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Thread: Very slow SDD/HDD performance

  1. #1
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    Very slow SDD/HDD performance

    My fresh Kubuntu 12.10 installation often (but not always) "blocks" when doing things like "sudo apt-get update" and often spends several minutes on "Reading package lists". Other things that take unusally long is the linking stage after compiling programs.

    My setup and symptoms are similar as the ones in this thread.
    I have a Dell Precision M4700, with one SSD and one HDD. Root is mounted on the SSD, and /home and /var are mounted on the HDD. I have /tmp mounted as tmpfs.

    Any suggestions?

  2. #2
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    Re: Very slow SDD/HDD performance

    The lags that happen during "apt-get update" and "apt-get upgrade" are not hardware-related, in all likelihood, they reflect congestion or lags at the repository server. I'm not sure about the linking issue. What makes you attribute the lag to hdd or ssd performance? Have you used hdparm to test the speed of your ssd and hdd?

    Code:
    sudo hdparm -tT /dev/sda
    If the speed figures are respectable (google will help you with that), then you can safely turn your attention to some other source of delay in linking.
    Intel Core i7-950 / Asus P6X58D-E / Nvidia GTX480 / siduction 64-bit on OCZ Revodrive SSD / KDE4.10.2/ Kubuntu 13.04

  3. #3
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    Re: Very slow SDD/HDD performance

    Thanks for your reply.

    Running hdparm -tT gives me reasonable results, I think: cached reads are around 4000 MB/s and buffered reads 100 MB/s for the HDD, and for the SSD I get between 4000 and 11000 MB/s cached reads, and 258 MB/s buffered reads.

    However, I don't think that the "Reading package lists" delay is related to network lag. I just tried "time sudo apt-get update", and it fetched all the data in 5 seconds, and while I'm writing this, it is slowly making its way through reading the downloaded package lists (currently at 7%, and I guess it will be done in a few minutes.)

    KDE's system load applet shows around 40% CPU time spent in I/O wait. A weird thing is that I don't see that when running htop. The line for "apt-get update" shows zero in the IO column.

    I hear a bit of intermittent HDD activity while doing this. I'm not sure which process is doing it though. Since only /home and /var are mounted on the HDD, I would assume that apt-get doesn't need to access the HDD at all.

  4. #4
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    Re: Very slow SDD/HDD performance

    Update: apt-get update just finished, and the result of "time sudo apt-get update" is

    real 34m36.434s
    user 0m28.938s
    sys 0m7.140s

  5. #5
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    Re: Very slow SDD/HDD performance

    I just learned that "time" can output a lot of other information as well. I timed "apt-get update" again, but this time with some more output. I've pasted the output below. I'm not sure what to make of this, though --- whether the volontary and involontary context switches are a problem, for example.

    Anyway, the fact that the process only spends seconds in user and kernel mode, while the wall-clock time is 28 minutes, is puzzling to me.

    Code:
    > 'time' -f "%E real, %U user, %S sys, %F faults, %I inputs, %O outputs, %R minor faults, %W swap, %c invol. cntx-switch, %w vol. cntx-switch" sudo apt-get update
    [sudo] password for martin: 
    Ign http://se.archive.ubuntu.com quantal InRelease
    Ign http://deb.opera.com stable InRelease                                                                                                                                                    
    Ign http://ppa.launchpad.net quantal InRelease                                                                                                                                               
    Hit http://repository.spotify.com stable InRelease                                                                                                                                           
    Hit http://deb.opera.com stable Release.gpg                                                                                                                                                  
    Hit http://deb.opera.com stable Release                                                                                                                                                      
    Ign http://ppa.launchpad.net precise InRelease                                                                                                                                               
    Ign http://extras.ubuntu.com quantal InRelease                                                                                                                                               
    Hit http://deb.opera.com stable/non-free i386 Packages                                                                                                                                       
    Hit http://repository.spotify.com stable/non-free Sources                                                                                                                                    
    Ign http://ppa.launchpad.net quantal InRelease                                                                                                                                               
    Hit http://extras.ubuntu.com quantal Release.gpg                                                                                                                                             
    Ign http://se.archive.ubuntu.com quantal-updates InRelease                                                                                                                                
    Hit http://repository.spotify.com stable/non-free i386 Packages                                                                                                     
    Ign http://ppa.launchpad.net quantal InRelease                                                                                                                      
    Ign http://ppa.launchpad.net quantal InRelease                                                                                                                      
    Ign http://se.archive.ubuntu.com quantal-backports InRelease                                                                                                        
    Ign http://security.ubuntu.com quantal-security InRelease                                                                              
    Hit http://ppa.launchpad.net quantal Release.gpg                                                                                       
    Hit http://extras.ubuntu.com quantal Release                                                                                           
    Hit http://se.archive.ubuntu.com quantal Release.gpg                                                                                                          
    Hit http://ppa.launchpad.net precise Release.gpg                                                                                                              
    Hit http://se.archive.ubuntu.com quantal-updates Release.gpg                                                                            
    Hit http://ppa.launchpad.net quantal Release.gpg                                                                                       
    Hit http://extras.ubuntu.com quantal/main Sources                                                                                      
    Get:1 http://security.ubuntu.com quantal-security Release.gpg [933 B]                                                                  
    Hit http://ppa.launchpad.net quantal Release.gpg                                                                                                                        
    Hit http://se.archive.ubuntu.com quantal-backports Release.gpg                                                                         
    Ign http://deb.opera.com stable/non-free Translation-en_US                                                                             
    Ign http://linux.dropbox.com precise InRelease                                                                                         
    Hit http://extras.ubuntu.com quantal/main i386 Packages                                                                                
    Ign http://deb.opera.com stable/non-free Translation-en                                                                                
    Hit http://se.archive.ubuntu.com quantal Release                                                                                       
    Hit http://ppa.launchpad.net quantal Release.gpg                                                                                                              
    Hit http://se.archive.ubuntu.com quantal-updates Release                                                                                                      
    Hit http://ppa.launchpad.net quantal Release                                                                                                                  
    Get:2 http://security.ubuntu.com quantal-security Release [49.6 kB]                                                                                           
    Hit http://se.archive.ubuntu.com quantal-backports Release                                                                                                              
    Hit http://ppa.launchpad.net precise Release                                                                                                     
    Hit http://ppa.launchpad.net quantal Release                                                                                                                            
    Hit http://se.archive.ubuntu.com quantal/main Sources                                                                                                                   
    Hit http://ppa.launchpad.net quantal Release                                                                                                                            
    Hit http://se.archive.ubuntu.com quantal/restricted Sources                                                                                                             
    Get:3 http://linux.dropbox.com precise Release.gpg [489 B]                                                                                                              
    Hit http://ppa.launchpad.net quantal Release                                                                                                                
    Ign http://repository.spotify.com stable/non-free Translation-en_US                                                                                                     
    Hit http://ppa.launchpad.net quantal/main Sources                                                                                                
    Ign http://repository.spotify.com stable/non-free Translation-en                                                           
    Hit http://se.archive.ubuntu.com quantal/universe Sources                                                                  
    Ign http://extras.ubuntu.com quantal/main Translation-en_US                                                          
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    Ign http://extras.ubuntu.com quantal/main Translation-en                                                                     
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    Get:6 http://linux.dropbox.com precise/main i386 Packages [1,148 B]                                               
    Hit http://ppa.launchpad.net quantal/main Sources                                                                             
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    Hit http://se.archive.ubuntu.com quantal/multiverse i386 Packages                                                      
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    Hit http://ppa.launchpad.net quantal/main Sources                                                    
    Hit http://ppa.launchpad.net quantal/main i386 Packages                                                           
    Hit http://se.archive.ubuntu.com quantal/main Translation-en                                                      
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    Hit http://se.archive.ubuntu.com quantal/multiverse Translation-en                                                
    Hit http://ppa.launchpad.net quantal/main Sources                                           
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    Hit http://se.archive.ubuntu.com quantal-updates/main Sources                                         
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    Get:11 http://security.ubuntu.com quantal-security/restricted i386 Packages [14 B]                                  
    Hit http://se.archive.ubuntu.com quantal-updates/main Translation-en                                                       
    Get:12 http://security.ubuntu.com quantal-security/universe i386 Packages [42.3 kB]           
    Hit http://se.archive.ubuntu.com quantal-updates/multiverse Translation-en                                                    
    Hit http://se.archive.ubuntu.com quantal-updates/restricted Translation-en                                                    
    Hit http://se.archive.ubuntu.com quantal-updates/universe Translation-en                                            
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    Get:13 http://security.ubuntu.com quantal-security/multiverse i386 Packages [1,397 B]         
    Hit http://se.archive.ubuntu.com quantal-backports/restricted Sources                                                            
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    Hit http://se.archive.ubuntu.com quantal-backports/main i386 Packages                         
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    Hit http://security.ubuntu.com quantal-security/main Translation-en                           
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    Ign http://ppa.launchpad.net quantal/main Translation-en_US                                 
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    Fetched 239 kB in 4s (49.3 kB/s)
    Reading package lists... Done
    28:53.26 real, 24.37 user, 5.55 sys, 20 faults, 2728 inputs, 3851424 outputs, 495023 minor faults, 0 swap, 1695 invol. cntx-switch, 394480 vol. cntx-switch

  6. #6
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    Re: Very slow SDD/HDD performance

    Hmmmmm -- yes, there is something off on that system. I just ran the same command (thanks for that!) on a fully-updated Kubuntu 12.10 system, and got this result:

    Code:
    0:09.01 real, 1.22 user, 0.51 sys, 43 faults, 206672 inputs, 161104 outputs, 22915 minor faults, 0 swap, 501 invol. cntx-switch, 864 vol. cntx-switch
    The dpkg system does its caching and logging in /var. It's not obvious to me, with what you've described about your system, why that would be relevant, but it is an unusual configuration to have /var mounted separately from the rest of the root filesystem. I still don't believe that hard drive performance is at the root of your issue, but possibly a caching function is not working correctly. As an experiment, could you mount /var on the SSD with the rest of the root filesystem? It might or might not reveal something about the source of the sluggishness.
    Last edited by dabl; February 27th, 2013 at 04:02 PM.
    Intel Core i7-950 / Asus P6X58D-E / Nvidia GTX480 / siduction 64-bit on OCZ Revodrive SSD / KDE4.10.2/ Kubuntu 13.04

  7. #7
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    Re: Very slow SDD/HDD performance

    this is your config right (this is how i do it with a ssd/hdd)
    /dev/sda is your ssd
    /dev/sdb is your hdd
    / is mounted to /dev/sda1
    /var is mounted to /dev/sdb1
    /home is mount to /dev/sdb2
    /tmp is mounted to the ram
    swap is mount to /dev/sdb3

    what is the free space in /var (/dev/sdb1) and / (/dev/sda1)

    i assume you have trim enabled (discard in /etc/fstab on /dev/sda1)
    your sata controller need to be in AHCI more for that to work BTW (set this in your BIOS)
    Laptop: ASUS A54C-NB91 (Storage: WD3200BEKT + MKNSSDCR60GB-DX); Desktop: Custom Build - Images included
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  8. #8
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    Re: Very slow SDD/HDD performance

    Actually, sda is my HDD and sdb is my SSD. I also have a few partitions that came with the computer, so to speak: a Dell recovery partition and a Windows partition.
    Following is the relevant output from "mount":

    Code:
    dev/sdb5 on / type ext4 (rw,noatime,nodiratime,errors=remount-ro,discard)
    /dev/sda8 on /home type ext4 (rw,relatime)
    /dev/sda6 on /var type ext4 (rw,relatime)
    tmpfs on /tmp type tmpfs (rw,mode=1777)
    And free space:

    Code:
    > df /var
    Filesystem      Size  Used Avail Use% Mounted on
    /dev/sda6       4.6G  2.0G  2.4G  46% /var
    
    > df /
    Filesystem      Size  Used Avail Use% Mounted on
    /dev/sdb5        55G  9.1G   43G  18% /
    I also have a 16-GB swap partition on /dev/sda5. And yes, I have set ACPI mode in BIOS.


    I will try mounting /var with the rest of the root file system on the SSD. But I don't know if I dare to do that while running? I think I'll try it next time I reboot.

  9. #9
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    Re: Very slow SDD/HDD performance

    I would change the mount line in /etc/fstab to reflect the new mount point, and then shutdown and reboot, to avoid disturbing the system logging processes.

    How about the dpkg cache --- has it been cleared lately?

    Code:
    sudo apt-get clean
    Intel Core i7-950 / Asus P6X58D-E / Nvidia GTX480 / siduction 64-bit on OCZ Revodrive SSD / KDE4.10.2/ Kubuntu 13.04

  10. #10
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    Re: Very slow SDD/HDD performance

    Question: Did you explicitly mount /tmp in /etc/fstab, or is that a default configuration? The reason I ask, my 12.10 system (a VM) does not show a separate mount or filesystem for /tmp.
    Last edited by dabl; February 28th, 2013 at 08:14 PM.
    Intel Core i7-950 / Asus P6X58D-E / Nvidia GTX480 / siduction 64-bit on OCZ Revodrive SSD / KDE4.10.2/ Kubuntu 13.04

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