Slow file access

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Here's the situation:

I have some large mysql db files on my main partition. For some strange reason, some of these files are very slow to be read off the disk: ~3MB/s (I'm SCPing them to another machine). File size doesn't seem to be relevant (other files of approximately same size are being transferred at ~20MB/s), and the speed is not the same throughout the file.

My first thought was that the file got very fragmented (I'm fairly sure that the partition was filled up to [almost] 100% at some point). Usually, that can be remedied by copying the file to another location on the same partition.. or rather, that's what would fix fragmented files on NTFS. When I tried that, the read speed of the new file was better by a small amount (up to ~5MB/s) - although that could be because the file was still in the memory cache.

I also thought that HD might be nearing the end of its useful lifetime (and has to re-read the sectors, causing the horrible slowdown), but I didn't notice any alerts from SMART (including the output of smartctl -a, anyway)

The partition is ~60-70% full, type ext3 with noatime enabled.
Speed tests were performed by "scp myfile localhost:/dev/null"



smartctl version 5.33 [i386-redhat-linux-gnu] Copyright (C) 2002-4 Bruce Allen
Home page is http://smartmontools.sourceforge.net/

=== START OF INFORMATION SECTION ===
Device Model:     ST3300831A
Serial Number:    3NF17FA8
Firmware Version: 3.04
User Capacity:    300,069,052,416 bytes
Device is:        Not in smartctl database [for details use: -P showall]
ATA Version is:   7
ATA Standard is:  Exact ATA specification draft version not indicated
Local Time is:    Tue Dec  4 14:01:27 2007 PST
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: 		 ( 430) 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: 	 (   1) minutes.
Extended self-test routine
recommended polling time: 	 ( 101) minutes.

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   062   050   006    Pre-fail  Always       -       217294
  3 Spin_Up_Time            0x0003   097   097   000    Pre-fail  Always       -       0
  4 Start_Stop_Count        0x0032   100   100   020    Old_age   Always       -       25
  5 Reallocated_Sector_Ct   0x0033   100   100   036    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x000f   081   060   030    Pre-fail  Always       -       8837462413
  9 Power_On_Hours          0x0032   084   084   000    Old_age   Always       -       14629
 10 Spin_Retry_Count        0x0013   100   100   097    Pre-fail  Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   020    Old_age   Always       -       59
194 Temperature_Celsius     0x0022   047   064   000    Old_age   Always       -       47 (Lifetime Min/Max 0/22)
195 Hardware_ECC_Recovered  0x001a   062   049   000    Old_age   Always       -       217294
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
200 Multi_Zone_Error_Rate   0x0000   100   253   000    Old_age   Offline      -       0
202 TA_Increase_Count       0x0032   100   253   000    Old_age   Always       -       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.

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