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Thread: New Install - Very slow at "Reading package lists..." in apt-get

  1. #1

    New Install - Very slow at "Reading package lists..." in apt-get

    I was running Ubuntu 12.10 on an older computer but on Friday I gathered a stack of new equipment and excitedly assembled a fresh new machine.

    The new machine has Intel i7, 32 GB ram, and a Samsung SSD (Pro 840). This should be a speedy machine.

    The Ubuntu install was very slow (took 6 hours, most of that was spent transferring from the CD to the SDD).

    After rebooting I noticed that performance was not great, so I went through the standard SSD tweaks and now I get very high numbers for both read and write.

    Performance is great except for one occasion, "apt-get update", or software center.

    I develop code under contract using this computer, so I primarily use the command line. However when I execute the update command "apt-get update" it has a performance issue.

    After downloading all the files it gets to the section of "Reading package lists..." and takes several minutes. I wrote this post and it is still going. I would estimate that it is more than 10 minutes. My old AMD Athon computer did this same process in seconds. Something is wrong.

    Anyone else ever experience a similar problem?

  2. #2
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    Re: New Install - Very slow at "Reading package lists..." in apt-get

    Have the same problem. It might not be that slow as you described it, but everytime using apt "reading package lists ... " takes about a minute or more. The installation also took quite long (longer than I experienced so far).

    My machine looks like this:
    intel i7, 24 Gig RAM and 2 SSDs - one for / and one for /home. (Corsair CSSD-F60GB2).

    I installed the 12.10 several day's ago. With 12.04 I did not have had this problem.


    By the way, what did you do, to speed up your system - regarding the SSD's?

    br
    Last edited by another1LinuxUser; January 14th, 2013 at 04:17 PM.

  3. #3
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    Re: New Install - Very slow at "Reading package lists..." in apt-get

    6 hours to install is crazy! What internet speed you got as am hoping its awful and the 6 hours was due to pulling in updates.

    Not sure if this is the issue you face but try hash our all the deb-src entries in

    Code:
    gksudo gedit /etc/apt/sources.list
    eg

    Code:
    # deb-src http://archive.canonical.com/ubuntu precise partner

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    Re: New Install - Very slow at "Reading package lists..." in apt-get

    My system is a 6 year old dual core with 4GB of RAM. It took about 9 minutes to install to my new SSD a year ago and new clean installs take about the same amount of time. I do install from ISO on hard drive to SSD.

    My Internet is fairly fast but it does take 10 to 20 minutes to download updates depending on how old ISO is to current and most of my configuration is now scripted so I have a full working install in about an hour.
    But even on my old laptop with hard drive from flash drive installed in 20 to 30 minutes.

    Something is really wrong if it is taking that much time.

    Is system in BIOS or UEFI mode? IF BIOS do you have AHCI on?

    Have you partitioned in advance or just used auto install?

    Is UEFI/BIOS up to date and SSDs version?

    https://wiki.archlinux.org/index.php/SSD_Benchmarking

    New SSDs have twice the speed as my low cost year old one.

    SSD speed
    fred@fred-Precise:~$ sudo hdparm -t /dev/sdd4
    /dev/sdd4:
    Timing buffered disk reads: 626 MB in 3.01 seconds = 208.20 MB/sec
    Older 160GB rotating drive:
    /dev/sdb4:
    Timing buffered disk reads: 212 MB in 3.01 seconds = 70.46 MB/sec
    Last edited by oldfred; January 14th, 2013 at 06:15 PM.
    For more info on UEFI boot install & repair - Regularly Updated :
    http://ubuntuforums.org/showthread.php?t=2147295
    Please use Thread Tools above first post to change to [Solved] when/if answered completely.

  5. #5

    Re: New Install - Very slow at "Reading package lists..." in apt-get

    Quote Originally Posted by another1LinuxUser View Post
    By the way, what did you do, to speed up your system - regarding the SSD's?
    Here are the instructions that I used to optimize Ubuntu for the SSD

    http://www.howtogeek.com/62761/how-t...r-performance/

    Sorry that yours is running slow, though I wish mine was done in a few minutes

  6. #6

    Re: New Install - Very slow at "Reading package lists..." in apt-get

    Quote Originally Posted by SlugSlug View Post
    6 hours to install is crazy! What internet speed you got as am hoping its awful and the 6 hours was due to pulling in updates.

    Not sure if this is the issue you face but try hash our all the deb-src entries in

    Code:
    gksudo gedit /etc/apt/sources.list
    eg

    Code:
    # deb-src http://archive.canonical.com/ubuntu precise partner
    Thank-you for the suggestion, but I do not think it has to do with the internet speed. I am on a 10 mbps connection and the download portion of any Ubuntu updates is very fast. It seems to have something to do with the local machine.

  7. #7

    Re: New Install - Very slow at "Reading package lists..." in apt-get

    Quote Originally Posted by oldfred View Post
    My system is a 6 year old dual core with 4GB of RAM. It took about 9 minutes to install to my new SSD a year ago and new clean installs take about the same amount of time. I do install from ISO on hard drive to SSD.

    My Internet is fairly fast but it does take 10 to 20 minutes to download updates depending on how old ISO is to current and most of my configuration is now scripted so I have a full working install in about an hour.
    But even on my old laptop with hard drive from flash drive installed in 20 to 30 minutes.

    Something is really wrong if it is taking that much time.

    Is system in BIOS or UEFI mode? IF BIOS do you have AHCI on?

    Have you partitioned in advance or just used auto install?

    Is UEFI/BIOS up to date and SSDs version?

    https://wiki.archlinux.org/index.php/SSD_Benchmarking

    New SSDs have twice the speed as my low cost year old one.

    SSD speed
    fred@fred-Precise:~$ sudo hdparm -t /dev/sdd4
    /dev/sdd4:
    Timing buffered disk reads: 626 MB in 3.01 seconds = 208.20 MB/sec
    Older 160GB rotating drive:
    /dev/sdb4:
    Timing buffered disk reads: 212 MB in 3.01 seconds = 70.46 MB/sec
    I started the install at 1:30 pm Saturday afternoon and walked away at 2:00. I came back every half hour or so to check on it... but it really took until 6:00 pm to finish. I guess that is not quite 6 hours, but it took a long time. I was so excited to see the performance of the new hardware.... this was not fun.

    I partitioned in advance. SSD is '/' and a 1TB platter is '/home/'.

    Good call on the BIOS revision. I checked and I am using a Gigabyte GA-P75-D3 and it has revision 3 of the BIOS. The current stable revision is 9 (beta is 10). I will try to install revision 9 now.

    As for the SSD, is there a way to check the firmware revision from Linux?

    Originally I had the system setup with IDE mode (BIOS came that way by default, but I switched it to AHCI which did not help.

    Here is what I got from hdparam:
    sudo hdparm -t /dev/sda1

    /dev/sda1:
    Timing buffered disk reads: 656 MB in 3.38 seconds = 194.06 MB/sec

    ran it a second time:
    sudo hdparm -t /dev/sda1

    /dev/sda1:
    Timing buffered disk reads: 64 MB in 3.04 seconds = 21.04 MB/sec

    That does not bode well....

  8. #8
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    Re: New Install - Very slow at "Reading package lists..." in apt-get

    Trim does not work unless you have AHCI on.

    New partition tools should set partition alignment correctly. All partitions starts should be divisible by 8. First partition start should be sector 2048.

    You may need to clean up SSD.

    I did not correctly enable trim with first install, so I ran this:
    fred@fred-Precise:~$ sudo fstrim -v /
    /: 23267893248 bytes were trimmed

    https://wiki.archlinux.org/index.php..._Cell_Clearing
    sudo hdparm -I /dev/sdX
    Alternate to discard, call fstrim via cron
    http://opensuse.14.n6.nabble.com/SSD...td3313048.html
    test if trim working using hdparm
    http://techgage.com/article/enabling..._under_linux/2
    For more info on UEFI boot install & repair - Regularly Updated :
    http://ubuntuforums.org/showthread.php?t=2147295
    Please use Thread Tools above first post to change to [Solved] when/if answered completely.

  9. #9
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    Re: New Install - Very slow at "Reading package lists..." in apt-get

    For the update issue you may want to change download server in update manager settings. If the operating system and download server are the same as the old AMD computer the problem may be elsewhere.

    Use software sources to change the sever so you don't have to wait for the update manager to finish before entering settings.
    Last edited by Frogs Hair; January 15th, 2013 at 03:50 PM.
    “Start where you are. Use what you have. Do what you can."

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  10. #10

    Re: New Install - Very slow at "Reading package lists..." in apt-get

    Quote Originally Posted by oldfred View Post
    Trim does not work unless you have AHCI on.

    New partition tools should set partition alignment correctly. All partitions starts should be divisible by 8. First partition start should be sector 2048.

    You may need to clean up SSD.

    I did not correctly enable trim with first install, so I ran this:
    fred@fred-Precise:~$ sudo fstrim -v /
    /: 23267893248 bytes were trimmed

    https://wiki.archlinux.org/index.php..._Cell_Clearing
    sudo hdparm -I /dev/sdX
    Alternate to discard, call fstrim via cron
    http://opensuse.14.n6.nabble.com/SSD...td3313048.html
    test if trim working using hdparm
    http://techgage.com/article/enabling..._under_linux/2

    1. I updated the BIOS and it did not help with performance.

    2. I do have the BIOS set to AHCI (was not during Ubuntu install)

    Thank-you for the links and suggestions. Here is what I found:

    $ sudo fstrim -v /
    /: 121008021504 bytes were trimmed


    $ sudo hdparm -I /dev/sda

    /dev/sda:

    ATA device, with non-removable media
    Model Number: Samsung SSD 840 PRO Series
    Serial Number: S12PNEACB11500H
    Firmware Revision: DXM03B0Q
    Media Serial Num: 00000000000000000000
    Transport: Serial, ATA8-AST, SATA 1.0a, SATA II Extensions, SATA Rev 2.5, SATA Rev 2.6, SATA Rev 3.0
    Standards:
    Used: unknown (minor revision code 0x0039)
    Supported: 9 8 7 6 5
    Likely used: 9
    Configuration:
    Logical max current
    cylinders 16383 16383
    heads 16 16
    sectors/track 63 63
    --
    CHS current addressable sectors: 16514064
    LBA user addressable sectors: 250069680
    LBA48 user addressable sectors: 250069680
    Logical Sector size: 512 bytes
    Physical Sector size: 512 bytes
    Logical Sector-0 offset: 0 bytes
    device size with M = 1024*1024: 122104 MBytes
    device size with M = 1000*1000: 128035 MBytes (128 GB)
    cache/buffer size = unknown
    Nominal Media Rotation Rate: Solid State Device
    Capabilities:
    LBA, IORDY(can be disabled)
    Queue depth: 32
    Standby timer values: spec'd by Standard, no device specific minimum
    R/W multiple sector transfer: Max = 16 Current = 16
    DMA: mdma0 mdma1 mdma2 udma0 udma1 udma2 udma3 udma4 udma5 *udma6
    Cycle time: min=120ns recommended=120ns
    PIO: pio0 pio1 pio2 pio3 pio4
    Cycle time: no flow control=120ns IORDY flow control=120ns
    Commands/features:
    Enabled Supported:
    * SMART feature set
    Security Mode feature set
    * Power Management feature set
    * Write cache
    * Look-ahead
    * Host Protected Area feature set
    * WRITE_BUFFER command
    * READ_BUFFER command
    * NOP cmd
    * DOWNLOAD_MICROCODE
    SET_MAX security extension
    * 48-bit Address feature set
    * Device Configuration Overlay feature set
    * Mandatory FLUSH_CACHE
    * FLUSH_CACHE_EXT
    * SMART error logging
    * SMART self-test
    * General Purpose Logging feature set
    * WRITE_{DMA|MULTIPLE}_FUA_EXT
    * 64-bit World wide name
    Write-Read-Verify feature set
    * WRITE_UNCORRECTABLE_EXT command
    * {READ,WRITE}_DMA_EXT_GPL commands
    * Segmented DOWNLOAD_MICROCODE
    * Gen1 signaling speed (1.5Gb/s)
    * Gen2 signaling speed (3.0Gb/s)
    * Gen3 signaling speed (6.0Gb/s)
    * Native Command Queueing (NCQ)
    * Phy event counters
    * unknown 76[15]
    * DMA Setup Auto-Activate optimization
    Device-initiated interface power management
    Asynchronous notification (eg. media change)
    * Software settings preservation
    unknown 78[8]
    * SMART Command Transport (SCT) feature set
    * SCT LBA Segment Access (AC2)
    * SCT Error Recovery Control (AC3)
    * SCT Features Control (AC4)
    * SCT Data Tables (AC5)
    * SET MAX SETPASSWORD/UNLOCK DMA commands
    * WRITE BUFFER DMA command
    * READ BUFFER DMA command
    * Data Set Management TRIM supported (limit 8 blocks)
    * Deterministic read ZEROs after TRIM
    Security:
    Master password revision code = 65534
    supported
    not enabled
    not locked
    frozen
    not expired: security count
    supported: enhanced erase
    2min for SECURITY ERASE UNIT. 2min for ENHANCED SECURITY ERASE UNIT.
    Logical Unit WWN Device Identifier: 500253855003dca4
    NAA : 5
    IEEE OUI : 002538
    Unique ID : 55003dca4
    Checksum: correct



    I am going to try to boot windows and see if the performance improves. Perhaps my drive is faulty.

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