Slow hard disk - Response time about 60 seconds

Hi all

I have recently installed a new hard disk (6 TB, WD Blue, SATA III) for storage. When accessing the disk on Manjaro it takes about 1 minute until the contents are shown. Same goes for opening folders on the disk, copying files and system shut down. The issue isn’t consistent, on some boots (rarely) it’s ok.
When accessing the disk with Windows 10 (dual boot) the device seems to work fine. I have formatted multiple times (ext4 - quick, NTFS - full), created new partition tables (GUID) and run S.M.A.R.T diagnostics all without resolving the issue. I am afraid I don’t know what else i can do. Does anybody understand what’s causing this problem? Maybe even know how to fix it?

Full system info here: paste. ubuntu. com /p/Jpgp5F8WXy (sorry can’t post links)

# inxi -Fazy
System:
  Kernel: 5.11.0-0-MANJARO x86_64 bits: 64 compiler: gcc v: 10.2.1 
  parameters: BOOT_IMAGE=/boot/vmlinuz-5.11-x86_64 
  root=UUID= <filter>  ro quiet apparmor=1 
  security=apparmor udev.log_priority=3 
  Desktop: Xfce 4.16.0 tk: Gtk 3.24.24 info: xfce4-panel wm: xfwm4 
  dm: LightDM 1.30.0 Distro: Manjaro Linux 
Machine:
  Type: Desktop System: ASUS product: N/A v: N/A serial: N/A 
  Mobo: ASUSTeK model: PRIME B550-PLUS v: Rev X.0x serial: <filter> 
  UEFI: American Megatrends v: 1202 date: 10/22/2020 
CPU:
  Info: 6-Core model: AMD Ryzen 5 5600X socket: AM4 bits: 64 type: MT MCP 
  arch: Zen 3 family: 19 (25) model-id: 21 (33) stepping: N/A 
  microcode: A201009 L1 cache: 384 KiB L2 cache: 3 MiB L3 cache: 31.2 MiB 
  flags: avx avx2 lm nx pae sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3 svm 
  bogomips: 88663 
  Speed: 2832 MHz min/max: 2200/5210 MHz base/boost: 3700/4650 boost: enabled 
  volts: 1.1 V ext-clock: 100 MHz Core speeds (MHz): 1: 2832 2: 2188 3: 2075 
  4: 2193 5: 2096 6: 2195 7: 2189 8: 2193 9: 2195 10: 2194 11: 2195 12: 2196 
  Vulnerabilities: Type: itlb_multihit status: Not affected 
  Type: l1tf status: Not affected 
  Type: mds status: Not affected 
  Type: meltdown status: Not affected 
  Type: spec_store_bypass 
  mitigation: Speculative Store Bypass disabled via prctl and seccomp 
  Type: spectre_v1 
  mitigation: usercopy/swapgs barriers and __user pointer sanitization 
  Type: spectre_v2 mitigation: Full AMD retpoline, IBPB: conditional, IBRS_FW, 
  STIBP: always-on, RSB filling 
  Type: srbds status: Not affected 
  Type: tsx_async_abort status: Not affected 
Graphics:
  Device-1: AMD Navi 21 [Radeon RX 6800/6800 XT / 6900 XT] 
  vendor: Sapphire Limited driver: amdgpu v: kernel bus ID: 09:00.0 
  chip ID: 1002:73bf class ID: 0300 
  Display: x11 server: X.Org 1.20.10 driver: loaded: amdgpu,ati 
  unloaded: modesetting,radeon alternate: fbdev,vesa display ID: :0.0 
  screens: 1 
  Screen-1: 0 s-res: 3840x2160 s-dpi: 96 s-size: 1016x571mm (40.0x22.5") 
  s-diag: 1165mm (45.9") 
  Monitor-1: DisplayPort-1 res: 3840x2160 hz: 60 dpi: 140 
  size: 698x393mm (27.5x15.5") diag: 801mm (31.5") 
  OpenGL: 
  renderer: AMD SIENNA_CICHLID (DRM 3.40.0 5.11.0-0-MANJARO LLVM 11.0.1) 
  v: 4.6 Mesa 21.1.0-devel (git-766538f83c) direct render: Yes 
Audio:
  Device-1: AMD driver: snd_hda_intel v: kernel bus ID: 09:00.1 
  chip ID: 1002:ab28 class ID: 0403 
  Device-2: AMD Starship/Matisse HD Audio vendor: ASUSTeK 
  driver: snd_hda_intel v: kernel bus ID: 0b:00.4 chip ID: 1022:1487 
  class ID: 0403 
  Sound Server: ALSA v: k5.11.0-0-MANJARO 
Network:
  Device-1: Realtek RTL8111/8168/8411 PCI Express Gigabit Ethernet 
  vendor: ASUSTeK driver: r8169 v: kernel port: f000 bus ID: 06:00.0 
  chip ID: 10ec:8168 class ID: 0200 
  IF: enp6s0 state: down mac: <filter> 
  Device-2: Realtek 802.11ac NIC type: USB driver: usb-network bus ID: 3-3:2 
  chip ID: 0bda:c811 class ID: 0000 serial: <filter> 
  IF-ID-1: <filter> 
  IF-ID-2: <filter>
Drives:
  Local Storage: total: 6.37 TiB used: 44.5 GiB (0.7%) 
  ID-1: /dev/nvme0n1 maj-min: 259:0 vendor: Western Digital 
  model: WDS100T2B0C-00PXH0 size: 931.51 GiB block size: physical: 512 B 
  logical: 512 B speed: 31.6 Gb/s lanes: 4 rotation: SSD serial: <filter> 
  rev: 211070WD temp: 46.9 C scheme: GPT 
  SMART: yes health: PASSED on: 54 hrs cycles: 21 read-units: 454,449 [232 GB] 
  written-units: 836,138 [428 GB] 
  ID-2: /dev/sda maj-min: 8:0 vendor: Western Digital model: WD60EZAZ-00ZGHB0 
  family: Blue (SMR) size: 5.46 TiB block size: physical: 4096 B 
  logical: 512 B sata: 3.1 speed: 6.0 Gb/s rotation: 5400 rpm serial: <filter> 
  rev: 0A80 temp: 34 C scheme: GPT 
  SMART: yes state: enabled health: PASSED on: 36 hrs cycles: 12 
Partition:
  ID-1: / raw size: 672.85 GiB size: 661.29 GiB (98.28%) 
  used: 42.56 GiB (6.4%) fs: ext4 block size: 4096 B dev: /dev/nvme0n1p4 
  maj-min: 259:4 
  ID-2: /boot/efi raw size: 100 MiB size: 96 MiB (96.00%) 
  used: 31.8 MiB (33.1%) fs: vfat block size: 512 B dev: /dev/nvme0n1p1 
  maj-min: 259:1 
Swap:
  Alert: No Swap data was found. 
Sensors:
  System Temperatures: cpu: 43.0 C mobo: N/A gpu: amdgpu temp: 60.0 C 
  mem: 66.0 C 
  Fan Speeds (RPM): N/A gpu: amdgpu fan: 874 
Info:
  Processes: 295 Uptime: 1h 00m wakeups: 0 Memory: 15.61 GiB 
  used: 3.34 GiB (21.4%) Init: systemd v: 247 Compilers: gcc: 10.2.0 
  clang: 11.0.1 Packages: pacman: 1211 lib: 379 flatpak: 0 Shell: Bash (su) 
  v: 5.1.0 running in: xfce4-terminal inxi: 3.3.01


# smartctl -a /dev/sda
smartctl 7.2 2020-12-30 r5155 [x86_64-linux-5.11.0-0-MANJARO] (local build)
Copyright (C) 2002-20, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Model Family:     Western Digital Blue (SMR)
Device Model:     WDC WD60EZAZ-00ZGHB0
Serial Number:    WD- <filter> 
LU WWN Device Id: 5 0014ee 2bdde1823
Firmware Version: 80.00A80
User Capacity:    6’001’175’126’016 bytes [6.00 TB]
Sector Sizes:     512 bytes logical, 4096 bytes physical
Rotation Rate:    5400 rpm
Form Factor:      3.5 inches
TRIM Command:     Available
Device is:        In smartctl database [for details use: -P show]
ATA Version is:   ACS-3 T13/2161-D revision 5
SATA Version is:  SATA 3.1, 6.0 Gb/s (current: 6.0 Gb/s)
Local Time is:    Tue Feb 16 08:16:42 2021 CET
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: 		(  180) seconds.
Offline data collection
capabilities: 			 (0x7b) SMART execute Offline immediate.
					Auto Offline data collection on/off support.
					Suspend Offline collection upon new
					command.
					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: 	 (   7) minutes.
Conveyance self-test routine
recommended polling time: 	 (   2) minutes.
SCT capabilities: 	       (0x3035)	SCT Status supported.
					SCT Feature Control supported.
					SCT Data Table supported.

SMART Attributes Data Structure revision number: 16
Vendor Specific SMART Attributes with Thresholds:
ID# ATTRIBUTE_NAME          FLAG     VALUE WORST THRESH TYPE      UPDATED  WHEN_FAILED RAW_VALUE
  1 Raw_Read_Error_Rate     0x002f   200   200   051    Pre-fail  Always       -       0
  3 Spin_Up_Time            0x0027   224   224   021    Pre-fail  Always       -       3766
  4 Start_Stop_Count        0x0032   100   100   000    Old_age   Always       -       13
  5 Reallocated_Sector_Ct   0x0033   200   200   140    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x002e   200   200   000    Old_age   Always       -       0
  9 Power_On_Hours          0x0032   100   100   000    Old_age   Always       -       35
 10 Spin_Retry_Count        0x0032   100   253   000    Old_age   Always       -       0
 11 Calibration_Retry_Count 0x0032   100   253   000    Old_age   Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       12
192 Power-Off_Retract_Count 0x0032   200   200   000    Old_age   Always       -       1
193 Load_Cycle_Count        0x0032   200   200   000    Old_age   Always       -       235
194 Temperature_Celsius     0x0022   121   105   000    Old_age   Always       -       29
196 Reallocated_Event_Count 0x0032   200   200   000    Old_age   Always       -       0
197 Current_Pending_Sector  0x0032   200   200   000    Old_age   Always       -       0
198 Offline_Uncorrectable   0x0030   100   253   000    Old_age   Offline      -       0
199 UDMA_CRC_Error_Count    0x0032   200   200   000    Old_age   Always       -       0
200 Multi_Zone_Error_Rate   0x0008   100   253   000    Old_age   Offline      -       0

SMART Error Log Version: 1
No Errors Logged

SMART Self-test log structure revision number 1
Num  Test_Description    Status                  Remaining  LifeTime(hours)  LBA_of_first_error
# 1  Extended offline    Aborted by host               90%        32         -
# 2  Short offline       Completed without error       00%        31         -
# 3  Short offline       Interrupted (host reset)      90%        17         -
# 4  Extended offline    Aborted by host               90%        17         -
>>> extensive test cancelled after 1 hour stuck at 10%

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.

# dmesg  >>> excerpt from original output, just what seemed most relevant to me

[    0.237514] ACPI: [Firmware Bug]: BIOS _OSI(Linux) query ignored
[    0.239533] ACPI: Interpreter enabled
[    0.239542] ACPI: (supports S0 S3 S4 S5)
[    0.239543] ACPI: Using IOAPIC for interrupt routing
[    0.239696] PCI: Using host bridge windows from ACPI; if necessary, use "pci=nocrs" and report a bug
[    0.239696] ACPI: Enabled 4 GPEs in block 00 to 1F
[    0.243754] ACPI: PCI Root Bridge [PCI0] (domain 0000 [bus 00-ff])
[    0.243758] acpi PNP0A08:00: _OSC: OS supports [ExtendedConfig ASPM ClockPM Segments MSI EDR HPX-Type3]
[    0.243894] acpi PNP0A08:00: _OSC: platform does not support [PCIeHotplug SHPCHotplug PME LTR DPC]
[    0.244023] acpi PNP0A08:00: _OSC: OS now controls [AER PCIeCapability]
[    0.244030] acpi PNP0A08:00: [Firmware Info]: MMCONFIG for domain 0000 [bus 00-7f] only partially covers this bridge
[    0.244263] PCI host bridge to bus 0000:00

[    3.162550] acpi PNP0C14:01: duplicate WMI GUID 05901221-D566-11D1-B2F0-00A0C9062910 (first instance was on PNP0C14:00)
[    3.162605] acpi PNP0C14:02: duplicate WMI GUID 05901221-D566-11D1-B2F0-00A0C9062910 (first instance was on PNP0C14:00)
[    3.162639] acpi PNP0C14:03: duplicate WMI GUID 05901221-D566-11D1-B2F0-00A0C9062910 (first instance was on PNP0C14:00)
[    3.162720] acpi PNP0C14:04: duplicate WMI GUID 05901221-D566-11D1-B2F0-00A0C9062910 (first instance was on PNP0C14:00)

[    3.213892] sp5100_tco: SP5100/SB800 TCO WatchDog Timer Driver
[    3.213948] sp5100-tco sp5100-tco: Using 0xfed80b00 for watchdog MMIO address
[    3.213954] sp5100-tco sp5100-tco: Watchdog hardware is disabled

[ 1631.312328] ata6.00: exception Emask 0x0 SAct 0x20000 SErr 0x50000 action 0x6 frozen
[ 1631.312333] ata6: SError: { PHYRdyChg CommWake }
[ 1631.312336] ata6.00: failed command: READ FPDMA QUEUED
[ 1631.312337] ata6.00: cmd 60/02:88:02:08:00/00:00:00:00:00/40 tag 17 ncq dma 1024 in
                        res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1631.312340] ata6.00: status: { DRDY }
[ 1631.312342] ata6: hard resetting link
[ 1631.778725] ata6: SATA link up 6.0 Gbps (SStatus 133 SControl 300)
[ 1631.779746] ata6.00: configured for UDMA/133
[ 1631.779791] ata6.00: device reported invalid CHS sector 0
[ 1631.779795] ata6: EH complete
[ 1632.718473] EXT4-fs (sda1): mounted filesystem with ordered data mode. Opts: (null). Quota mode: none.
´´´

check cables on the disk

I replaced the data cable and used another available power cable.
Wondering a bit how, but that definitively solved the problem.
Thank you for helping, much appreciated! :relaxed:

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