$(nvidia-smi -L | wc -l)        # number of GPUs on node
+    gpu_ids=$(seq -s ' ' 0 $(($gpu_count-1))) # 0,1,2,...,gpu_count-1
+    device_opts="-g $gpu_ids"
+    n_test_threads=`expr $gpu_count \* 2`
+fi
+
+./mfc.sh test -a -j $n_test_threads $device_opts -- -c phoenix
+

.github/workflows/pretty.yml

@@ -0,0 +1,21 @@
+name: Pretty
+
+on:
+  push:
+
+  pull_request:
+
+  workflow_dispatch:
+
+jobs:
+  docs:
+    name:    Code formatting
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Check formatting
+      run: |
+        ./mfc.sh format
+        git diff --exit-code

.github/workflows/spelling.yml

@@ -12,4 +12,4 @@ jobs:
       uses: actions/checkout@v3
 
     - name: Spell Check
-      uses: crate-ci/typos@master
+      uses: crate-ci/typos@master

.github/workflows/ci.yml → .github/workflows/test.yml

@@ -109,24 +109,22 @@ jobs:
         device: ['cpu', 'gpu']
     runs-on:
       group:  phoenix
-      labels: self-hosted
+      labels: gt
     steps:
       - name: Clone
         uses: actions/checkout@v3
 
-      - name: Build
-        run:  |
-          . ./mfc.sh load -c p -m gpu
-          ./mfc.sh build -j 2 $(if [ '${{ matrix.device }}' == 'gpu' ]; then echo '--gpu'; fi)
+      - name: Build & Test
+        run:  bash .github/workflows/phoenix/submit.sh .github/workflows/phoenix/test.sh ${{ matrix.device }}
 
-      - name: Test
-        run: |
-          . ./mfc.sh load -c p -m gpu
-          mv misc/run-phoenix-release-${{ matrix.device }}.sh ./
-          sbatch run-phoenix-release-${{ matrix.device }}.sh
+      - name: Print Logs
+        if:   always()
+        run:  cat test-${{ matrix.device }}.out
 
-      - name: Print
-        if: always()
-        run: |
-          cat test.out
+      - name: Archive Logs
+        uses: actions/upload-artifact@v3
+        if:   always()
+        with:
+          name: logs
+          path: test-${{ matrix.device }}.out
 

.gitignore

@@ -1,3 +1,8 @@
+node_modules/
+package.json
+yarn.lock
+docker-compose.yml
+
 /build/
 .vscode/
 src/*/include/case.fpp
@@ -19,8 +24,6 @@ __pycache__
 /tests/*/**
 !/tests/*/golden.txt
 !/tests/*/golden-metadata.txt
-!/tests/*/case.py
-!/tests/*/README.md
 
 # NVIDIA Nsight Compute
 *.nsys-rep

.link_config.json

@@ -0,0 +1,32 @@
+{
+  "ignorePatterns": [
+    {
+      "pattern": "examples.md"
+    }
+  ],
+  "replacementPatterns": [
+    {
+      "pattern": "^.attachments",
+      "replacement": "file://some/conventional/folder/.attachments"
+    },
+    {
+      "pattern": "^/",
+      "replacement": "{{BASEURL}}/"
+    }
+  ],
+  "httpHeaders": [
+    {
+      "urls": ["https://example.com"],
+      "headers": {
+        "Authorization": "Basic Zm9vOmJhcg==",
+        "Foo": "Bar"
+      }
+    }
+  ],
+  "timeout": "20s",
+  "retryOn429": true,
+  "retryCount": 5,
+  "fallbackRetryDelay": "30s",
+  "aliveStatusCodes": [200, 206, 403]
+}
+

.typos.toml

@@ -10,10 +10,6 @@ AttributeIDSupressMenu = "AttributeIDSupressMenu"
 INOUT = "INOUT"
 WRONLY = "WRONLY"
 nd = "nd"
-# Childs = "Childs"
-# myu = "myu"
-
-
 
 [files]
 extend-exclude = ["docs/documentation/references*", "tests/"]