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roboto
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PostPosted: Tue Jul 18, 2017 12:34 am    Post subject: [SOLVED] Initramfs disappeared after halting while on i3wm Reply with quote

So, I typed halt in LXTerminal while in i3wm. After I turned it on, I noticed a very noticeable decrease in speed of everything on my laptop. I noticed that the initramfs line during boot was not there, instead it said error: ata1: device not ready.

I had a huge decrease of speed when starting X. Before: 3 seconds. After: 14 seconds.
Firefox launching. Before: 5 seconds. After: 27 seconds.

Boot time was terrible. Before: 27 seconds. After: Four minutes.

I chrooted into the environment and reinstalled genkernel and recreated initramfs, and update grub, and rebooted.

Still the same.

This is merely one of the reasons why I prefer systemd.
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eccerr0r
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PostPosted: Tue Jul 18, 2017 12:45 am    Post subject: Reply with quote

So I'm not sure, does the rescue CD boot any different than before?

The only gut feel I have is that you have the wrong IDE driver in the kernel if it wasn't a spontaneous hardware. Then again not sure why the initramfs disappeared? Are you using grub2 + grub2-mkconfig?

As an aside I don't quite understand your systemd comment and why you prefer it, or do you mean it sarcastically?
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Last edited by eccerr0r on Tue Jul 18, 2017 12:50 am; edited 1 time in total
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PostPosted: Tue Jul 18, 2017 12:50 am    Post subject: Reply with quote

I used the official Gentoo minimal installation CD and the boot output was the same.

I haven't configured the kernel at all since I installed it on this laptop. The initramfs problem never occurred until now.

Yes and no. I'm being sarcastic while blaming OpenRC for breaking initramfs.
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PostPosted: Tue Jul 18, 2017 12:55 am    Post subject: Reply with quote

Could you rule out hardware problems/hard drive failure? Anything dmesg?

Is ata1 used for your hard drive or CD or ??
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PostPosted: Tue Jul 18, 2017 1:03 am    Post subject: Reply with quote

I'm not sure on how I can test my hard drive. GNOME disks shows no bad sectors.
I literally have no idea where to look into dmesg. Please tell me what to do with dmesg next time.
https://www.zerobin.net/?cd042683bcd8f1ca#tM7ueshfTnAAAZCHwAGaapvkLxEB8GpsqA4ctyqIjws=

ata1 is my hard drive.
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PostPosted: Tue Jul 18, 2017 1:27 am    Post subject: Reply with quote

OpenRC is very unlikely to spontaneously delete your initramfs. If it went missing, I would suspect filesystem corruption (possibly induced by failed hard drive sectors). How old is the drive? How old is the laptop? When did you install Gentoo on the laptop? What is the output of smartctl -a /dev/sda (substitute drive as appropriate)?
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PostPosted: Tue Jul 18, 2017 1:28 am    Post subject: Reply with quote

Your dmesg looks OK other than that spurious

[ 1.984035] ata1: softreset failed (device not ready)
[ 1.984128] ata1: applying PMP SRST workaround and retrying

See if you can find a copy of "smartctl" in smartmontools - If your system otherwise looks like it's working, you can emerge smartmontools and run

# smartctl -a /dev/sda

Then post the results.
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PostPosted: Tue Jul 18, 2017 1:45 am    Post subject: Reply with quote

Code:
smartctl -a /dev/sda1

smartctl 6.4 2015-06-04 r4109 [x86_64-linux-4.9.16-gentoo] (local build)
Copyright (C) 2002-15, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Device Model:     Seagate ST320LT020-9YG142
Serial Number:    W049CB7Y
LU WWN Device Id: 5 000c50 05c53a0c5
Firmware Version: 0003TSM1
User Capacity:    320,072,933,376 bytes [320 GB]
Sector Sizes:     512 bytes logical, 4096 bytes physical
Rotation Rate:    5400 rpm
Device is:        Not in smartctl database [for details use: -P showall]
ATA Version is:   ATA8-ACS T13/1699-D revision 4
SATA Version is:  SATA 2.6, 3.0 Gb/s
Local Time is:    Mon Jul 17 20:45:07 2017 CDT
SMART support is: Available - device has SMART capability.
SMART support is: Enabled

=== START OF READ SMART DATA SECTION ===
SMART overall-health self-assessment test result: PASSED

General SMART Values:
Offline data collection status:  (0x00)   Offline data collection activity
               was never started.
               Auto Offline Data Collection: Disabled.
Self-test execution status:      (   0)   The previous self-test routine completed
               without error or no self-test has ever
               been run.
Total time to complete Offline
data collection:       (    0) seconds.
Offline data collection
capabilities:           (0x73) SMART execute Offline immediate.
               Auto Offline data collection on/off support.
               Suspend Offline collection upon new
               command.
               No Offline surface scan supported.
               Self-test supported.
               Conveyance Self-test supported.
               Selective Self-test supported.
SMART capabilities:            (0x0003)   Saves SMART data before entering
               power-saving mode.
               Supports SMART auto save timer.
Error logging capability:        (0x01)   Error logging supported.
               General Purpose Logging supported.
Short self-test routine
recommended polling time:     (   2) minutes.
Extended self-test routine
recommended polling time:     (  83) minutes.
Conveyance self-test routine
recommended polling time:     (   3) minutes.
SCT capabilities:           (0x303f)   SCT Status supported.
               SCT Error Recovery Control supported.
               SCT Feature Control supported.
               SCT Data Table supported.

SMART Attributes Data Structure revision number: 10
Vendor Specific SMART Attributes with Thresholds:
ID# ATTRIBUTE_NAME          FLAG     VALUE WORST THRESH TYPE      UPDATED  WHEN_FAILED RAW_VALUE
  1 Raw_Read_Error_Rate     0x000f   120   099   006    Pre-fail  Always       -       3104
  3 Spin_Up_Time            0x0003   099   099   085    Pre-fail  Always       -       0
  4 Start_Stop_Count        0x0032   095   095   020    Old_age   Always       -       5725
  5 Reallocated_Sector_Ct   0x0033   100   100   036    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x000f   081   060   030    Pre-fail  Always       -       142570607
  9 Power_On_Hours          0x0032   093   093   000    Old_age   Always       -       6539
 10 Spin_Retry_Count        0x0013   100   100   097    Pre-fail  Always       -       0
 12 Power_Cycle_Count       0x0032   099   099   020    Old_age   Always       -       1668
184 End-to-End_Error        0x0032   100   100   099    Old_age   Always       -       0
187 Reported_Uncorrect      0x0032   097   097   000    Old_age   Always       -       3
188 Command_Timeout         0x0032   100   098   000    Old_age   Always       -       166
189 High_Fly_Writes         0x003a   100   100   000    Old_age   Always       -       0
190 Airflow_Temperature_Cel 0x0022   059   047   045    Old_age   Always       -       41 (Min/Max 30/41)
191 G-Sense_Error_Rate      0x0032   100   100   000    Old_age   Always       -       365
192 Power-Off_Retract_Count 0x0032   100   100   000    Old_age   Always       -       25
193 Load_Cycle_Count        0x0032   001   001   000    Old_age   Always       -       243904
194 Temperature_Celsius     0x0022   041   053   000    Old_age   Always       -       41 (0 19 0 0 0)
195 Hardware_ECC_Recovered  0x001a   055   049   000    Old_age   Always       -       3104
197 Current_Pending_Sector  0x0012   100   100   000    Old_age   Always       -       0
198 Offline_Uncorrectable   0x0010   100   100   000    Old_age   Offline      -       0
199 UDMA_CRC_Error_Count    0x003e   200   200   000    Old_age   Always       -       0
240 Head_Flying_Hours       0x0000   100   253   000    Old_age   Offline      -       5716 (16 97 0)
241 Total_LBAs_Written      0x0000   100   253   000    Old_age   Offline      -       3474722940
242 Total_LBAs_Read         0x0000   100   253   000    Old_age   Offline      -       3509725149
250 Read_Error_Retry_Rate   0x0000   100   001   000    Old_age   Offline      -       9092
251 Unknown_Attribute       0x0000   100   001   000    Old_age   Offline      -       668
252 Unknown_Attribute       0x0000   100   001   000    Old_age   Offline      -       61
254 Free_Fall_Sensor        0x0032   100   100   000    Old_age   Always       -       0

SMART Error Log Version: 1
ATA Error Count: 3
   CR = Command Register [HEX]
   FR = Features Register [HEX]
   SC = Sector Count Register [HEX]
   SN = Sector Number Register [HEX]
   CL = Cylinder Low Register [HEX]
   CH = Cylinder High Register [HEX]
   DH = Device/Head Register [HEX]
   DC = Device Command Register [HEX]
   ER = Error register [HEX]
   ST = Status register [HEX]
Powered_Up_Time is measured from power on, and printed as
DDd+hh:mm:SS.sss where DD=days, hh=hours, mm=minutes,
SS=sec, and sss=millisec. It "wraps" after 49.710 days.

Error 3 occurred at disk power-on lifetime: 6390 hours (266 days + 6 hours)
  When the command that caused the error occurred, the device was active or idle.

  After command completion occurred, registers were:
  ER ST SC SN CL CH DH
  -- -- -- -- -- -- --
  40 51 00 ff ff ff 0f  Error: WP at LBA = 0x0fffffff = 268435455

  Commands leading to the command that caused the error were:
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name
  -- -- -- -- -- -- -- --  ----------------  --------------------
  61 00 08 80 08 80 40 00      00:34:11.838  WRITE FPDMA QUEUED
  61 00 08 00 08 80 40 00      00:34:11.838  WRITE FPDMA QUEUED
  61 00 70 38 26 41 40 00      00:34:11.838  WRITE FPDMA QUEUED
  61 00 f8 40 25 41 40 00      00:34:11.837  WRITE FPDMA QUEUED
  61 00 98 a0 24 41 40 00      00:34:11.836  WRITE FPDMA QUEUED

Error 2 occurred at disk power-on lifetime: 6390 hours (266 days + 6 hours)
  When the command that caused the error occurred, the device was active or idle.

  After command completion occurred, registers were:
  ER ST SC SN CL CH DH
  -- -- -- -- -- -- --
  40 51 00 ff ff ff 0f  Error: UNC at LBA = 0x0fffffff = 268435455

  Commands leading to the command that caused the error were:
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name
  -- -- -- -- -- -- -- --  ----------------  --------------------
  60 00 08 ff ff ff 4f 00      00:34:07.869  READ FPDMA QUEUED
  60 00 08 ff ff ff 4f 00      00:34:07.859  READ FPDMA QUEUED
  60 00 08 ff ff ff 4f 00      00:34:07.808  READ FPDMA QUEUED
  60 00 10 ff ff ff 4f 00      00:34:07.770  READ FPDMA QUEUED
  60 00 48 ff ff ff 4f 00      00:34:07.738  READ FPDMA QUEUED

Error 1 occurred at disk power-on lifetime: 6390 hours (266 days + 6 hours)
  When the command that caused the error occurred, the device was active or idle.

  After command completion occurred, registers were:
  ER ST SC SN CL CH DH
  -- -- -- -- -- -- --
  40 51 00 ff ff ff 0f  Error: UNC at LBA = 0x0fffffff = 268435455

  Commands leading to the command that caused the error were:
  CR FR SC SN CL CH DH DC   Powered_Up_Time  Command/Feature_Name
  -- -- -- -- -- -- -- --  ----------------  --------------------
  60 00 30 ff ff ff 4f 00      00:33:10.504  READ FPDMA QUEUED
  60 00 08 ff ff ff 4f 00      00:33:10.503  READ FPDMA QUEUED
  60 00 08 ff ff ff 4f 00      00:33:10.503  READ FPDMA QUEUED
  60 00 08 ff ff ff 4f 00      00:33:10.503  READ FPDMA QUEUED
  60 00 08 ff ff ff 4f 00      00:33:10.502  READ FPDMA QUEUED

SMART Self-test log structure revision number 1
Num  Test_Description    Status                  Remaining  LifeTime(hours)  LBA_of_first_error
# 1  Short offline       Completed without error       00%      6336         -
# 2  Short offline       Completed without error       00%      6326         -
# 3  Short offline       Completed without error       00%         1         -
# 4  Short offline       Completed without error       00%         1         -
# 5  Short offline       Completed without error       00%         1         -

SMART Selective self-test log data structure revision number 1
 SPAN  MIN_LBA  MAX_LBA  CURRENT_TEST_STATUS
    1        0        0  Not_testing
    2        0        0  Not_testing
    3        0        0  Not_testing
    4        0        0  Not_testing
    5        0        0  Not_testing
Selective self-test flags (0x0):
  After scanning selected spans, do NOT read-scan remainder of disk.
If Selective self-test is pending on power-up, resume after 0 minute delay.


This looks like my hard drive is failing?

[Moderator edit: added [code] tags to preserve output layout. -Hu]
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PostPosted: Tue Jul 18, 2017 2:03 am    Post subject: Reply with quote

It's had trouble in the past but not exactly "dead"...

The hard drive has thought it has gotten close or has exceeded its designed load cycles:

Code:
1 Raw_Read_Error_Rate 0x000f 120 099 006 Pre-fail Always - 3104
7 Seek_Error_Rate 0x000f 081 060 030 Pre-fail Always - 142570607
193 Load_Cycle_Count 0x0032 001 001 000 Old_age Always - 243904


These should be "acceptable" but have shown some signs of wear.

How does the disk benchmark with hdparm,

# hdparm -t /dev/sda

?

[Moderator edit: added [code] tags to preserve output layout. -Hu]
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PostPosted: Tue Jul 18, 2017 2:14 am    Post subject: Reply with quote

hdparm -t /dev/sda1

/dev/sda1:
Timing buffered disk reads: 266 MB in 3.02 seconds = 88.07 MB/sec
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PostPosted: Tue Jul 18, 2017 2:26 am    Post subject: Reply with quote

Put your dmesg into pastebin and provide the link, please.
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PostPosted: Tue Jul 18, 2017 2:45 am    Post subject: Reply with quote

Why?

The link works just fine.
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PostPosted: Tue Jul 18, 2017 2:47 am    Post subject: Reply with quote

roboto wrote:
hdparm -t /dev/sda1

/dev/sda1:
Timing buffered disk reads: 266 MB in 3.02 seconds = 88.07 MB/sec

Is this from normal boot or from a boot CD?

This seems healthy...
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PostPosted: Tue Jul 18, 2017 2:50 am    Post subject: Reply with quote

This is on normal boot.
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PostPosted: Tue Jul 18, 2017 3:48 am    Post subject: Reply with quote

Nevertheless, here is the link:

https://paste.pound-python.org/show/l8ZmCqSbfVq6LCpqxcPr/
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PostPosted: Tue Jul 18, 2017 8:18 am    Post subject: Reply with quote

roboto,

Did you do a kernel update with genkernel and fill up /boot ?
Its possible that the new kernel would have been written but not the initrd, du to lack of space.
You missed the error, updated grub and the initrd for the new kernel is missing.

What does
Code:
ls -l /boot
show?

Your HDD looks healthy from smartctl.
Head load cycles may or may not be something to worry about.
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PostPosted: Tue Jul 18, 2017 12:03 pm    Post subject: Reply with quote

roboto wrote:
Nevertheless, here is the link:

https://paste.pound-python.org/show/l8ZmCqSbfVq6LCpqxcPr/


You are booting the kernel from June 23, where is the new kernel you said you built?
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PostPosted: Tue Jul 18, 2017 2:54 pm    Post subject: Reply with quote

Hmm... this looks suspicious

[ 47.116630] CE: hpet increased min_delta_ns to 20115 nsec
[ 47.116630] CE: hpet increased min_delta_ns to 30172 nsec
[ 47.116630] CE: hpet increased min_delta_ns to 45258 nsec
[ 47.116630] CE: hpet increased min_delta_ns to 67887 nsec
[ 47.116630] CE: hpet increased min_delta_ns to 101830 nsec
[ 47.120657] CE: hpet increased min_delta_ns to 152745 nsec

I recall one of my machines having problems with hpet and forced to use another timebase. With the defective hpet, the machine was running real slow. But again this should not have happened spontaneously.
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PostPosted: Tue Jul 18, 2017 3:11 pm    Post subject: Reply with quote

Code:
ls -l /boot
total 20244
-rw-r--r-- 1 root root  103373 Jun 23 12:22 config-4.9.16-gentoo
-rw-r--r-- 1 root root  100599 Jun 21 12:07 config-4.9.16-gentoo.old
drwxr-xr-x 6 root root    4096 Jun 25 23:13 grub
-rw-r--r-- 1 root root 1333604 Jun 25 23:13 initramfs-genkernel-x86_64-4.9.16-gentoo
-rw-r--r-- 1 root root 2731576 Jun 23 12:22 System.map-4.9.16-gentoo
-rw-r--r-- 1 root root 2692472 Jun 21 12:07 System.map-4.9.16-gentoo.old
-rw-r--r-- 1 root root 6919152 Jun 23 12:22 vmlinuz-4.9.16-gentoo
-rw-r--r-- 1 root root 6829040 Jun 21 12:07 vmlinuz-4.9.16-gentoo.old


Jaglover,

I haven't turned on this laptop since June 23. I didn't build a new kernel, I used genkernel for initramfs, the manual configuration method was done by me during the installation, that's all.



Now, I remember, I did reconfigure the kernel and recompile it back when I was having wifi problems and sound problems. That might explain the *.old files in /boot.

I see initramfs in /boot, why isn't it doing anything?

And I'm never going to upgrade the kernel. The version on mine works just fine. So let it be that way.
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PostPosted: Tue Jul 18, 2017 4:43 pm    Post subject: Reply with quote

How do I suppress hpet if it's slowing down my machine?
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eccerr0r
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PostPosted: Tue Jul 18, 2017 5:03 pm    Post subject: Reply with quote

Does your old kernel exhibit the slow boot problem too?

I highly doubt the hpet problem would spontaneously show up. You could try on your kernel commandline

clocksource=pit

or

hpet=disable

But I kind of doubt that this is the problem if it was working before, plus if your kernel clock remains correct. I had clearly broken hardware so it worked, sort of. The PIT is the pits as a timesource however, but it was way more accurate than a broken hpet.

It still does not explain the initramfs, which I'm at a total loss at.
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PostPosted: Tue Jul 18, 2017 10:52 pm    Post subject: Reply with quote

No, there was no slow boot on my previous kernel.

both clocksource=pit or hpet=disable have no noticeable effect upon my exceptionally slow speed.

Aside from all this, I just happened to go into htop and noticed a process taking up 10% of the CPU all the time.

Process: kworker/1:3

Does this mean anything?

EDIT: And I noticed a few other things take up more RAM than usual. i.e. htop itself took up 7 MB of RAM instead of 3.
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eccerr0r
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PostPosted: Wed Jul 19, 2017 1:21 am    Post subject: Reply with quote

If the old kernel worked and the new kernel is going bonkers I'd do a diff of the .configs.

Kworker is a internal kernel thread...so something you did is causing to work the kernel harder than normal. Is it due to your wifi interrupts?

cat /proc/interrupts

Any lines there with very large numbers after a fresh boot with the afflicted kernel?
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PostPosted: Wed Jul 19, 2017 2:48 am    Post subject: Reply with quote

Code:
cat /proc/interrupts
           CPU0       CPU1       
  0:       2204      32931   IO-APIC   2-edge      timer
  1:         13        193   IO-APIC   1-edge      i8042
  8:          0          2   IO-APIC   8-edge      rtc0
  9:          0          1   IO-APIC   9-fasteoi   acpi
 12:          0          2   IO-APIC  12-edge      i8042
 14:          0          0   IO-APIC  14-edge      pata_atiixp
 15:          0          0   IO-APIC  15-edge      pata_atiixp
 16:       3227     722441   IO-APIC  16-fasteoi   ohci_hcd:usb2, snd_hda_intel:card2
 17:         42       2527   IO-APIC  17-fasteoi   ohci_hcd:usb3, ohci_hcd:usb5
 18:          0          0   IO-APIC  18-fasteoi   ohci_hcd:usb4, ohci_hcd:usb6
 20:          0          2   IO-APIC  20-fasteoi   ehci_hcd:usb1
 22:        450       8494   IO-APIC  22-fasteoi   ahci[0000:00:12.0]
 26:         33       1071   PCI-MSI 606208-edge      radeon
 27:         95       1602   PCI-MSI 4718592-edge      enp9s0
NMI:          0          0   Non-maskable interrupts
LOC:      87934      70311   Local timer interrupts
SPU:          0          0   Spurious interrupts
PMI:          0          0   Performance monitoring interrupts
IWI:          0          0   IRQ work interrupts
RTR:          0          0   APIC ICR read retries
RES:      40097      33007   Rescheduling interrupts
CAL:       4241       7679   Function call interrupts
TLB:       4139       7624   TLB shootdowns
THR:          0          0   Threshold APIC interrupts
DFR:          0          0   Deferred Error APIC interrupts
MCE:          0          0   Machine check exceptions
MCP:          1          1   Machine check polls
ERR:          1
MIS:          0
PIN:          0          0   Posted-interrupt notification event
PIW:          0          0   Posted-interrupt wakeup event


Ok, I think downgrading my .config to the .old one will not work because I configured and compiled the kernel many times a while ago when I was having problems with my laptop. I might have configured the wifi a couple of configs back.

Should I just go ahead and disable everything that I remember enabling before (wifi, sound, touchpad)?
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eccerr0r
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PostPosted: Wed Jul 19, 2017 2:59 am    Post subject: Reply with quote

Is this a fairly fresh boot? IRQ16 seems to have a lot of events if it's a fresh reboot.

What's connected to your usb2?

Code:
lsusb|grep "Bus 002"


Did you play a lot of music this boot? If not and this is a fresh boot, I'd start with investigating sound and why it's doing interrupts.
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