Significant slowdown in boot; thunderbolt driver error

Ubuntu Version:
24.04LTS

Desktop Environment (if applicable):
GNOME

Problem Description:

After the last system updates on May 12th, I have noticed that my system has significantly slowed down. For example:

  • Aprox 6 second to boot desktop (was 2s)
  • emacs boot time with my setup from 2s to 8s
  • Opening tilix I have a lag of around 2s until the zsh shows up (was almost instantaneous before)
cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=24.04
DISTRIB_CODENAME=noble
DISTRIB_DESCRIPTION=“Ubuntu 24.04.4 LTS”
uname -a
Linux 840g5 6.8.0-117-generic #117-Ubuntu SMP PREEMPT_DYNAMIC Tue May  5 19:26:24 UTC 2026 x86_64 x86_64 x86_64 GNU/Linux

Messages in dmesg that I didn’t see before:

[    8.668081] Bluetooth: hci0: Reading supported features failed (-16)
[    8.668089] Bluetooth: hci0: Error reading debug features
[    8.668092] Bluetooth: hci0: HCI LE Coded PHY feature bit is set, but its usage is not supported.

[   15.746351] set_capacity_and_notify: 42 callbacks suppressed

[   33.619389] kauditd_printk_skb: 194 callbacks suppressed

[   69.040561] workqueue: delayed_fput hogged CPU for >13333us 4 times, consider switching to WQ_UNBOUND

[   72.531188] pcieport 0000:00:1c.4: Intel SPT PCH root port ACS workaround enabled
[   73.555224] pcieport 0000:00:1c.4: broken device, retraining non-functional downstream link at 2.5GT/s
[   74.557128] pcieport 0000:00:1c.4: retraining failed
[   74.560144] pcieport 0000:00:1c.4: Data Link Layer Link Active not set in 100 msec
[   74.560217] pcieport 0000:00:1c.4: pciehp: Slot(4): Card not present
[   74.623330] xhci_hcd 0000:3a:00.0: Controller not ready at resume -19
[   74.623349] xhci_hcd 0000:3a:00.0: PCI post-resume error -19!
[   74.623364] xhci_hcd 0000:3a:00.0: HC died; cleaning up
[   74.623470] xhci_hcd 0000:3a:00.0: remove, state 4

[   74.624446] usb usb3: USB disconnect, device number 1
[   74.626105] xhci_hcd 0000:3a:00.0: Host halt failed, -19
[   74.626126] xhci_hcd 0000:3a:00.0: Host not accessible, reset failed.
[   74.627479] xhci_hcd 0000:3a:00.0: USB bus 3 deregistered
[   74.681874] ------------[ cut here ]------------
[   74.681887] thunderbolt 0000:04:00.0: interrupt for TX ring 0 is already enabled
[   74.682053] WARNING: CPU: 0 PID: 10 at drivers/thunderbolt/nhi.c:146 ring_interrupt_active+0x270/0x350 [thunderbolt]
[   74.682186] Modules linked in: ccm rfcomm snd_seq_dummy snd_hrtimer vboxnetadp(OE) vboxnetflt(OE) vboxdrv(OE) qrtr cmac algif_hash algif_skcipher af_alg snd_ctl_led ledtrig_audio snd_hda_codec_conexant snd_hda_codec_generic bnep snd_sof_pci_intel_skl snd_sof_intel_hda_common soundwire_intel snd_sof_intel_hda_mlink soundwire_cadence snd_sof_intel_hda snd_hda_codec_hdmi snd_sof_pci snd_sof_xtensa_dsp snd_sof intel_uncore_frequency intel_uncore_frequency_common intel_pmc_core_pltdrv intel_pmc_core snd_sof_utils intel_vsec soundwire_generic_allocation pmt_telemetry pmt_class soundwire_bus intel_tcc_cooling x86_pkg_temp_thermal snd_soc_avs snd_soc_hda_codec snd_soc_skl intel_powerclamp snd_soc_hdac_hda snd_hda_ext_core snd_soc_sst_ipc snd_soc_sst_dsp coretemp snd_soc_acpi_intel_match snd_soc_acpi kvm_intel snd_soc_core snd_compress binfmt_misc ac97_bus snd_pcm_dmaengine kvm snd_hda_intel snd_intel_dspcfg snd_intel_sdw_acpi snd_hda_codec irqbypass crct10dif_pclmul polyval_clmulni polyval_generic snd_hda_core snd_hwdep
[   74.682432]  ghash_clmulni_intel snd_pcm sha256_ssse3 iwlmvm sha1_ssse3 snd_seq_midi nls_iso8859_1 aesni_intel snd_seq_midi_event ee1004 mei_pxp mei_hdcp intel_rapl_msr i915 crypto_simd mac80211 snd_rawmidi btusb cryptd libarc4 uvcvideo btrtl videobuf2_vmalloc snd_seq btintel uvc drm_buddy rapl processor_thermal_device_pci_legacy hp_wmi btbcm videobuf2_memops btmtk hp_bioscfg videobuf2_v4l2 sparse_keymap ttm processor_thermal_device hid_apple intel_wmi_thunderbolt intel_cstate firmware_attributes_class platform_profile snd_seq_device bluetooth iwlwifi videodev drm_display_helper snd_timer processor_thermal_wt_hint videobuf2_common i2c_i801 processor_thermal_rfim ecdh_generic cec processor_thermal_rapl wmi_bmof mc apple_mfi_fastcharge ecc snd i2c_smbus rc_core intel_rapl_common cfg80211 processor_thermal_wt_req processor_thermal_power_floor mei_me soundcore processor_thermal_mbox mei intel_soc_dts_iosf i2c_algo_bit intel_xhci_usb_role_switch intel_pch_thermal int3403_thermal int340x_thermal_zone acpi_pad
[   74.682702]  wireless_hotkey int3400_thermal acpi_thermal_rel input_leds joydev mac_hid serio_raw sch_fq_codel msr parport_pc ppdev lp parport efi_pstore nfnetlink dmi_sysfs ip_tables x_tables autofs4 usbhid hid_multitouch hid_generic video crc32_pclmul nvme psmouse thunderbolt e1000e nvme_core intel_lpss_pci ucsi_acpi intel_lpss i2c_hid_acpi typec_ucsi xhci_pci i2c_hid nvme_auth typec idma64 xhci_pci_renesas hid wmi pinctrl_sunrisepoint
[   74.682858] CPU: 0 PID: 10 Comm: kworker/0:1 Tainted: G           OE      6.8.0-117-generic #117-Ubuntu
[   74.682872] Hardware name: HP HP EliteBook 840 G5/83B2, BIOS Q78 Ver. 01.29.01 09/21/2024
[   74.682880] Workqueue: pm pm_runtime_work
[   74.682898] RIP: 0010:ring_interrupt_active+0x270/0x350 [thunderbolt]
[   74.683016] Code: 89 5d c8 44 89 45 d4 e8 fe f1 2c ce 44 8b 45 d4 48 8b 4d c0 49 89 d9 48 8b 55 b8 48 89 c6 48 c7 c7 98 90 54 c0 e8 90 e0 82 cd <0f> 0b 4d 8b 7f 08 44 8b 5d c8 49 8b 77 18 45 84 ed 0f 85 d9 fe ff
[   74.683027] RSP: 0018:ffffd397000f7c38 EFLAGS: 00010046
[   74.683040] RAX: 0000000000000000 RBX: ffffffffc054dc3b RCX: 0000000000000000
[   74.683049] RDX: 0000000000000000 RSI: 0000000000000000 RDI: 0000000000000000
[   74.683056] RBP: ffffd397000f7c88 R08: 0000000000000000 R09: 0000000000000000
[   74.683063] R10: 0000000000000000 R11: 0000000000000000 R12: 0000000000000001
[   74.683070] R13: 0000000000000001 R14: 0000000000038200 R15: ffff8e508a0906c0
[   74.683078] FS:  0000000000000000(0000) GS:ffff8e53af400000(0000) knlGS:0000000000000000
[   74.683088] CS:  0010 DS: 0000 ES: 0000 CR0: 0000000080050033
[   74.683097] CR2: 0000126b44367000 CR3: 000000016483a002 CR4: 00000000003706f0
[   74.683106] Call Trace:
[   74.683113]  <TASK>
[   74.683129]  ? __pfx_pci_pm_runtime_resume+0x10/0x10
[   74.683148]  tb_ring_start+0x166/0x330 [thunderbolt]
[   74.683270]  tb_ctl_start+0x1d/0xc0 [thunderbolt]
[   74.683392]  tb_domain_runtime_resume+0x19/0x50 [thunderbolt]
[   74.683533]  nhi_runtime_resume+0x64/0x80 [thunderbolt]
[   74.683652]  pci_pm_runtime_resume+0x94/0xf0
[   74.683667]  __rpm_callback+0x4d/0x170
[   74.683681]  rpm_callback+0x6d/0x80
[   74.683690]  ? __pfx_pci_pm_runtime_resume+0x10/0x10
[   74.683703]  rpm_resume+0x594/0x7e0
[   74.683718]  pm_runtime_work+0x80/0xe0
[   74.683730]  process_one_work+0x181/0x3a0
[   74.683746]  worker_thread+0x306/0x440
[   74.683759]  ? _raw_spin_lock_irqsave+0xe/0x20
[   74.683774]  ? __pfx_worker_thread+0x10/0x10
[   74.683785]  kthread+0xef/0x120
[   74.683800]  ? __pfx_kthread+0x10/0x10
[   74.683815]  ret_from_fork+0x44/0x70
[   74.683828]  ? __pfx_kthread+0x10/0x10
[   74.683842]  ret_from_fork_asm+0x1b/0x30
[   74.683862]  </TASK>
[   74.683867] ---[ end trace 0000000000000000 ]---
[   74.683942] ------------[ cut here ]------------
[   74.683948] thunderbolt 0000:04:00.0: interrupt for RX ring 0 is already enabled
[   74.684081] WARNING: CPU: 0 PID: 10 at drivers/thunderbolt/nhi.c:146 ring_interrupt_active+0x270/0x350 [thunderbolt]
[   74.684203] Modules linked in: ccm rfcomm snd_seq_dummy snd_hrtimer vboxnetadp(OE) vboxnetflt(OE) vboxdrv(OE) qrtr cmac algif_hash algif_skcipher af_alg snd_ctl_led ledtrig_audio snd_hda_codec_conexant snd_hda_codec_generic bnep snd_sof_pci_intel_skl snd_sof_intel_hda_common soundwire_intel snd_sof_intel_hda_mlink soundwire_cadence snd_sof_intel_hda snd_hda_codec_hdmi snd_sof_pci snd_sof_xtensa_dsp snd_sof intel_uncore_frequency intel_uncore_frequency_common intel_pmc_core_pltdrv intel_pmc_core snd_sof_utils intel_vsec soundwire_generic_allocation pmt_telemetry pmt_class soundwire_bus intel_tcc_cooling x86_pkg_temp_thermal snd_soc_avs snd_soc_hda_codec snd_soc_skl intel_powerclamp snd_soc_hdac_hda snd_hda_ext_core snd_soc_sst_ipc snd_soc_sst_dsp coretemp snd_soc_acpi_intel_match snd_soc_acpi kvm_intel snd_soc_core snd_compress binfmt_misc ac97_bus snd_pcm_dmaengine kvm snd_hda_intel snd_intel_dspcfg snd_intel_sdw_acpi snd_hda_codec irqbypass crct10dif_pclmul polyval_clmulni polyval_generic snd_hda_core snd_hwdep
[   74.684439]  ghash_clmulni_intel snd_pcm sha256_ssse3 iwlmvm sha1_ssse3 snd_seq_midi nls_iso8859_1 aesni_intel snd_seq_midi_event ee1004 mei_pxp mei_hdcp intel_rapl_msr i915 crypto_simd mac80211 snd_rawmidi btusb cryptd libarc4 uvcvideo btrtl videobuf2_vmalloc snd_seq btintel uvc drm_buddy rapl processor_thermal_device_pci_legacy hp_wmi btbcm videobuf2_memops btmtk hp_bioscfg videobuf2_v4l2 sparse_keymap ttm processor_thermal_device hid_apple intel_wmi_thunderbolt intel_cstate firmware_attributes_class platform_profile snd_seq_device bluetooth iwlwifi videodev drm_display_helper snd_timer processor_thermal_wt_hint videobuf2_common i2c_i801 processor_thermal_rfim ecdh_generic cec processor_thermal_rapl wmi_bmof mc apple_mfi_fastcharge ecc snd i2c_smbus rc_core intel_rapl_common cfg80211 processor_thermal_wt_req processor_thermal_power_floor mei_me soundcore processor_thermal_mbox mei intel_soc_dts_iosf i2c_algo_bit intel_xhci_usb_role_switch intel_pch_thermal int3403_thermal int340x_thermal_zone acpi_pad
[   74.684707]  wireless_hotkey int3400_thermal acpi_thermal_rel input_leds joydev mac_hid serio_raw sch_fq_codel msr parport_pc ppdev lp parport efi_pstore nfnetlink dmi_sysfs ip_tables x_tables autofs4 usbhid hid_multitouch hid_generic video crc32_pclmul nvme psmouse thunderbolt e1000e nvme_core intel_lpss_pci ucsi_acpi intel_lpss i2c_hid_acpi typec_ucsi xhci_pci i2c_hid nvme_auth typec idma64 xhci_pci_renesas hid wmi pinctrl_sunrisepoint
[   74.684858] CPU: 0 PID: 10 Comm: kworker/0:1 Tainted: G        W  OE      6.8.0-117-generic #117-Ubuntu
[   74.684871] Hardware name: HP HP EliteBook 840 G5/83B2, BIOS Q78 Ver. 01.29.01 09/21/2024
[   74.684878] Workqueue: pm pm_runtime_work
[   74.684893] RIP: 0010:ring_interrupt_active+0x270/0x350 [thunderbolt]
[   74.685009] Code: 89 5d c8 44 89 45 d4 e8 fe f1 2c ce 44 8b 45 d4 48 8b 4d c0 49 89 d9 48 8b 55 b8 48 89 c6 48 c7 c7 98 90 54 c0 e8 90 e0 82 cd <0f> 0b 4d 8b 7f 08 44 8b 5d c8 49 8b 77 18 45 84 ed 0f 85 d9 fe ff
[   74.685019] RSP: 0018:ffffd397000f7c38 EFLAGS: 00010046
[   74.685031] RAX: 0000000000000000 RBX: ffffffffc054dc3b RCX: 0000000000000000
[   74.685039] RDX: 0000000000000000 RSI: 0000000000000000 RDI: 0000000000000000
[   74.685046] RBP: ffffd397000f7c88 R08: 0000000000000000 R09: 0000000000000000
[   74.685053] R10: 0000000000000000 R11: 0000000000000000 R12: 0000000000001000
[   74.685060] R13: 0000000000000001 R14: 0000000000038200 R15: ffff8e5082275840
[   74.685068] FS:  0000000000000000(0000) GS:ffff8e53af400000(0000) knlGS:0000000000000000
[   74.685077] CS:  0010 DS: 0000 ES: 0000 CR0: 0000000080050033
[   74.685084] CR2: 0000126b44367000 CR3: 000000016483a002 CR4: 00000000003706f0
[   74.685093] Call Trace:
[   74.685098]  <TASK>
[   74.685109]  ? __pfx_pci_pm_runtime_resume+0x10/0x10
[   74.685123]  tb_ring_start+0x166/0x330 [thunderbolt]
[   74.685240]  tb_ctl_start+0x27/0xc0 [thunderbolt]
[   74.685360]  tb_domain_runtime_resume+0x19/0x50 [thunderbolt]
[   74.685497]  nhi_runtime_resume+0x64/0x80 [thunderbolt]
[   74.685611]  pci_pm_runtime_resume+0x94/0xf0
[   74.685626]  __rpm_callback+0x4d/0x170
[   74.685640]  rpm_callback+0x6d/0x80
[   74.685649]  ? __pfx_pci_pm_runtime_resume+0x10/0x10
[   74.685661]  rpm_resume+0x594/0x7e0
[   74.685676]  pm_runtime_work+0x80/0xe0
[   74.685688]  process_one_work+0x181/0x3a0
[   74.685703]  worker_thread+0x306/0x440
[   74.685715]  ? _raw_spin_lock_irqsave+0xe/0x20
[   74.685730]  ? __pfx_worker_thread+0x10/0x10
[   74.685742]  kthread+0xef/0x120
[   74.685756]  ? __pfx_kthread+0x10/0x10
[   74.685771]  ret_from_fork+0x44/0x70
[   74.685783]  ? __pfx_kthread+0x10/0x10
[   74.685798]  ret_from_fork_asm+0x1b/0x30
[   74.685818]  </TASK>
[   74.685824] ---[ end trace 0000000000000000 ]---
[   95.408915] thunderbolt 0000:04:00.0: failed to send driver ready to ICM
[  101.031091] warning: `ThreadPoolForeg' uses wireless extensions which will stop working for Wi-Fi 7 hardware; use nl80211



Additional data from dmesg:

  [   47.549743] i915 0000:00:02.0: [drm] *ERROR* Atomic update failure on pipe A (start=3737 end=3738) time 581 us, min 1073, max 1079, scanline start 1059, end 1098 

And:

I have disabled Thunderbolt in the BIOS with no improvement,

Can you provide the list of packages that got upgraded? (/var/log/apt/history*)

Maybe these are also relevant.

Have the stack traces disappeared afterwards? I believe with all the fancy UEFI interactions, Linux might be able to still talk to such devices, unless being explicitly prevented from accessing it by the firmware.
Or Thunderbolt is not the actual cause; see the other dmesg lines above.

So thunderbolt seemed to be one of the culprits. Disabling it made the traces go.

Additionally, I noticed that the powermode had gone from balanced to powersave without my asking to do so…

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