Add HPC tuning: PCIe ASPM off, C-states, performance CPU governor

- grub.cfg + isolinux/live.cfg.in: add pcie_aspm=off,
  intel_idle.max_cstate=1 and processor.max_cstate=1 to all
  non-failsafe boot entries
- bee-hpc-tuning: new script that sets all CPU cores to performance
  governor via sysfs and logs THP state at boot
- bee-hpc-tuning.service: runs before bee-nvidia and bee-audit
- 9000-bee-setup.hook.chroot: enable service and mark script executable

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

audit/internal/collector/pcie.go

@@ -2,6 +2,7 @@ package collector
 
 import (
 	"bee/audit/internal/schema"
+	"fmt"
 	"log/slog"
 	"os/exec"
 	"strconv"
@@ -172,6 +173,9 @@ func parseLspciDevice(fields map[string]string) schema.HardwarePCIeDevice {
 
 	// SVendor/SDevice available but not in schema — skip
 
+	// Warn if PCIe link is running below its maximum negotiated speed.
+	applyPCIeLinkSpeedWarning(&dev)
+
 	return dev
 }
 
@@ -241,6 +245,41 @@ func readPCIStringAttribute(bdf, attribute string) (string, bool) {
 	return value, true
 }
 
+// applyPCIeLinkSpeedWarning sets the device status to Warning if the current PCIe link
+// speed is below the maximum negotiated speed supported by both ends.
+func applyPCIeLinkSpeedWarning(dev *schema.HardwarePCIeDevice) {
+	if dev.LinkSpeed == nil || dev.MaxLinkSpeed == nil {
+		return
+	}
+	if pcieLinkSpeedRank(*dev.LinkSpeed) < pcieLinkSpeedRank(*dev.MaxLinkSpeed) {
+		warn := statusWarning
+		dev.Status = &warn
+		desc := fmt.Sprintf("PCIe link speed degraded: running at %s, capable of %s", *dev.LinkSpeed, *dev.MaxLinkSpeed)
+		dev.ErrorDescription = &desc
+	}
+}
+
+// pcieLinkSpeedRank returns a numeric rank for a normalized Gen string (e.g. "Gen4" → 4).
+// Returns 0 for unrecognised values so comparisons fail safe.
+func pcieLinkSpeedRank(gen string) int {
+	switch gen {
+	case "Gen1":
+		return 1
+	case "Gen2":
+		return 2
+	case "Gen3":
+		return 3
+	case "Gen4":
+		return 4
+	case "Gen5":
+		return 5
+	case "Gen6":
+		return 6
+	default:
+		return 0
+	}
+}
+
 func normalizePCILinkSpeed(raw string) string {
 	raw = strings.TrimSpace(strings.ToLower(raw))
 	switch {

audit/internal/collector/pcie_filter_test.go

@@ -1,6 +1,7 @@
 package collector
 
 import (
+	"bee/audit/internal/schema"
 	"encoding/json"
 	"strings"
 	"testing"
@@ -141,3 +142,77 @@ func TestNormalizePCILinkSpeed(t *testing.T) {
 		}
 	}
 }
+
+func TestApplyPCIeLinkSpeedWarning(t *testing.T) {
+	ptr := func(s string) *string { return &s }
+
+	tests := []struct {
+		name        string
+		linkSpeed   *string
+		maxSpeed    *string
+		wantWarning bool
+		wantGenIn   string // substring expected in ErrorDescription when warning
+	}{
+		{
+			name:        "degraded Gen1 vs Gen5",
+			linkSpeed:   ptr("Gen1"),
+			maxSpeed:    ptr("Gen5"),
+			wantWarning: true,
+			wantGenIn:   "Gen1",
+		},
+		{
+			name:        "at max Gen5",
+			linkSpeed:   ptr("Gen5"),
+			maxSpeed:    ptr("Gen5"),
+			wantWarning: false,
+		},
+		{
+			name:        "degraded Gen4 vs Gen5",
+			linkSpeed:   ptr("Gen4"),
+			maxSpeed:    ptr("Gen5"),
+			wantWarning: true,
+			wantGenIn:   "Gen4",
+		},
+		{
+			name:        "missing current speed — no warning",
+			linkSpeed:   nil,
+			maxSpeed:    ptr("Gen5"),
+			wantWarning: false,
+		},
+		{
+			name:        "missing max speed — no warning",
+			linkSpeed:   ptr("Gen1"),
+			maxSpeed:    nil,
+			wantWarning: false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			dev := schema.HardwarePCIeDevice{}
+			ok := statusOK
+			dev.Status = &ok
+			dev.LinkSpeed = tt.linkSpeed
+			dev.MaxLinkSpeed = tt.maxSpeed
+
+			applyPCIeLinkSpeedWarning(&dev)
+
+			gotWarn := dev.Status != nil && *dev.Status == statusWarning
+			if gotWarn != tt.wantWarning {
+				t.Fatalf("wantWarning=%v gotWarning=%v (status=%v)", tt.wantWarning, gotWarn, dev.Status)
+			}
+			if tt.wantWarning {
+				if dev.ErrorDescription == nil {
+					t.Fatal("expected ErrorDescription to be set")
+				}
+				if !strings.Contains(*dev.ErrorDescription, tt.wantGenIn) {
+					t.Fatalf("ErrorDescription %q does not contain %q", *dev.ErrorDescription, tt.wantGenIn)
+				}
+			} else {
+				if dev.ErrorDescription != nil {
+					t.Fatalf("unexpected ErrorDescription: %s", *dev.ErrorDescription)
+				}
+			}
+		})
+	}
+}

audit/internal/platform/techdump.go

@@ -20,6 +20,7 @@ var techDumpFixedCommands = []struct {
 	{Name: "dmidecode", Args: []string{"-t", "4"}, File: "dmidecode-type4.txt"},
 	{Name: "dmidecode", Args: []string{"-t", "17"}, File: "dmidecode-type17.txt"},
 	{Name: "lspci", Args: []string{"-vmm", "-D"}, File: "lspci-vmm.txt"},
+	{Name: "lspci", Args: []string{"-vvv"}, File: "lspci-vvv.txt"},
 	{Name: "lsblk", Args: []string{"-J", "-d", "-o", "NAME,TYPE,SIZE,SERIAL,MODEL,TRAN,HCTL"}, File: "lsblk.json"},
 	{Name: "sensors", Args: []string{"-j"}, File: "sensors.json"},
 	{Name: "ipmitool", Args: []string{"fru", "print"}, File: "ipmitool-fru.txt"},

iso/builder/config/bootloaders/grub-pc/grub.cfg

@@ -11,18 +11,18 @@ echo "  Hardware Audit LiveCD"
 echo ""
 
 menuentry "EASY-BEE" {
-    linux   @KERNEL_LIVE@ @APPEND_LIVE@ nomodeset bee.nvidia.mode=normal net.ifnames=0 biosdevname=0 mitigations=off transparent_hugepage=always numa_balancing=disable nowatchdog nosoftlockup
+    linux   @KERNEL_LIVE@ @APPEND_LIVE@ nomodeset bee.nvidia.mode=normal net.ifnames=0 biosdevname=0 mitigations=off transparent_hugepage=always numa_balancing=disable pcie_aspm=off intel_idle.max_cstate=1 processor.max_cstate=1 nowatchdog nosoftlockup
     initrd  @INITRD_LIVE@
 }
 
 submenu "EASY-BEE (advanced options) -->" {
     menuentry "EASY-BEE — GSP=off" {
-        linux   @KERNEL_LIVE@ @APPEND_LIVE@ nomodeset bee.nvidia.mode=gsp-off net.ifnames=0 biosdevname=0 mitigations=off transparent_hugepage=always numa_balancing=disable nowatchdog nosoftlockup
+        linux   @KERNEL_LIVE@ @APPEND_LIVE@ nomodeset bee.nvidia.mode=gsp-off net.ifnames=0 biosdevname=0 mitigations=off transparent_hugepage=always numa_balancing=disable pcie_aspm=off intel_idle.max_cstate=1 processor.max_cstate=1 nowatchdog nosoftlockup
         initrd  @INITRD_LIVE@
     }
 
     menuentry "EASY-BEE — KMS (no nomodeset)" {
-        linux   @KERNEL_LIVE@ @APPEND_LIVE@ bee.nvidia.mode=normal net.ifnames=0 biosdevname=0 mitigations=off transparent_hugepage=always numa_balancing=disable nowatchdog nosoftlockup
+        linux   @KERNEL_LIVE@ @APPEND_LIVE@ bee.nvidia.mode=normal net.ifnames=0 biosdevname=0 mitigations=off transparent_hugepage=always numa_balancing=disable pcie_aspm=off intel_idle.max_cstate=1 processor.max_cstate=1 nowatchdog nosoftlockup
         initrd  @INITRD_LIVE@
     }
 

iso/builder/config/bootloaders/isolinux/live.cfg.in

@@ -3,31 +3,31 @@ label live-@FLAVOUR@-normal
     menu default
     linux @LINUX@
     initrd @INITRD@
-    append @APPEND_LIVE@ bee.nvidia.mode=normal
+    append @APPEND_LIVE@ bee.nvidia.mode=normal pcie_aspm=off intel_idle.max_cstate=1 processor.max_cstate=1
 
 label live-@FLAVOUR@-kms
     menu label EASY-BEE (^graphics/KMS)
     linux @LINUX@
     initrd @INITRD@
-    append @APPEND_LIVE@ bee.display=kms bee.nvidia.mode=normal
+    append @APPEND_LIVE@ bee.display=kms bee.nvidia.mode=normal pcie_aspm=off intel_idle.max_cstate=1 processor.max_cstate=1
 
 label live-@FLAVOUR@-toram
     menu label EASY-BEE (^load to RAM)
     linux @LINUX@
     initrd @INITRD@
-    append @APPEND_LIVE@ toram bee.nvidia.mode=normal
+    append @APPEND_LIVE@ toram bee.nvidia.mode=normal pcie_aspm=off intel_idle.max_cstate=1 processor.max_cstate=1
 
 label live-@FLAVOUR@-gsp-off
     menu label EASY-BEE (^NVIDIA GSP=off)
     linux @LINUX@
     initrd @INITRD@
-    append @APPEND_LIVE@ nomodeset bee.nvidia.mode=gsp-off
+    append @APPEND_LIVE@ nomodeset bee.nvidia.mode=gsp-off pcie_aspm=off intel_idle.max_cstate=1 processor.max_cstate=1
 
 label live-@FLAVOUR@-kms-gsp-off
     menu label EASY-BEE (g^raphics/KMS, GSP=off)
     linux @LINUX@
     initrd @INITRD@
-    append @APPEND_LIVE@ bee.display=kms bee.nvidia.mode=gsp-off
+    append @APPEND_LIVE@ bee.display=kms bee.nvidia.mode=gsp-off pcie_aspm=off intel_idle.max_cstate=1 processor.max_cstate=1
 
 label live-@FLAVOUR@-failsafe
     menu label EASY-BEE (^fail-safe)

iso/builder/config/hooks/normal/9000-bee-setup.hook.chroot

@@ -25,6 +25,7 @@ ensure_bee_console_user() {
 ensure_bee_console_user
 
 # Enable common bee services
+systemctl enable bee-hpc-tuning.service
 systemctl enable bee-network.service
 systemctl enable bee-preflight.service
 systemctl enable bee-audit.service
@@ -55,6 +56,7 @@ fi
 # nogpu: no GPU services needed
 
 # Ensure scripts are executable
+chmod +x /usr/local/bin/bee-hpc-tuning  2>/dev/null || true
 chmod +x /usr/local/bin/bee-network.sh  2>/dev/null || true
 chmod +x /usr/local/bin/bee-sshsetup   2>/dev/null || true
 chmod +x /usr/local/bin/bee-smoketest  2>/dev/null || true

iso/overlay/etc/systemd/system/bee-hpc-tuning.service

@@ -0,0 +1,14 @@
+[Unit]
+Description=Bee: HPC tuning (CPU governor, C-states)
+After=local-fs.target
+Before=bee-nvidia.service bee-audit.service
+
+[Service]
+Type=oneshot
+ExecStart=/usr/local/bin/bee-log-run /appdata/bee/export/bee-hpc-tuning.log /usr/local/bin/bee-hpc-tuning
+StandardOutput=journal
+StandardError=journal
+RemainAfterExit=yes
+
+[Install]
+WantedBy=multi-user.target

iso/overlay/usr/local/bin/bee-hpc-tuning

@@ -0,0 +1,41 @@
+#!/bin/sh
+# bee-hpc-tuning — apply HPC tuning for deterministic benchmarking
+# Called by bee-hpc-tuning.service at boot.
+
+log() { echo "[bee-hpc-tuning] $*"; }
+
+# ── CPU governor ────────────────────────────────────────────────────────────
+# Set all CPU cores to performance governor via sysfs.
+# cpupower is not available; write directly to scaling_governor.
+governor_ok=0
+governor_fail=0
+for gov_path in /sys/devices/system/cpu/cpu*/cpufreq/scaling_governor; do
+    [ -f "$gov_path" ] || continue
+    if echo performance > "$gov_path" 2>/dev/null; then
+        governor_ok=$((governor_ok + 1))
+    else
+        governor_fail=$((governor_fail + 1))
+    fi
+done
+
+if [ "$governor_ok" -gt 0 ] && [ "$governor_fail" -eq 0 ]; then
+    log "CPU governor set to performance on ${governor_ok} core(s)"
+elif [ "$governor_ok" -gt 0 ]; then
+    log "WARN: CPU governor: ${governor_ok} OK, ${governor_fail} failed"
+elif [ "$governor_fail" -gt 0 ]; then
+    log "WARN: failed to set CPU governor on ${governor_fail} core(s)"
+else
+    log "WARN: no cpufreq scaling_governor paths found (C-state governor or HW-controlled)"
+fi
+
+# ── Transparent Huge Pages ───────────────────────────────────────────────────
+# Kernel cmdline sets transparent_hugepage=always at boot, but confirm and log.
+thp_path=/sys/kernel/mm/transparent_hugepage/enabled
+if [ -f "$thp_path" ]; then
+    current=$(cat "$thp_path" 2>/dev/null)
+    log "transparent_hugepage: ${current}"
+else
+    log "WARN: transparent_hugepage sysfs path not found"
+fi
+
+log "done"