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I have set up a machine that I use as a server using Ubuntu 20.04 . The machine worked perfectly but lately, it started giving me a really strange behavior. One time while I was working remotely suddenly I could not use anything. All the binaries were unreachable and whenever I was trying to invoke them using their path as /usr/bin/echo "Test" for example I was prompted a cannot <command>: Input/Output error.

After looking online I found out that this may be due to a hard-drive problem. But my question is, how can I resolve this? Obviously, the system's condition is not stable and it has to be resolved. Any suggestions?

Here is a sample from the dmesg -T --level=warn,err log after the machine was rebooted from a colleague, although I cannot see it linking the issue to the hard disk somehow. dmesg output

smartmontools log (sudo smartctl -a /dev/sda)

smartctl 7.1 2019-12-30 r5022 [x86_64-linux-5.4.0-47-generic] (local build)
Copyright (C) 2002-19, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Model Family:     Toshiba X300
Device Model:     TOSHIBA HDWE140
Serial Number:    69F9K2YWFBBG
LU WWN Device Id: 5 000039 95bb0145e
Firmware Version: FP1R
User Capacity:    4,000,787,030,016 bytes [4.00 TB]
Sector Sizes:     512 bytes logical, 4096 bytes physical
Rotation Rate:    7200 rpm
Form Factor:      3.5 inches
Device is:        In smartctl database [for details use: -P show]
ATA Version is:   ATA8-ACS (minor revision not indicated)
SATA Version is:  SATA 3.0, 6.0 Gb/s (current: 6.0 Gb/s)
Local Time is:    Fri Sep 25 15:35:54 2020 CEST
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:  (0x82) Offline data collection activity
                    was completed without error.
                    Auto Offline Data Collection: Enabled.
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:        (  120) seconds.
Offline data collection
capabilities:            (0x5b) SMART execute Offline immediate.
                    Auto Offline data collection on/off support.
                    Suspend Offline collection upon new
                    command.
                    Offline surface scan supported.
                    Self-test supported.
                    No 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:    ( 479) minutes.
SCT capabilities:          (0x003d) SCT Status supported.
                    SCT Error Recovery Control 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     0x000b   100   100   050    Pre-fail  Always       -       0
  2 Throughput_Performance  0x0005   100   100   050    Pre-fail  Offline      -       0
  3 Spin_Up_Time            0x0027   100   100   001    Pre-fail  Always       -       4092
  4 Start_Stop_Count        0x0032   100   100   000    Old_age   Always       -       12
  5 Reallocated_Sector_Ct   0x0033   100   100   050    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x000b   100   100   050    Pre-fail  Always       -       0
  8 Seek_Time_Performance   0x0005   100   100   050    Pre-fail  Offline      -       0
  9 Power_On_Hours          0x0032   096   096   000    Old_age   Always       -       1886
 10 Spin_Retry_Count        0x0033   100   100   030    Pre-fail  Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       12
191 G-Sense_Error_Rate      0x0032   100   100   000    Old_age   Always       -       6
192 Power-Off_Retract_Count 0x0032   100   100   000    Old_age   Always       -       8
193 Load_Cycle_Count        0x0032   100   100   000    Old_age   Always       -       12
194 Temperature_Celsius     0x0022   100   100   000    Old_age   Always       -       48 (Min/Max 26/55)
196 Reallocated_Event_Count 0x0032   100   100   000    Old_age   Always       -       0
197 Current_Pending_Sector  0x0032   100   100   000    Old_age   Always       -       0
198 Offline_Uncorrectable   0x0030   100   100   000    Old_age   Offline      -       0
199 UDMA_CRC_Error_Count    0x0032   200   253   000    Old_age   Always       -       0
220 Disk_Shift              0x0002   100   100   000    Old_age   Always       -       0
222 Loaded_Hours            0x0032   096   096   000    Old_age   Always       -       1886
223 Load_Retry_Count        0x0032   100   100   000    Old_age   Always       -       0
224 Load_Friction           0x0022   100   100   000    Old_age   Always       -       0
226 Load-in_Time            0x0026   100   100   000    Old_age   Always       -       573
240 Head_Flying_Hours       0x0001   100   100   001    Pre-fail  Offline      -       0


SMART Error Log Version: 1
No Errors Logged


SMART Self-test log structure revision number 1
No self-tests have been logged.  [To run self-tests, use: smartctl -t]


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.
ex1led
  • 286
  • First sudo apt install smartmontools then post the output of sudo smartctl -a /dev/sda. Your dmesg doesn't contain any relevant info. journalctl -k could be more useful. – Artem S. Tashkinov Sep 25 '20 at 13:29
  • @ArtemS.Tashkinov done. – ex1led Sep 25 '20 at 13:38
  • Your disk looks perfectly fine and I've no idea what could be the source of your errors. But then smartctl log doesn't always paint the full picture, e.g. you might have faulty cables or interference. – Artem S. Tashkinov Sep 25 '20 at 17:22
  • @ArtemS.Tashkinov So, where else should I look in order to resolve this problem? – ex1led Sep 28 '20 at 06:08
  • How often does this happen to you? Can you try changing the cable? – Artem S. Tashkinov Sep 29 '20 at 10:07
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    The period of the occurrences is not fixed. Nor do I have in mind a specific event that raises such kind of errors on the system because it happened in situations that were irrelevant to each other. Since this machine is located in my office at a remote location I cannot access it to change the disk cable but I will bear that in mind and try to change it when I will be able to do so. This happened 3 times in total up to my knowledge with the last 2 occuring within a week. During that time the machine was running some C++ code. – ex1led Oct 02 '20 at 12:10

1 Answers1

1

So, finally, I had a chance to take look at the actual machine and perform some changes.

The issue, (at least it seems like that) was solved by doing the following; The SATA port#0 on the Motherboard, had a dangling cable that was NOT connected to any HDD or SSD. Instead, my HDD was connected with another cable on SATA port#1. It is true that in many cases, the motherboard prioritizes the SATA slots according to their ID ( 0 > 1 > 2 > 3 > ... ).

So, I removed the dangling cable (which honestly, I have no idea who put it up there on the first place), and then I booted up the machine.

Ever since I did this stupid change, namely removing a dangling cable from the SATA hub on the motherboard, the problem did not appear again. Obviously it was not a matter of a faulty disk partition since all of the disks were new and in great shape.

ex1led
  • 286