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  • Find and free disk space that is unused but unavailable (due to file system error, etc.)

    - by Voyagerfan5761
    Sometimes I get the feeling that if an app such as μTorrent allocates files on my FAT32-formatted flash drive, but then is killed or crashes (as happens more than a few times a month), that space just disappears from my file system. Whether or not that is the case, sometimes I do get a chill from wondering if I've lost hundreds of MB in available storage due to carelessness or malfunctions. Checking my disk with WinDirStat just makes it worse, because I see the huge "<Unknown>" item at the disk root staring at me, eating up well over a gigabyte. It might be FS inefficiency (due to 32 or 64kb sector/cluster size and a lot of tiny files) or it might be a glitch... Is there a tool I can download and run to check my file system and make sure that there aren't any unused allocated blocks on the disk? I want to make sure I'm not losing any disk space to I/O errors, etc.

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  • Why do [flush-8:16] and [jbd2/sdb2-8] occasionally use 99.99% disk IO?

    - by ændrük
    Approximately twice a week, the entire graphical interface will lock up for about 10-20 seconds without warning while I am doing simple tasks such as browsing the web or writing a paper. When this happens, GUI elements do not respond to mouse or keyboard input, and the System Monitor applet displays 100% IOWait processor usage. Today, I finally happened to have GNOME Terminal already open when the problem started. Despite other applications such as Google Chrome, Firefox, GNOME Do, and GNOME Panel being unresponsive, the terminal was usable. I ran iotop and observed that commands named [flush-8:16] and [jbd2/sdb2-8] were alternately using 99.99% IO. What are these, and how can I prevent them from causing GUI unresponsiveness? Here is dumpe2fs /dev/sdb2, if it's relevant.

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  • When to use Truecrypt, and when not to?

    - by tm77
    I have about 30 (this number will most likely grow over the next few years to 50 or more) unencrypted laptops that I have been tasked to encrypt (entire drive). These machines will be used off site regularly by my users. These machines are running Windows 7 and XP (about 50/50), but more Windows 7 every month. I have experience with Truecrypt, and have had no issues. It appears to be THE solution for a free solution. My concern with Truecrypt is that my users will have 2 passswords needed to login to their machines. Also, I need to choose to either have 1 password for my organization, or carefully document each machine's password (management nightmare). In my mind, choosing between a managed and a free encryption solution is primarily based on the NUMBER of machines that will be encrypted and supported. Two questions: From a management standpoint, what is the tipping point of users where a managed solution would pay for itself over Truecrypt? What are some good third party solutions? (I will consider Bitlocker, but the price to upgrade Windows 7 licenses is a turn-off) I would love to hear from some admins with experience in supporting encrypted machines in a corporate environment. Many thanks in advance!

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  • Automount of external hard disk

    - by moose
    I have an Intenso 6002560 1TB Memory Station - an external hard disk. This hard disk gets connected via Y-USB cable. When I connect both USB-ends to my Notebook, it gets recognized by my Ubuntu 10.04.4 LTS system: moose@pc07:~$ lsusb [...] Bus 002 Device 005: ID 13fd:1840 Initio Corporation [...] and Disk /dev/sda: 320.1 GB, 320072933376 bytes 255 heads, 63 sectors/track, 38913 cylinders Units = cylinders of 16065 * 512 = 8225280 bytes Sector size (logical/physical): 512 bytes / 512 bytes I/O size (minimum/optimal): 512 bytes / 512 bytes Disk identifier: 0x00065e10 Device Boot Start End Blocks Id System /dev/sda1 * 1 37810 303704064 83 Linux /dev/sda2 37810 38914 8864769 5 Extended /dev/sda5 37810 38914 8864768 82 Linux swap / Solaris Disk /dev/sdc: 1000.2 GB, 1000204886016 bytes 255 heads, 63 sectors/track, 121601 cylinders Units = cylinders of 16065 * 512 = 8225280 bytes Sector size (logical/physical): 512 bytes / 512 bytes I/O size (minimum/optimal): 512 bytes / 512 bytes Disk identifier: 0x0d6ea32a Device Boot Start End Blocks Id System /dev/sdc1 1 121601 976759008+ c W95 FAT32 (LBA) But it did not get mounted: moose@pc07:/dev$ mount -l /dev/sda1 on / type ext4 (rw,errors=remount-ro,user_xattr) proc on /proc type proc (rw,noexec,nosuid,nodev) none on /sys type sysfs (rw,noexec,nosuid,nodev) none on /sys/fs/fuse/connections type fusectl (rw) none on /sys/kernel/debug type debugfs (rw) none on /sys/kernel/security type securityfs (rw) none on /dev type devtmpfs (rw,mode=0755) none on /dev/pts type devpts (rw,noexec,nosuid,gid=5,mode=0620) none on /dev/shm type tmpfs (rw,nosuid,nodev) none on /var/run type tmpfs (rw,nosuid,mode=0755) none on /var/lock type tmpfs (rw,noexec,nosuid,nodev) none on /lib/init/rw type tmpfs (rw,nosuid,mode=0755) binfmt_misc on /proc/sys/fs/binfmt_misc type binfmt_misc (rw,noexec,nosuid,nodev) gvfs-fuse-daemon on /home/moose/.gvfs type fuse.gvfs-fuse-daemon (rw,nosuid,nodev,user=moose) However, I could mount it manually with mount -t vfat /dev/sdc1 /mnt/sdc1 as you can see here: moose@pc07:~$ mount -l /dev/sda1 on / type ext4 (rw,errors=remount-ro,user_xattr) proc on /proc type proc (rw,noexec,nosuid,nodev) none on /sys type sysfs (rw,noexec,nosuid,nodev) none on /sys/fs/fuse/connections type fusectl (rw) none on /sys/kernel/debug type debugfs (rw) none on /sys/kernel/security type securityfs (rw) none on /dev type devtmpfs (rw,mode=0755) none on /dev/pts type devpts (rw,noexec,nosuid,gid=5,mode=0620) none on /dev/shm type tmpfs (rw,nosuid,nodev) none on /var/run type tmpfs (rw,nosuid,mode=0755) none on /var/lock type tmpfs (rw,noexec,nosuid,nodev) none on /lib/init/rw type tmpfs (rw,nosuid,mode=0755) binfmt_misc on /proc/sys/fs/binfmt_misc type binfmt_misc (rw,noexec,nosuid,nodev) gvfs-fuse-daemon on /home/moose/.gvfs type fuse.gvfs-fuse-daemon (rw,nosuid,nodev,user=moose) /dev/sdc1 on /mnt/sdc1 type vfat (rw) edit: Another command: moose@pc07:~$ sudo blkid -o list device fs_type label mount point UUID ---------------------------------------------------------------------------------------------------------------------- /dev/sda1 ext4 / 45eb611b-517e-425b-8057-0391726cccd5 /dev/sda5 swap <swap> e9dc42f3-594c-4b62-874a-305eda5eed41 moose@pc07:~$ blkid -o list device fs_type label mount point UUID ---------------------------------------------------------------------------------------------------------------------- /dev/sda1 ext4 / 45eb611b-517e-425b-8057-0391726cccd5 /dev/sda5 swap <swap> e9dc42f3-594c-4b62-874a-305eda5eed41 /dev/sdc1 /mnt/sdc1 edit: another command: moose@pc07:~$ ls -l /dev/disk/by-uuid/ total 0 lrwxrwxrwx 1 root root 10 2012-09-30 09:31 45eb611b-517e-425b-8057-0391726cccd5 -> ../../sda1 lrwxrwxrwx 1 root root 10 2012-09-30 09:31 e9dc42f3-594c-4b62-874a-305eda5eed41 -> ../../sda5 Here is a link to a Launchpad question about this problem. But I would like it to mount automatically. What do I have to do?

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  • How to create VHD disk image from a Linux live system?

    - by Federico
    Once more, I have to resort at the experts here at SuperUser, as my other sources (mainly Google ;-)) didn't prove very helpful... So basically, I would like to create a VHD image of a physical disk to be archived/accessed/maybe even mounted in a virtual machine. Now, there are dozens of articles and tutorials on how to do that on the web, but none that meets exactly the conditions I would like to achieve: I would like the destination file to be a VHD image, as Windows 7 can mount it natively, even over the network and many other programs can use it (VirtualBox, ...) The disk I'm trying to image contains a Windows XP install, so in theory, I could use the disk2vhd utility, but I would like to find a solution that doesn't require booting that Windows XP install (ie keep the disk read-only) Thus I was searching for a solution involving some sort of live system (running from a USB stic or the network) However, all the solutions that I've came across either make use of disk2vhd or use the dd command under linux, which does a complete copy of the disk (ie even empty blocks) and does not output a VHD file. Is there a tool/program under Linux that can directly create a VHD file? Or is is possible to convert a raw disk image created using dd to a VHD file, without allocating space for the empty blocks? How would you proceed? As always, any advice or comment is highly appreciated!!

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  • CentOS 5.5 installation on disk image

    - by Dima
    Today, in order to install CentOS 5.5 I'm using kickstart script. I would like to install CentOS on different way: Create disk image (using dd command) Create filesystem on this disk image using mkfs.ext3 Install CentOS on this filesystem Make this disk image bootable (using grub-install) Copy the disk image to the physical hard disk (using dd command) I know to do all these items except 3. Is it possible to do it? If yes, how can I install CentOS on the disk image?

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  • limit linux background flush (dirty pages)

    - by korkman
    Background flushing in linux happens when either too much written data is pending (adjustable via /proc/sys/vm/dirty_background_ratio) or a timeout for pending writes is reached (/proc/sys/vm/dirty_expire_centisecs). Unless another limit is being hit (/proc/sys/vm/dirty_ratio), more written data may be cached. Further writes will block. In theory, this should create a background process writing out dirty pages without disturbing other processes. In practice, it does disturb any process doing uncached reading or synchronous writing. Badly. This is because the background flush actually writes at 100% device speed and any other device requests at this time will be delayed (because all queues and write-caches on the road are filled). Is there any way to limit the amount of requests per second the flushing process performs, or otherwise effectively prioritize other device I/O?

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  • Disallow user from decrypting the startup disk

    - by Blacklight Shining
    When you enable FileVault's full-disk encryption, it asks for the password of each account on the system to allow every user to decrypt the disk. You can simply choose not to have a user enter their password, and they will not be able to decrypt the disk. However, if you create an account after enabling disk encryption, the user is automatically allowed to decrypt the disk. How do I disallow a user from decrypting the startup disk?

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  • Ubuntu 12.04.1 LTS USB not being detected after formatting with Startup Disk Creator

    - by Zach
    sudo fdisk -l lists the drive, however, I cannot find it in the file explorer. Disk /dev/sda: 250.1 GB, 250059350016 bytes 255 heads, 63 sectors/track, 30401 cylinders, total 488397168 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 512 bytes I/O size (minimum/optimal): 512 bytes / 512 bytes Disk identifier: 0x000d871e Device Boot Start End Blocks Id System /dev/sda1 * 2048 486322175 243160064 83 Linux /dev/sda2 486324222 488396799 1036289 5 Extended /dev/sda5 486324224 488396799 1036288 82 Linux swap / Solaris Disk /dev/sdb: 8195 MB, 8195480064 bytes 253 heads, 62 sectors/track, 1020 cylinders, total 16006797 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 512 bytes I/O size (minimum/optimal): 512 bytes / 512 bytes Disk identifier: 0x00027ae4 Device Boot Start End Blocks Id System /dev/sdb1 * 62 15999719 M 7999829 c W95 FAT32 (LBA) Manually mounting it produces this error message :~$ sudo mount -t vfat /dev/sdb1 /media/external -ouiduid=1000,gid=1000,utf8,dmask=027,fmask=137 mount: wrong fs type, bad option, bad superblock on /dev/sdb1, missing codepage or helper program, or other error In some cases useful info is found in syslog - try dmesg | tail or so Is the usb toast?

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  • Sparse virtual machine disk image resizing weirdness?

    - by Matt H
    I have a partitioned virtual machine disk image created by vmware. What I want to do is resize that by 10GB. The file size is showing as 64424509440. Or 60GB. So I ran this: dd if=/dev/zero of=./win7.img seek=146800640 count=0 It ran without errors and I can verify the new size is in fact 75161927680 bytes or 70GB. This is where it gets a little odd. I started the guest domain in xen which is a Windows 7 enterprise machine. What I was expecting to see in diskmgmt.msc is 2 partitions. 1 system partition at the start of around 100MB and near 60GB partition (which is C drive) followed by around 10GB of free space. Actually what I saw was a 70GB partition!?! That confused me... so I decided to run the Check Disk which when you set it on the C drive it asks you to reboot so it'll run on boot. So I did that and during the boot it ran the checks. It got all the way through stage 3 and didn't show any errors at all. Looked at the partitions in disk manager and now C drive has shrunk back to 60GB and there is no free space. What gives? Ok, I thought I'd try mounting it under Dom0 and examining it with fdisk. This is what I get when mounted sudo xl block-attach 0 tap:aio:/home/xen/vms/otoy_v1202-xen.img xvda w sudo fdisk -l /dev/xvda Disk /dev/xvda: 64.4 GB, 64424509440 bytes 255 heads, 63 sectors/track, 7832 cylinders Units = cylinders of 16065 * 512 = 8225280 bytes Sector size (logical/physical): 512 bytes / 512 bytes I/O size (minimum/optimal): 512 bytes / 512 bytes Disk identifier: 0x582dfc96 Device Boot Start End Blocks Id System /dev/xvda1 * 1 13 102400 7 HPFS/NTFS Partition 1 does not end on cylinder boundary. /dev/xvda2 13 7833 62810112 7 HPFS/NTFS Note the cylinder boundary comment. When I run sudo cfdisk /dev/xvda I get: FATAL ERROR: Bad primary partition 1: Partition ends in the final partial cylinder Press any key to exit cfdisk So I guess this is a bigger problem than first thought. How can I fix this? EDIT: Oops, the cylinder boundary thing is not a problem at all since disks have used LBA etc. So that threw me for a moment... still the problem exists... Now this output looks a little different. sudo sfdisk -uS -l /dev/xvda Disk /dev/xvda: 7832 cylinders, 255 heads, 63 sectors/track Units = sectors of 512 bytes, counting from 0 Device Boot Start End #sectors Id System /dev/xvda1 * 2048 206847 204800 7 HPFS/NTFS /dev/xvda2 206848 125827071 125620224 7 HPFS/NTFS /dev/xvda3 0 - 0 0 Empty /dev/xvda4 0 - 0 0 Empty BTW: I do have a backup of the image so if you help me mess it up that's ok. EDIT: sudo parted /dev/xvda print free Model: Xen Virtual Block Device (xvd) Disk /dev/xvda: 64.4GB Sector size (logical/physical): 512B/512B Partition Table: msdos Number Start End Size Type File system Flags 32.3kB 1049kB 1016kB Free Space 1 1049kB 106MB 105MB primary ntfs boot 2 106MB 64.4GB 64.3GB primary ntfs 64.4GB 64.4GB 1049kB Free Space Cool. Linux is showing free space is 10GB which is what I expect. The problem is windows isn't seeing this?

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  • MSA20 RAID5 recovery failure due to URE on another disk

    - by Andrey
    I have MSA20 with one disk array on 12 disks and 3 LUNs on it (each raid 5). A few days ago one disk in one of the LUNs was failed and I replaced it. But raid5 recovering failed at 13% and I see in ADU report that one of the disk has "Errors Logged = 5566" and according SCSI specifications it is URE (Sense Code=0x11, Qualifier=0x00). In serial log I also see URE error. It seems that Raid5 can't be rebuilt because of this. So I have a few questions: Is there a way to recover raid5 still? If I leave new disk that was replaced and remove disk with URE, will other LUNs be destroyed or just failed LUN? If all LUNs will fail what is the sense to make each LUN with own raid on one disk group array if 2 failed disk can destroy all? As I understand the preferred way is to create one disk array for one LUN in future and not one array with few LUNs? Thanks.

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  • Ubuntu doesn't "see" external USB Hard Disk

    - by Mina Michael
    It's NTFS. It's USB2. I'm using Ubuntu 13.04. It works perfectly fine on Windows (which excludes cable and hardware problems). I have two Ubuntu computers and it's not detected on either. It's about 500 GB. Edits: Following the first link, I input sudo lsusb in a terminal; before and after connecting the HDD. The difference was Bus 001 Device 012: ID 14cd:6116 Super Top M6116 SATA Bridge. There it is! ("sata bridge" used to appear in a windows notification when I plugged in the HDD in!). ...This means that Ubuntu detects it but is it not mounting it? I tried this: sudo mount /dev/sdb1 /mnt But gives this: mount: special device /dev/sdb1 does not exist I also tried: sudo mount /dev/sdc1 /mnt but it stays with no output forever. I left it in background for about 30 min.s. sudo fdisk -l gives out this: Disk /dev/sda: 160.0 GB, 160041885696 bytes 255 heads, 63 sectors/track, 19457 cylinders, total 312581808 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 512 bytes I/O size (minimum/optimal): 512 bytes / 512 bytes Disk identifier: 0xa42d04a3 Device Boot Start End Blocks Id System /dev/sda1 63 80324 40131 de Dell Utility /dev/sda2 * 80325 102481919 51200797+ 7 HPFS/NTFS/exFAT /dev/sda3 263874558 312580095 24352769 5 Extended /dev/sda4 102481920 263872511 80695296 7 HPFS/NTFS/exFAT /dev/sda5 263874560 310505471 23315456 83 Linux /dev/sda6 310507520 312580095 1036288 82 Linux swap / Solaris Partition table entries are not in disk order Disk /dev/sdc: 500.1 GB, 500107862016 bytes 255 heads, 63 sectors/track, 60801 cylinders, total 976773168 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 512 bytes I/O size (minimum/optimal): 512 bytes / 512 bytes Disk identifier: 0x5822aaea Device Boot Start End Blocks Id System /dev/sdc1 2048 976769023 488383488 7 HPFS/NTFS/exFAT The part below "Partition table entries are not in disk order" takes about 5 minutes to appear. The outputs of ls /dev/ | grep sd before and after connecting the HDD: before: sda sda1 sda2 sda3 sda4 sda5 sda6 ,after: sda sda1 sda2 sda3 sda4 sda5 sda6 sdd sdd1 The second output has the lines sdd and sdd1 different from the first one. IT SHOWED THE FILES!! The command sudo mount /dev/sdd1 /mnt worked after I typed in sudo fdisk -l!!! Thanks a million!! :) :)

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  • Problem in booting Windows Vista after repairing using a boot repair disk

    - by Pubudu
    Been using Vista and I recently installed Ubuntu 11 in a separate hard disk(in BIOS, this hard disk was set for the 'Boot from' option)..Apart from the partitions used for Ubuntu, there are 2 more partitions(NTFS) in that hard disk..Then I installed Windows 7 on one of those partitions (just to see which Windows operating system I'd like to keep on using, along with Ubuntu)..But after installing Windows 7, the OS selection menu didn't appear anymore and had to fix it using the Boot-Repair-Disk... It kinda worked.. Now the OS selection menu is displayed.. But whenever I select Vista, it boots Windows 7...any thoughts on how to fix this? here's the link to the log generated by boot repair http://paste.debian.net/202691 I'm new to Ubuntu btw..

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  • hd0 out of disk error results to low graphics mode

    - by msPeachy
    Yesterday, I have reinstalled Ubuntu due to a error: hd0 out of disk on boot. Everything went fine, I've installed apps, perform updates and upgraded the kernel. I've even restarted it a few times just to check if I would encounter boot issues and was glad that everything was working perfectly, then powered it down. The next morning when I boot, I got this error: hd0 out of disk error. Press any key to continue... again! After pressing a key, it took 10 minutes for the Ubuntu logo to appear with it's 5 dots. After another 5 minutes, Ubuntu started checking the disk and displayed a message that / has errors, I pressed F to fix the errors. After which Ubuntu tells me that /tmp is not yet ready for mounting so I pressed S to skip mounting it, then Ubuntu restarted. On boot I saw the error: hd0 out of disk error. Press any key to continue... again. This time it took only a minute for the Ubuntu logo to appear and after another minute a dialog box appeared with the following message: The system is running in low-graphics mode. Your screen, graphics card, and input settings could not be detected correctly. You will have to configure these yourself. What would you like to do? Run in low-graphics mode for just one session Reconfigure graphics Troubleshoot the error Exit to console login Whichever option I choose I ended up with a console prompt: grub-editenv: error: cannot read the file /boot/grub/grubenv. _ I can't do anything on this console, whatever I type nothing happens. I've rebooted several times and I get same error every time. I don't quite understand what is wrong with Ubuntu or with my installation. I've encountered this hd0 out of disk error several times already and always ended up reinstalling. I'd really really appreciate it if you guys can help me fix this. Thank you and good day.

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  • How does the process of disk partitioning actually work on most HDD's?

    - by Dark Templar
    From what I know of most laptops, you are able to "partition" your disk into as many other drives as you please. The more you cut it up, the smaller your partitions are, but from an organizational point of view, this may be desirable... I was wondering how the filesystem itself becomes partitioned underneath the partitions visible to the user. For instance, a laptop disk is usually divided into platters, each with two surfaces. The surfaces are further divided into "tracks". I guess what I am asking is, is it possible to identify how the disk itself keeps track of partitions? (whether each partition has its own platter? each partition has its own set of adjacent tracks? or some other configuration, or whether the data from different partitions are just randomly interleaved and scattered throughout the disk?)

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  • Hard disk error

    - by Nadim A. Hachem
    I got this error during installation. "The installer encountered an error copying files to the hard disk: [Errno 5] Input/output error This is often due to a faulty CD/DVD disk or drive, or a faulty hard disk. It may help to clean the CD/DVD, to burn the CD/DVD at a lower speed, to clean the CD/DVD drive lens (cleaning kits are often available from electronics suppliers), to check whether the hard disk is old and in need of replacement, or to move the system to a cooler environment." how can i fix this and what does it mean specifically? i'm installing via usb so it can't be the CD. the laptop is recent so it cant be an old HD.

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  • Somebody knows why the sectors of the IBM floppy disk are named 1 to 8 (and not 0 to 7 )

    - by Olivier Briand
    I am now programming on a 8 bits Z80 computer with CP/M 2.2, (as a hobby) and the floppy disk format is IBM, 40 tracks, 8 sectors per track, 512 bytes per sector. free space is 154 Ko on each face of the disk. Why the sectors are indexed 1 to 8 (and not zero to seven, as usually is seen with computers)? The catalog of the floppy disk is on the track 1 (sector 1 to 4, 64 entries). I'm wondering is the catalog on track zero? Is the zero track reserved to included a system (as track 0 & 1 are reserved to the system on a CP/M floppy disk, and catalog is on track 2)?

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  • I (stupidly) converted a TrueCrypt encrypted disk to GPT in Disk Management: now TrueCrypt won't mount it

    - by asilentfire
    Backstory: After moving a Macrium Reflect disk image from my TrueCrypt external drive (with whole disk encryption) onto a unencrypted drive and using Windows PE with Macrium Reflect to restore my internal disk to the recovery image on the external unencrypted drive, my Windows 8 failed to boot. I then went back and also recovered the System Partition (looking now, it is currently EFI), but I still couldn't boot into my backup.. I was in a hurry to get online for something so I just did a clean install of Windows 8, without the backup.. After I installed Windows 8, I went into Disk Management out of curiosity to see if there were other partitions with Windows 8 that Macruim might have missed, and there is (by default) a Recovery Partition of 100MB. My memory of this is hazy, as I was trying to get up and running for an exam at 4 AM: Something in Disk Management prompted me to convert my encrypted external drive to GPT.. I have no idea why I did this, but I went ahead and allowed it to convert my TrueCrypt drive to GPT. Now, I can't mount the drive in TrueCrypt.. Disk Management sees it as Disk 1, Basic, and Unallocated. I tried converting it back to MBR with Disk Management, but no dice with TrueCrypt :( If I try to mount the disk in TrueCrypt I get the message: Incorrect password or not a TrueCrypt volume I should never have messed with a Truecrypt drive in Disk Management, but I did. I have important college work in that drive, and fear I have lost it forever. PLEASE HELP

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  • PowerShell script to find files that are consuming the most disk space

    As you know, SQL Server databases and backup files can take up a lot of disk space. When disk is running low and you need to troubleshoot disk space issues, the first thing to do is to find large files that are consuming disk space. In this article I will show you a PowerShell script that you can use to find large files on your disks. 12 essential tools for database professionalsThe SQL Developer Bundle contains 12 tools designed with the SQL Server developer and DBA in mind. Try it now.

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  • On Disk Substring index

    - by emeryc
    I have a file (fasta file to be specific) that I would like to index, so that I can quickly locate any substring within the file and then find the location within the original fasta file. This would be easy to do in many cases, using a Trie or substring array, unfortunately the strings I need to index are 800+ MBs which means that doing them in memory in unacceptable, so I'm looking for a reasonable way to create this index on disk, with minimal memory usage. (edit for clarification) I am only interested in the headers of proteins, so for the largest database I'm interested in, this is about 800 MBs of text. I would like to be able to find an exact substring within O(N) time based on the input string. This must be useable on 32 bit machines as it will be shipped to random people, who are not expected to have 64 bit machines. I want to be able to index against any word break within a line, to the end of the line (though lines can be several MBs long). Hopefully this clarifies what is needed and why the current solutions given are not illuminating. I should also add that this needs to be done from within java, and must be done on client computers on various operating systems, so I can't use any OS Specific solution, and it must be a programatic solution.

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  • Ubuntu 12.04 Install - Black Screen - No Grub - Have run Boot Repair Disk

    - by Pat
    Day 4 of my purgatory. History: Had problems with live CD at first, had to set the "nomodeset" option ... and then it worked fine. Installed Ubuntu "Alongside" Windows XP from live CD (NOT wubi) Upon reboot after installation, I get the BIOS ... and then a black screen. If I hit shift after the BIOS screen I get text that says "loading GRUB ..", but then no GRUB ... just a black screen. What I have tried to do: Total re-installation ... 3 times now. Also tried with wubi, same black screen. Have gone back to the normal (non-wubi) install. After installation, I tried re-booting the live cd ... and trying to change GRUB file using: sudo gedit /etc/default/grub ... to "nomodeset" and "timeout=10" ... but won't let me save my changes because I'm using the live cd "in memory" system and don't have permissions to the disks (I think). I tried logging in ... but it won't let me. I then read many posts on this site. I'm stuck. This morning, I ran the "boot repair disk". Results here: http://paste.ubuntu.com/1132333/ What I think is wrong: Since I can get the live CD to run (perfectly) with the "nomodeset" option, I think all I need to do is get to GRUB to change that ... but I can't get to GRUB. Appreciate any advice. Pat Day 5 ... I downloaded "Super Grub 2 Disk" from: http://www.supergrubdisk.org/super-grub2-disk/ This looks promising. I can boot the disk and it brings me to a GRUB program that allows me to: 1) Boot to Windows ... which works 2) Boot to Ubuntu ... which does NOT work When I choose boot to Ubuntu, I get lines across the screen which is an obvious video card problem. Likely because I need to set the "nomodeset" option. So, I attempted to use super grub2 to edit the grub file ... but it is TOTALLY different than the Ubuntu grub file ... and I don't know where to put the "nomodeset" option. Still stuck ... The bottom line is that: 1) I need to edit /etc/default/grub on sda(1) ... which is my boot drive ... to add the "nomodeset" option 2) To do that I need to get into grub ... but, I can't. Holding down shift just echo's "loading grub .." and then takes me to a black screen 3) I can boot to the live CD by setting nomodeset .... but I cannot access the hard disk as root ... I can't save my changes! Can anyone tell me how to login as root for the filesystem from the live CD ... so I can edit the grub file on the HARD DISK ... and then run update-grub??

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  • Disk IO Performance Limitations based on numbers of folders/files

    - by Josh
    I have an application where users are allowed to upload images to the server. Our Web Server is a windows 2008 server and we have a site (images.mysite.com) that points to a shared drive on a unix box. The code used to do the uploading is C# 3.5. The system currently supports a workflow where after a threshold is met a new subfolder can be generated. The question we have is how many files and/or subfolders can you have in a single folder before there is a degredation in performance - in serving the images up through IIS 7 and reading/writing through code?

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  • Dell 2950 Perc 6/i "physical disk" and "Enclosure(Backplane)" under Connector 1 in OMSA tree- Troubleshoot help

    - by user66357
    Just looking for someone who might know why this could occur... In OMSA, on my Dell 2950, there usually is only one "Physical Disks" child under "Enclosure (Backplane)" in the tree view. Currently, the tree looks like this: Dell PERC 6/i Integrated Connector 1 (RAID) Enclosure (Backplane) Physical Disks (1:04 good, 1:05 removed) Physical Disks (1:33 Ready but unused) Normally it's like this: Connector 1 (RAID) Enclosure (Backplane) Physical Disks (1:04 good, 1:05 good) From the front, 6 of 6 3.5" SAS drives are connected. The server is showing Slot 5 as bad and the disk as removed. It seems that the drive in Slot 5 is being sensed as external to the Enclosure. Any ideas why this would happen? Think I can get away with rebuilding the virtual disk by replacing 1:05 with 1:33? Thanks. UPDATE: The only options on the Physical Disk 1:33 were Assign as Global Hot Spare and Clear... After clearing, I assigned it as the Global Hot Spare. This allowed the rebuilding of the virtual disk. Hopefully it won't fail. I'm still unsure of the reason for this odd behavior. I'm checking the firmware next.

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