Squashed commit of the following:

commit d792c63
Author: Weiqun Zhang <[email protected]>
Date:   Wed Sep 11 10:07:00 2024 -0500

    Simplify cache cleanup actions (AMReX-Fluids#129)

    In our old approach, a workflow file contains a job that uploads the PR
    number as an artifact. While the PR is still open, the workflow_run
    triggered by it will download the artifact and use the information to
    clean up all except the last used cache associated with that original
    workflow. When a PR is merged or closed, there will be a post-pr
    workflow that uploads the PR number as an artifact and triggers a
    workflow_run that clean up all caches associated with the PR. The reason
    we did it this way was in the cache cleanup workflows, we did not find
    an easy way to get the number of the PR triggering them. This is not
    convenient because we have to add jobs uploading artifacts to workflow
    files.

    After some experiments, we have found a reliable way to find the PR
    number without using artifacts. The workflow_run's payload always
    contains the head SHA of the commit that triggers it, whether the PR
    comes from a fork or not. We can then use `gh pr list` to search for
    that head and obtain the PR number.

commit a007c21
Author: Candace Gilet <[email protected]>
Date:   Wed Sep 11 16:57:56 2024 +0200

    Fix case of multiple tracers with default initial conditions. Issue (AMReX-Fluids#132)

    introduced in PR#131

.github/workflows/cleanup-cache-postpr.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   CleanUpCcacheCachePostPR:
-    name: Clean Up Ccahe Cache Post PR
+    name: Clean Up Ccache Cache Post PR
     runs-on: ubuntu-latest
     permissions:
       actions: write
@@ -17,21 +17,27 @@ jobs:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v4
-      - name: Clean up ccahe
+      - name: Clean up ccache
         run: |
           gh extension install actions/gh-actions-cache
 
           REPO=${{ github.repository }}
 
-          gh run download ${{ github.event.workflow_run.id }} -n pr_number
-          pr_number=`cat pr_number.txt`
+          # For debugging cat ${GITHUB_EVENT_PATH} to see the payload.
+
+          pr_head_sha=${{ github.event.workflow_run.head_sha }}
+          pr_number=$(gh pr list --state all --search $pr_head_sha --json number --jq '.[0].number')
+          echo "Post-PR cache cleanup for PR ${pr_number}"
           BRANCH=refs/pull/${pr_number}/merge
 
           # Setting this to not fail the workflow while deleting cache keys.
           set +e
 
           keys=$(gh actions-cache list -L 100 -R $REPO -B $BRANCH | cut -f 1)
+          # $keys might contain spaces. Thus we set IFS to \n.
+          IFS=$'\n'
           for k in $keys
           do
-            gh actions-cache delete $k -R $REPO -B $BRANCH --confirm
+            gh actions-cache delete "$k" -R $REPO -B $BRANCH --confirm
           done
+          unset IFS

.github/workflows/cleanup-cache.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   CleanUpCcacheCache:
-    name: Clean Up Ccahe Cache for ${{ github.event.workflow_run.name }}
+    name: Clean Up Ccache Cache for ${{ github.event.workflow_run.name }}
     runs-on: ubuntu-latest
     permissions:
       actions: write
@@ -17,7 +17,7 @@ jobs:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v4
-      - name: Clean up ccahe
+      - name: Clean up ccache
         run: |
           gh extension install actions/gh-actions-cache
 
@@ -27,11 +27,14 @@ jobs:
           EVENT=${{ github.event.workflow_run.event }}
 
           # Triggering workflow run name (e.g., LinuxClang)
-          WORKFLOW_NAME=${{ github.event.workflow_run.name }}
+          WORKFLOW_NAME="${{ github.event.workflow_run.name }}"
+
+          # For debugging, cat ${GITHUB_EVENT_PATH} to see the payload.
 
           if [[ $EVENT == "pull_request" ]]; then
-            gh run download ${{ github.event.workflow_run.id }} -n pr_number
-            pr_number=`cat pr_number.txt`
+            pr_head_sha=${{ github.event.workflow_run.head_sha }}
+            pr_number=$(gh pr list --search $pr_head_sha --json number --jq '.[0].number')
+            echo "Clean up cache for PR ${pr_number}"
             BRANCH=refs/pull/${pr_number}/merge
           else
             BRANCH=refs/heads/${{ github.event.workflow_run.head_branch }}
@@ -45,16 +48,20 @@ jobs:
           # The goal is to keep the last used key of each job and delete all others.
 
           # something like ccache-LinuxClang-
-          keyprefix=ccache-${WORKFLOW_NAME}-
+          keyprefix="ccache-${WORKFLOW_NAME}-"
 
-          cached_jobs=$(gh actions-cache list -L 100 -R $REPO -B $BRANCH --key $keyprefix | awk -F '-git-' '{print $1}' | sort | uniq)
+          cached_jobs=$(gh actions-cache list -L 100 -R $REPO -B $BRANCH --key "$keyprefix" | awk -F '-git-' '{print $1}' | sort | uniq)
 
           # cached_jobs is something like "ccache-LinuxClang-configure-1d ccache-LinuxClang-configure-2d".
+          # It might also contain spaces. Thus we set IFS to \n.
+          IFS=$'\n'
           for j in $cached_jobs
           do
-            old_keys=$(gh actions-cache list -L 100 -R $REPO -B $BRANCH --key ${j}-git- --sort last-used | cut -f 1 | tail -n +2)
+            # Delete all entries except the last used one
+            old_keys=$(gh actions-cache list -L 100 -R $REPO -B $BRANCH --key "${j}-git-" --sort last-used | cut -f 1 | tail -n +2)
             for k in $old_keys
             do
-              gh actions-cache delete $k -R $REPO -B $BRANCH --confirm
+              gh actions-cache delete "$k" -R $REPO -B $BRANCH --confirm
             done
           done
+          unset IFS

.github/workflows/cuda.yml

@@ -143,18 +143,3 @@ jobs:
 
         ccache -s
         du -hs ~/.cache/ccache
-
-  save_pr_number:
-    if: github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Save PR number
-        env:
-          PR_NUMBER: ${{ github.event.number }}
-        run: |
-          echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pr_number
-          path: pr_number.txt
-          retention-days: 1

.github/workflows/gcc.yml

@@ -322,18 +322,3 @@ jobs:
         export OMP_NUM_THREADS=2
         cd ${{ github.workspace }}/incflo
         build/incflo.ex test_no_eb_2d/benchmark.bouss_bubble_god max_step=10 incflo.verbose=1 mac_proj.verbose=1 nodal_proj.verbose=1
-
-  save_pr_number:
-    if: github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Save PR number
-        env:
-          PR_NUMBER: ${{ github.event.number }}
-        run: |
-          echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pr_number
-          path: pr_number.txt
-          retention-days: 1

.github/workflows/hip.yml

@@ -75,18 +75,3 @@ jobs:
 
         ccache -s
         du -hs ~/.cache/ccache
-
-  save_pr_number:
-    if: github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Save PR number
-        env:
-          PR_NUMBER: ${{ github.event.number }}
-        run: |
-          echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pr_number
-          path: pr_number.txt
-          retention-days: 1

.github/workflows/post-pr.yml

@@ -4,17 +4,13 @@ on:
     types:
       - closed
 
+# This workflow does not have the permission to clean up cache for PRs
+# originated from a fork. The purpose here is to trigger a workflow_run
+# cleanup-cache-postpr.yml that has the right permission.
+
 jobs:
-  cleanup:
+  noop:
     runs-on: ubuntu-latest
     steps:
-      - name: Save PR number
-        env:
-          PR_NUMBER: ${{ github.event.number }}
-        run: |
-          echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pr_number
-          path: pr_number.txt
-          retention-days: 1
+      - name: No OP
+        run: echo "This workflow is going to trigger CleanUpCachePostPR."

.github/workflows/sycl.yml

@@ -74,18 +74,3 @@ jobs:
 
         ccache -s
         du -hs ~/.cache/ccache
-
-  save_pr_number:
-    if: github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Save PR number
-        env:
-          PR_NUMBER: ${{ github.event.number }}
-        run: |
-          echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pr_number
-          path: pr_number.txt
-          retention-days: 1

src/setup/init.cpp

@@ -123,13 +123,23 @@ void incflo::ReadParameters ()
             amrex::Abort("We currently require cfl <= 1.0 when using this advection scheme");
         }
 
+        pp.query("ntrac", m_ntrac);
+
+        if (m_ntrac <= 0) m_advect_tracer = false;
+
+        if (m_ntrac < 1) {
+            amrex::Abort("We currently require at least one tracer");
+        }
+
         // Initial conditions
         pp.query("probtype", m_probtype);
         pp.query("ic_u", m_ic_u);
         pp.query("ic_v", m_ic_v);
         pp.query("ic_w", m_ic_w);
         pp.query("ic_p", m_ic_p);
-        pp.queryarr("ic_t", m_ic_t);
+        if ( !pp.queryarr("ic_t", m_ic_t, 0, m_ntrac) ) {
+            m_ic_t.resize(m_ntrac, 0.);
+        }
 
         // Viscosity (if constant)
         pp.query("mu", m_mu);
@@ -138,14 +148,6 @@ void incflo::ReadParameters ()
         pp.query("ro_0", m_ro_0);
         AMREX_ALWAYS_ASSERT(m_ro_0 >= 0.0);
 
-        pp.query("ntrac", m_ntrac);
-
-        if (m_ntrac <= 0) m_advect_tracer = false;
-
-        if (m_ntrac < 1) {
-            amrex::Abort("We currently require at least one tracer");
-        }
-
         // Scalar diffusion coefficients
         m_mu_s.resize(m_ntrac, 0.0);
         pp.queryarr("mu_s", m_mu_s, 0, m_ntrac );