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benchmarks hardening! #1078
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benchmarks hardening! #1078
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e8090bd
benchmarks hardening!
sbryngelson 8c01b99
lint error
sbryngelson 2e1eb87
minor
sbryngelson 0668fed
forks look nicer now i think
sbryngelson f79f4d1
more fixing!
sbryngelson 76a6e63
clean linter
sbryngelson 7333098
fix some more suggestions
sbryngelson b62854c
more hardening :O
sbryngelson adc26a0
fix bug
sbryngelson 0b31278
harden against h5dump missing
sbryngelson b0eca32
debug
sbryngelson 0589b85
lint fix
sbryngelson 6d830f3
fix brokenness
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,139 @@ | ||
| #!/bin/bash | ||
| # Monitor a SLURM job and stream its output in real-time | ||
| # Usage: monitor_slurm_job.sh <job_id> <output_file> | ||
|
|
||
| set -e | ||
|
|
||
| if [ $# -ne 2 ]; then | ||
| echo "Usage: $0 <job_id> <output_file>" | ||
| exit 1 | ||
| fi | ||
|
|
||
| job_id="$1" | ||
| output_file="$2" | ||
|
|
||
| echo "Submitted batch job $job_id" | ||
| echo "Monitoring output file: $output_file" | ||
|
|
||
| # Wait for file to appear with retry logic for transient squeue failures | ||
| echo "Waiting for job to start..." | ||
| squeue_retries=0 | ||
| max_squeue_retries=5 | ||
| while [ ! -f "$output_file" ]; do | ||
| # Check if job is still queued/running | ||
| if squeue -j "$job_id" &>/dev/null; then | ||
| squeue_retries=0 # Reset on success | ||
| sleep 5 | ||
| else | ||
| squeue_retries=$((squeue_retries + 1)) | ||
| if [ $squeue_retries -ge $max_squeue_retries ]; then | ||
| # Job not in queue and output file doesn't exist | ||
| if [ ! -f "$output_file" ]; then | ||
| echo "ERROR: Job $job_id not in queue and output file not created" | ||
| exit 1 | ||
| fi | ||
| break | ||
| fi | ||
| # Exponential backoff | ||
| sleep_time=$((2 ** squeue_retries)) | ||
| echo "Warning: squeue check failed, retrying in ${sleep_time}s..." | ||
| sleep $sleep_time | ||
| fi | ||
| done | ||
|
|
||
| echo "=== Streaming output for job $job_id ===" | ||
| # Stream output while job runs | ||
| tail -f "$output_file" & | ||
| tail_pid=$! | ||
|
|
||
| # Wait for job to complete with retry logic for transient squeue failures | ||
| squeue_failures=0 | ||
| while true; do | ||
| if squeue -j "$job_id" &>/dev/null; then | ||
| squeue_failures=0 | ||
| else | ||
| squeue_failures=$((squeue_failures + 1)) | ||
| # Check if job actually completed using sacct (if available) | ||
| if [ $squeue_failures -ge 3 ]; then | ||
| if command -v sacct >/dev/null 2>&1; then | ||
| state=$(sacct -j "$job_id" --format=State --noheader 2>/dev/null | head -n1 | awk '{print $1}') | ||
| # Consider job done only if it reached a terminal state | ||
| case "$state" in | ||
| COMPLETED|FAILED|CANCELLED|TIMEOUT|OUT_OF_MEMORY) | ||
| break | ||
| ;; | ||
| *) | ||
| # treat as transient failure, reset failures and continue polling | ||
| squeue_failures=0 | ||
| ;; | ||
| esac | ||
| else | ||
| # No sacct: avoid false positive by doing an extra check cycle | ||
| squeue_failures=2 | ||
| fi | ||
| fi | ||
| fi | ||
| sleep 5 | ||
| done | ||
|
|
||
| # Wait for output file to finish growing (stabilize) before stopping tail | ||
| if [ -f "$output_file" ]; then | ||
| last_size=-1 | ||
| same_count=0 | ||
| while true; do | ||
| size=$(stat -c%s "$output_file" 2>/dev/null || echo -1) | ||
| if [ "$size" -eq "$last_size" ] && [ "$size" -ge 0 ]; then | ||
| same_count=$((same_count + 1)) | ||
| else | ||
| same_count=0 | ||
| last_size=$size | ||
| fi | ||
| # two consecutive stable checks (~10s) implies file likely flushed | ||
| if [ $same_count -ge 2 ]; then | ||
| break | ||
| fi | ||
| sleep 5 | ||
| done | ||
| fi | ||
|
|
||
| # Stop tailing | ||
| kill $tail_pid 2>/dev/null || true | ||
|
|
||
| echo "" | ||
| echo "=== Final output ===" | ||
| cat "$output_file" | ||
|
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||
| # Check exit status with sacct fallback | ||
| exit_code="" | ||
|
|
||
| # Try scontrol first (works for recent jobs) | ||
| scontrol_output=$(scontrol show job "$job_id" 2>/dev/null || echo "") | ||
| if [ -n "$scontrol_output" ]; then | ||
| exit_code=$(echo "$scontrol_output" | grep -oE 'ExitCode=[0-9]+:[0-9]+' | cut -d= -f2 || echo "") | ||
| fi | ||
|
|
||
| # If scontrol failed or returned invalid job, try sacct (for completed/aged-out jobs) | ||
| if [ -z "$exit_code" ]; then | ||
| echo "Warning: scontrol failed to get exit code, trying sacct..." | ||
| sacct_output=$(sacct -j "$job_id" --format=ExitCode --noheader --parsable2 2>/dev/null | head -n1 || echo "") | ||
| if [ -n "$sacct_output" ]; then | ||
| exit_code="$sacct_output" | ||
| fi | ||
| fi | ||
|
|
||
| # If we still can't determine exit code, fail explicitly | ||
| if [ -z "$exit_code" ]; then | ||
| echo "ERROR: Unable to determine exit status for job $job_id" | ||
| echo "Both scontrol and sacct failed to return valid exit code" | ||
| exit 1 | ||
| fi | ||
|
|
||
| # Check if job succeeded | ||
| if [ "$exit_code" != "0:0" ]; then | ||
| echo "ERROR: Job $job_id failed with exit code $exit_code" | ||
| exit 1 | ||
| fi | ||
|
|
||
| echo "Job $job_id completed successfully" | ||
| exit 0 | ||
|
|
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