Fix self-hosted CI robustness: build cache, SLURM QOS, and submit resilience

.github/scripts/run_monitored_slurm_job.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+# Run monitor_slurm_job.sh and recover if the monitor is killed (e.g. SIGKILL
+# from the runner OS) before the SLURM job completes.  When the monitor exits
+# non-zero, sacct is used to verify the job's actual final state; if the SLURM
+# job succeeded we exit 0 so the CI step is not falsely marked as failed.
+#
+# Usage: run_monitored_slurm_job.sh <job_id> <output_file>
+
+set -euo pipefail
+
+if [ $# -ne 2 ]; then
+    echo "Usage: $0 <job_id> <output_file>"
+    exit 1
+fi
+
+job_id="$1"
+output_file="$2"
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+monitor_exit=0
+bash "$SCRIPT_DIR/monitor_slurm_job.sh" "$job_id" "$output_file" || monitor_exit=$?
+
+if [ "$monitor_exit" -ne 0 ]; then
+    echo "Monitor exited with code $monitor_exit; re-checking SLURM job $job_id final state..."
+    # Give the SLURM epilog time to finalize if the job just finished
+    sleep 30
+    final_state=$(sacct -j "$job_id" -n -X -P -o State 2>/dev/null | head -n1 | cut -d'|' -f1 | tr -d ' ' || echo "UNKNOWN")
+    final_exit=$(sacct -j "$job_id" -X --format=ExitCode --noheader --parsable2 2>/dev/null | head -n1 | tr -d ' ' || echo "")
+    echo "Final SLURM state=$final_state exit=$final_exit"
+    if [ "$final_state" = "COMPLETED" ] && [ "$final_exit" = "0:0" ]; then
+        echo "SLURM job $job_id completed successfully despite monitor failure — continuing."
+    else
+        echo "ERROR: SLURM job $job_id did not complete successfully (state=$final_state exit=$final_exit)"
+        exit 1
+    fi
+fi

.github/scripts/submit_and_monitor_bench.sh

@@ -14,12 +14,18 @@ device="$2"
 interface="$3"
 cluster="$4"
 
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
 echo "[$dir] Submitting benchmark for $device-$interface on $cluster..."
 cd "$dir"
 
-# Submit and monitor job (submit.sh auto-detects bench mode from script name)
-bash .github/workflows/$cluster/submit.sh \
-    .github/workflows/$cluster/bench.sh "$device" "$interface"
+# Always use the PR's submit.sh so both master and PR builds benefit from the
+# run_monitored_slurm_job.sh SIGKILL recovery wrapper.  The bench script is
+# still resolved relative to the current directory (master/ or pr/) so the
+# correct branch code is benchmarked.  SLURM_SUBMIT_DIR ensures the job runs
+# in the right directory regardless of which submit.sh is invoked.
+PR_SUBMIT="${SCRIPT_DIR}/../workflows/${cluster}/submit.sh"
+bash "$PR_SUBMIT" .github/workflows/$cluster/bench.sh "$device" "$interface"
 
 # Verify the YAML output file was created
 job_slug="bench-$device-$interface"

.github/workflows/bench.yml

@@ -88,7 +88,7 @@ jobs:
     runs-on:
       group: ${{ matrix.group }}
       labels: ${{ matrix.labels }}
-    timeout-minutes: 480
+    timeout-minutes: 240
     steps:
       - name: Clone - PR
         uses: actions/checkout@v4

.github/workflows/frontier/bench.sh

@@ -2,8 +2,11 @@
 
 source .github/scripts/bench-preamble.sh
 
+# Cap parallel jobs at 64 to avoid overwhelming MPI daemons on large nodes.
+n_jobs=$(( $(nproc) > 64 ? 64 : $(nproc) ))
+
 if [ "$job_device" = "gpu" ]; then
     ./mfc.sh bench --mem 4 -j $n_ranks -o "$job_slug.yaml" -- -c $job_cluster $device_opts -n $n_ranks
 else
-    ./mfc.sh bench --mem 1 -j $(nproc) -o "$job_slug.yaml" -- -c $job_cluster $device_opts -n $n_ranks
+    ./mfc.sh bench --mem 1 -j $n_jobs -o "$job_slug.yaml" -- -c $job_cluster $device_opts -n $n_ranks
 fi

.github/workflows/frontier/build.sh

@@ -20,10 +20,7 @@ build_opts="$gpu_opts"
 
 . ./mfc.sh load -c $compiler_flag -m $([ "$job_device" = "gpu" ] && echo "g" || echo "c")
 
-# Only set up build cache for test suite, not benchmarks
-if [ "$run_bench" != "bench" ]; then
-    source .github/scripts/setup-build-cache.sh "$cluster_name" "$job_device" "$job_interface"
-fi
+rm -rf build
 
 source .github/scripts/retry-build.sh
 if [ "$run_bench" == "bench" ]; then

.github/workflows/frontier/submit.sh

@@ -25,13 +25,6 @@ else
     exit 1
 fi
 
-# Detect job type from submitted script basename
-script_basename="$(basename "$1" .sh)"
-case "$script_basename" in
-    bench*) job_type="bench" ;;
-    *)      job_type="test"  ;;
-esac
-
 if [ "$2" = "cpu" ]; then
     sbatch_device_opts="\
 #SBATCH -n 32                       # Number of cores required"
@@ -44,17 +37,10 @@ else
 fi
 
 # Select SBATCH params based on job type
-if [ "$job_type" = "bench" ]; then
-    sbatch_account="#SBATCH -A ENG160"
-    sbatch_time="#SBATCH -t 05:59:00"
-    sbatch_partition="#SBATCH -p extended"
-    sbatch_extra=""
-else
-    sbatch_account="#SBATCH -A CFD154"
-    sbatch_time="#SBATCH -t 01:59:00"
-    sbatch_partition="#SBATCH -p batch"
-    sbatch_extra="#SBATCH --qos=normal"
-fi
+sbatch_account="#SBATCH -A CFD154"
+sbatch_time="#SBATCH -t 01:59:00"
+sbatch_partition="#SBATCH -p batch"
+sbatch_extra="#SBATCH --qos=normal"
 
 shard_suffix=""
 if [ -n "$4" ]; then
@@ -102,5 +88,4 @@ fi
 
 echo "Submitted batch job $job_id"
 
-# Use resilient monitoring instead of sbatch -W
-bash "$SCRIPT_DIR/../../scripts/monitor_slurm_job.sh" "$job_id" "$output_file"
+bash "$SCRIPT_DIR/../../scripts/run_monitored_slurm_job.sh" "$job_id" "$output_file"

.github/workflows/phoenix/bench.sh

@@ -2,7 +2,11 @@
 
 source .github/scripts/bench-preamble.sh
 
-tmpbuild=/storage/scratch1/6/sbryngelson3/mytmp_build
+# Cap parallel jobs at 64 to avoid overwhelming MPI daemons on large nodes
+# (GNR nodes have 192 cores but nproc is too aggressive for build/bench).
+n_jobs=$(( $(nproc) > 64 ? 64 : $(nproc) ))
+
+tmpbuild=/storage/project/r-sbryngelson3-0/sbryngelson3/mytmp_build
 currentdir=$tmpbuild/run-$(( RANDOM % 900 ))
 mkdir -p $tmpbuild
 mkdir -p $currentdir
@@ -15,10 +19,12 @@ else
     bench_opts="--mem 1"
 fi
 
+rm -rf build
+
 source .github/scripts/retry-build.sh
-RETRY_CLEAN_CMD="./mfc.sh clean" retry_build ./mfc.sh build -j $(nproc) $build_opts || exit 1
+RETRY_CLEAN_CMD="./mfc.sh clean" retry_build ./mfc.sh build -j $n_jobs $build_opts || exit 1
 
-./mfc.sh bench $bench_opts -j $(nproc) -o "$job_slug.yaml" -- -c phoenix-bench $device_opts -n $n_ranks
+./mfc.sh bench $bench_opts -j $n_jobs -o "$job_slug.yaml" -- -c phoenix-bench $device_opts -n $n_ranks
 
 sleep 10
 rm -rf "$currentdir" || true

.github/workflows/phoenix/submit.sh

@@ -94,6 +94,5 @@ fi
 
 echo "Submitted batch job $job_id"
 
-# Use resilient monitoring instead of sbatch -W
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-bash "$SCRIPT_DIR/../../scripts/monitor_slurm_job.sh" "$job_id" "$output_file"
+bash "$SCRIPT_DIR/../../scripts/run_monitored_slurm_job.sh" "$job_id" "$output_file"

.github/workflows/phoenix/test.sh

@@ -3,11 +3,10 @@
 source .github/scripts/gpu-opts.sh
 build_opts="$gpu_opts"
 
-# Set up persistent build cache
-source .github/scripts/setup-build-cache.sh phoenix "$job_device" "$job_interface"
+rm -rf build
 
-# Build with retry; smoke-test cached binaries to catch architecture mismatches
-# (SIGILL from binaries compiled on a different compute node).
+# Build with retry; smoke-test the freshly built syscheck binary to catch
+# architecture mismatches (SIGILL from binaries compiled on a different compute node).
 source .github/scripts/retry-build.sh
 RETRY_VALIDATE_CMD='syscheck_bin=$(find build/install -name syscheck -type f 2>/dev/null | head -1); [ -z "$syscheck_bin" ] || "$syscheck_bin" > /dev/null 2>&1' \
     retry_build ./mfc.sh test -v --dry-run -j 8 $build_opts || exit 1

CMakeLists.txt

@@ -224,13 +224,24 @@ endif()
 
 if (CMAKE_BUILD_TYPE STREQUAL "Release")
     # Processor tuning: Check if we can target the host's native CPU's ISA.
-    CHECK_FORTRAN_COMPILER_FLAG("-march=native" SUPPORTS_MARCH_NATIVE)
-    if (SUPPORTS_MARCH_NATIVE)
-        add_compile_options($<$<COMPILE_LANGUAGE:Fortran>:-march=native>)
-    else()
-    	CHECK_FORTRAN_COMPILER_FLAG("-mcpu=native" SUPPORTS_MCPU_NATIVE)
-        if (SUPPORTS_MCPU_NATIVE)
-            add_compile_options($<$<COMPILE_LANGUAGE:Fortran>:-mcpu=native>)
+    # Skip for gcov builds — -march=native on newer CPUs (e.g. Granite Rapids)
+    # can emit instructions the system assembler doesn't support.
+    if (NOT MFC_GCov)
+        CHECK_FORTRAN_COMPILER_FLAG("-march=native" SUPPORTS_MARCH_NATIVE)
+        if (SUPPORTS_MARCH_NATIVE)
+            add_compile_options($<$<COMPILE_LANGUAGE:Fortran>:-march=native>)
+            # Disable AVX-512 FP16: gfortran ≥12 emits vmovw instructions on
+            # Granite Rapids CPUs, but binutils <2.38 cannot assemble them.
+            # FP16 is unused in MFC's double-precision computations.
+            CHECK_FORTRAN_COMPILER_FLAG("-mno-avx512fp16" SUPPORTS_MNO_AVX512FP16)
+            if (SUPPORTS_MNO_AVX512FP16)
+                add_compile_options($<$<COMPILE_LANGUAGE:Fortran>:-mno-avx512fp16>)
+            endif()
+        else()
+            CHECK_FORTRAN_COMPILER_FLAG("-mcpu=native" SUPPORTS_MCPU_NATIVE)
+            if (SUPPORTS_MCPU_NATIVE)
+                add_compile_options($<$<COMPILE_LANGUAGE:Fortran>:-mcpu=native>)
+            endif()
         endif()
     endif()
 

benchmarks/5eq_rk3_weno3_hllc/case.py

@@ -191,8 +191,8 @@
             "cyl_coord": "F",
             "dt": dt,
             "t_step_start": 0,
-            "t_step_stop": ARGS["steps"] if ARGS["steps"] is not None else int(7 * (5 * size + 5)),
-            "t_step_save": ARGS["steps"] if ARGS["steps"] is not None else int(7 * (5 * size + 5)),
+            "t_step_stop": ARGS["steps"] if ARGS["steps"] is not None else int(2 * (5 * size + 5)),
+            "t_step_save": ARGS["steps"] if ARGS["steps"] is not None else int(2 * (5 * size + 5)),
             # Simulation Algorithm Parameters
             "num_patches": 3,
             "model_eqns": 2,

benchmarks/hypo_hll/case.py

@@ -44,8 +44,8 @@
             "p": Nz,
             "dt": 1e-8,
             "t_step_start": 0,
-            "t_step_stop": ARGS["steps"] if ARGS["steps"] is not None else int(7 * (5 * size + 5)),
-            "t_step_save": ARGS["steps"] if ARGS["steps"] is not None else int(7 * (5 * size + 5)),
+            "t_step_stop": ARGS["steps"] if ARGS["steps"] is not None else int(2 * (5 * size + 5)),
+            "t_step_save": ARGS["steps"] if ARGS["steps"] is not None else int(2 * (5 * size + 5)),
             # Simulation Algorithm Parameters
             "num_patches": 2,
             "model_eqns": 2,

benchmarks/ibm/case.py

@@ -48,8 +48,8 @@
             "p": Nz,
             "dt": mydt,
             "t_step_start": 0,
-            "t_step_stop": ARGS["steps"] if ARGS["steps"] is not None else int(7 * (5 * size + 5)),
-            "t_step_save": ARGS["steps"] if ARGS["steps"] is not None else int(7 * (5 * size + 5)),
+            "t_step_stop": ARGS["steps"] if ARGS["steps"] is not None else int(2 * (5 * size + 5)),
+            "t_step_save": ARGS["steps"] if ARGS["steps"] is not None else int(2 * (5 * size + 5)),
             # Simulation Algorithm Parameters
             "num_patches": 1,
             "model_eqns": 2,

benchmarks/igr/case.py

@@ -63,8 +63,8 @@
             "cyl_coord": "F",
             "dt": dt,
             "t_step_start": 0,
-            "t_step_stop": ARGS["steps"] if ARGS["steps"] is not None else int(7 * (5 * size + 5)),
-            "t_step_save": ARGS["steps"] if ARGS["steps"] is not None else int(7 * (5 * size + 5)),
+            "t_step_stop": ARGS["steps"] if ARGS["steps"] is not None else int(2 * (5 * size + 5)),
+            "t_step_save": ARGS["steps"] if ARGS["steps"] is not None else int(2 * (5 * size + 5)),
             # Simulation Algorithm Parameters
             "num_patches": 1,
             "model_eqns": 2,

benchmarks/viscous_weno5_sgb_acoustic/case.py

@@ -94,8 +94,8 @@
             "p": Nz,
             "dt": dt,
             "t_step_start": 0,
-            "t_step_stop": ARGS["steps"] if ARGS["steps"] is not None else int(6 * (5 * size + 5)),
-            "t_step_save": ARGS["steps"] if ARGS["steps"] is not None else int(6 * (5 * size + 5)),
+            "t_step_stop": ARGS["steps"] if ARGS["steps"] is not None else int(2 * (5 * size + 5)),
+            "t_step_save": ARGS["steps"] if ARGS["steps"] is not None else int(2 * (5 * size + 5)),
             # Simulation Algorithm Parameters
             "num_patches": 2,
             "model_eqns": 2,

toolchain/mfc/build.py

@@ -1,6 +1,7 @@
 import os, typing, hashlib, dataclasses, subprocess, re, time, sys, threading, queue
 
 from rich.panel import Panel
+from rich.text  import Text
 from rich.progress import Progress, SpinnerColumn, BarColumn, TextColumn, TimeElapsedColumn, TaskProgressColumn
 
 from .case    import Case
@@ -273,14 +274,14 @@ def _show_build_error(result: subprocess.CompletedProcess, stage: str):
         stdout_text = result.stdout if isinstance(result.stdout, str) else result.stdout.decode('utf-8', errors='replace')
         stdout_text = stdout_text.strip()
         if stdout_text:
-            cons.raw.print(Panel(stdout_text, title="Output", border_style="yellow"))
+            cons.raw.print(Panel(Text(stdout_text), title="Output", border_style="yellow"))
 
     # Show stderr if available
     if result.stderr:
         stderr_text = result.stderr if isinstance(result.stderr, str) else result.stderr.decode('utf-8', errors='replace')
         stderr_text = stderr_text.strip()
         if stderr_text:
-            cons.raw.print(Panel(stderr_text, title="Errors", border_style="red"))
+            cons.raw.print(Panel(Text(stderr_text), title="Errors", border_style="red"))
 
     cons.print()