External Drive Disk Errors

AKGeoChad
I work primarily on my desktop at work and keep all my data and PDFs on my D:\ drive. I placed my zotero database on my D:\drive. I sync my D:\ drive with an external drive so that I can work on my laptop at home. Zotero is great in that I can choose where to store the database so that I can work on different computers and still use the entire citation database and preserve all the links to my PDFs.

However, after working at home editing the citations in Zotero I came back to work to sync the changes to my desktop. When I tried to sync my changes to my desktop drive the sync program alerted me that some of the files were corrupt. Most of the corrupted files were Zotero database files. I ran Windows Check Disk and it found many errors but was able to repair the disk. This happened to me twice. After the second time I assumed the disk was bad so I sent it in for a warranty replacement.

I bought a new external drive and synced my D:\ drive to the new drive. However, it happened again. I made some edits to my Zotero citations using my laptop. After I was done working I shut down my laptop with the external drive still connected. When I turned the computer back on Windows detected errors on the external disk and automatically started Check Disk. This time it again found extensive errors on the disk, mostly in Zotero files but also many other files.

I'm assuming from these two experiences that working with Zotero on an external drive is "unstable" and probably causes registry errors. This issue needs to be addressed. It doesn't happen if I just make a few minor changes to my citation database but only after making extensive changes.

I'm using version 2.1b2. Windows XP at work and Windows 7 on my laptop at home.
  • dstillman
    I can't tell you how that's happening, but Zotero has no way of corrupting files at the filesystem level—and I'm not sure even Firefox could.

    Corrupting files is one thing, but filesystem corruption suggests a hardware or OS problem.
  • AKGeoChad
    Then why has it only happened while using Zotero? Twice I got disk errors after making extensive edits in Zotero and not working on anything else (on two different disks). The evidence strongly supports my assumption that Zotero is causing a problem.
  • dstillman
    A program that makes high-level file calls can't be responsible for filesystem corruption—only an OS or hardware bug (or some other low-level program that's interfering with basic disk calls) can do that. You can believe me or not, but there's really nothing else I can tell you.

    (In general, I would suggest trying to safely unmount the drive before shutting down the computer and unplugging it on the off-chance that that's causing the problem, but that's beyond the scope of these forums.)
  • adamsmith
    edited December 15, 2010
    edit: [what Dan said].
  • AKGeoChad
    Update: Now both of my computers are running Windows 7. The problem still exists. Whenever I use my laptop with my synced external drive and open Firefox with Zotero I get a disk error when I plug it back into my desktop.

    I understand Dan's point that Zotero doesn't mess with the registry, that the operating system controls the disk. However, why is Zotero the only program that causes a problem? I think there is an issue of HOW Zotero communicates with Windows to change things on the disk. Maybe Zotero is constantly changing things or is always in the middle of changing things, so when the disk is removed the changes are interrupted. Zotero automatically updates many of the citation library files every time it is opened, so maybe this background operation doesn't complete properly.

    Bottom line: Zotero is the only program that is associated with getting disk errors, so Zotero is to blame.

    Can someone at Zotero please test this and fix the problem?
  • dstillman
    The answer here hasn't changed. Zotero has literally no way of corrupting a filesystem.
    Maybe Zotero is constantly changing things or is always in the middle of changing things, so when the disk is removed the changes are interrupted.
    What does disk activity have to do with anything? You shouldn't be pulling the drive while anything on it is in use. You'd absolutely get corruption if you did that.
  • timtak
    edited April 17, 2012
    I use zotero to a flash drive all the time without problems. The drive is a solid stage hard drive, a Buffalo SDH-UHR64GS, soon to be replaced by a SDH-P series, again 64GB.

    Rash and foolish that I am, I do not make sure that I safely unmount the drive (though I would recommend that others do).

    However, I do not physically unplug the drive while it is in use. As Dan Stillman says, that would result in corruption.

    In order to ensure that I do not unplug the drive while in use
    1) I don't unplug it while I am saving something, obviously.
    2) I have turned off automatic syncing in the preferences. I sync from time to time, and not no unplug while the sync is in progress. The sync has a progress bar and a cancel sync button for those times when I am in a rush to leave and the sync has not finished.

    Tim
  • dstillman
    No—"in use" doesn't just mean actively being used. You should never unmount a disk while any program has files open for writing on that disk. That's how you get corruption.

    If you have Zotero pointed at an external drive, you absolutely need to close Firefox/Standalone before unmounting the drive.
  • timtak
    Sorry yes, I quite agree. Good point.
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