After receiving a private reply, I’ve tried to replicate the original issue. Alas I cannot, which leaves me in the odd position of wanting to try this app but also being a bit tentative in that it may randomly decide not to save.
I would like to mention that the person who PM’ed me said that we are likely experiencing diverse issues and self-diagnosing it as the same issue. The implication is that these smaller issues are being solved and it’s just not being mentioned here… so with this: If you do have a data-loss event happen, it might be good to post it as a new issue rather than reply here, and if the developers think it’s this issue they can move it here.
If there are no more posts after this one, you can assume the app works I guess.
I have also experienced what I think is this bug today (2022-02-10), but with a twist: I wrote a few paragraphs, and attempted to open a different extant file. That file failed to open, and in the filesystem I later discovered it had gone to zero bytes, and the original file I was working in lost the few paragraphs of changes I had made. I have plenty of space on the filesystem, so it’s not a space issue. MacOS 10.15.6, Obsidian insiders v0.13.24.
Today I made my very first note and experimented with the markdown syntax (which I’m not familiar with yet). My very first 30 minutes of ‘work’ with Obsidian was lost. Off to a rough start…
I’m on an old machine (MB Air mid 2012), up-to-date with not much additional programs. I like to keep the things as they ship. Same for Obsidian: no plugins or anything. Switching to light mode was the only change I made to this program.
As previously mentioned, I as well got the ‘File system operation timed out.’ warning, but didn’t take it seriously (I’m coming from windows…). Not only the progress was not saved, but the whole file was wiped. Since it was the only file in this vault at the time, I can’t even be sure that not everything would have been wiped if more would have existed.
I browsed all the relevant threads on this in this forum, but no one seems to be able to provide a solution - which seems odd to me, since data loss is the single most fundamental thing to prevent as a note taking app… I type information, so I don’t have to remember it. Typing information only makes sense, if it is stays where I put it. But this thread exists since early 2021… Is there something people do to be able to live with this? Did I miss something? I want to use Obsidian so badly, but I can’t (with this problem).
If there is information that I can provide so the problem can be better understood, I’m more than glad to help. But I might need a step-by-step guide on how and what.
Happy note-taking everyone. For now I stay with my txt files…
@rnax Nope you didn’t miss anything. I’m sorry this happened to you (and sad this was your first experience with Obsidian) but luckily you didn’t lose anything important.
I’m not sure whether this is just a low priority for the developer or (more likely) just something that is unfixable due to a combination of being quite hard to reliably reproduce and also very likely an “upstream” bug—meaning the bug is in the Electron framework itself or in one of the modules that Obsidian uses like CodeMirror.
I agree with you that the #1 priority for a note taking “second brain” app should be making sure the stuff you type in gets saved. But Obsidian is so freaking good at everything else that even with that (scary) shortcoming, myself and others continue to accept that risk.
I sincerely hope that this bug gets fixed one day but it’s looking less and less likely as months turn into years and people continue to report this issue. Maybe it will just magically disappear one day when Electron fixes it, which seems to be what happened to the kernel panic bug that was really big a while back.
What I’ve done to protect myself is:
set snapshot period to 1 minute
script that makes hourly backups of my vault and preserves the last 30 days
script to monitor my vault and pop up an alert the moment it detects an “empty” file that was created >2 min ago
Even with all of this, I still hit the bug sometimes and just deal with it. I’m still hoping one day I figure out a way to trigger it so we can at least have hope of a fix.
A bug that causes a kernel panic is very different than one that simply causes a file to be truncated. Only very low level bugs can cause KPs and so it makes sense that that one needed help from Apple to fix.
Contrast that to this data loss bug which seems much more like a race condition or some other side effect. While it may be true that it only affects macOS at this point, that does not mean the bug isn’t in Electron, CodeMirror, or Obsidian. In fact, it’s highly likely that this is NOT a macOS bug because to my knowledge it has only been reported with Obsidian (again, contrast to the KPs which were also widely reported in other popular Electron apps such as VSCode and Discord)
Sad to hear there is not much I can do. I did (1), but this won’t solve the problem at all since said snapshots are wiped as well. Do you know of any public plugin that could take care of (2) and (3) for me?
I just can’t wrap my head around how this is a problem people life with. If I can’t solve the initial problem, I try to fight the symptoms and put something in place that counter steers the problem, doesn’t I? This is a paid product after all. Somewhere I read about a warning banner being added in v0.13.25 that doesn’t vanish after a second, but this seems barely adequate to a bug like this. Especially so, because people are claiming they can’t even copy and paste their data out of it at that point.
Nevertheless I see the potential in this app that you called ‘freaking good’ after playing around with it today a bit more. Still not putting my data in…
So the first question is ‘Did the file written in Obsidian ever get written to the disc?’
Followed by ‘Does Obsidian have permission to write to the folder you were trying to save in?’
If it’s not written in the first place, it’s quite a different problem to the original data being lost during an edit.
Then ‘Is there a sync service running?’
If you get a File System error, you do need to pay attention because it means that the file system isn’t working at that moment and data may not be being written to disc at all. Sometimes the message can be intermittent if two programs are attempting to access that file at the same time.
txt and md are the same - it’s only the extension that’s different.
You can write markdown syntax into txt files. You can write markdown into any txt file, whether it supports markdown or not. Obsidian doesn’t fully support any extension except md, but there is a plugin which shows you the syntax in action.
Some markdown editors fully support txt as an extension.
It’s a bit difficult to recollect the exact sequence of actions for me now. Following with a grain of salt. If there is somewhere log-data I can provide, I’ll gladly share that. To answer the question: I think it did. I was fiddling with the Markdown syntax (new for me) and wanted to see it through the TextEditor. Closed Obsidian (proper quit) and opened the file with the TextEditor to see how it looks without rendering. Closed the file and reopened Obsidian. Continued writing the file when at some point the warning popped up. I thought this would resolve itself at some point and continued writing. Closed Obsidian some time after. After reopening it, the file was wiped. 0 KB.
As I said, switching to light theme was the only change I made to Obsidian. For the files I made a folder locally.
First time user and got this error within the first 10 minutes of experience. Created a test2, could enter text, but it didn’t save. Started in my root dropbox folder. Connecting to internet through a known flaky work vpn. mac v0.13.23. No plugins setup by me, perhaps some by default. I did get the warning dialogue but just kept going cuz, uh, I’ve been trained to ignore most such warnings. Restarting working fine but test2 was empty (but created).
Sounds like dropbox and maybe the vpn is contributing to the issue. Other apps (and I use a lot) deal with this fine. Worst case they delay a couple of seconds while trying to open or save something.
Here is an attempt to gather information about the error condition. I hope I managed to catch even some new information to help remedy the situation.
I have used Obsidian now for a month or two and have written about three hundred files to my vault. I have experienced this bug for two or three times on macOS and one time on iOS. I do not know if the iOS bug was the same as this one though, I did not have opportunity at the time to look at it in any detail.
In chronological order. I’m annoyed in retrospect for not recording time stamps.
Obsidian gave a popup that the file system operation timed out.
I checked for zero size files in Finder and the current file I was editing shows it has no content on disk.
The contents were still on screen so I copied the text to another program.
I then tested if I could write to the folder with TextEdit and it worked fine.
Finder shows the iCloud cloud symbol on the vault folder, icon has a mouse over text “Downloading”
On the subfolder the iCloud icon mouse over is “Waiting to Update”
No files in the folder show the cloud icon.
After awhile the Vault cloud icon mouse over text changed to “Waiting to Update” also.
The issue has not resolved in about half an hour.
My vault folder shows that 3 bytes are left from the download, seems stuck.
Writing to the vault with Obsidian on my iPhone works ok.
Phone also sees the current file that I was working on as empty.
Obsidian still shows the popup infrequently that the filesystem operation timed out.
Also tried to use another Electron app Discord to save an image to the vault folder and it worked ok.
Tried creating a new file with Obsidian and it does not react to the command.
I divided the workspace to two panes and the new pane shows that no file is open and displays the buttons to create or open files.
Tried creating a new file by pressing the button, but with no reaction from Obsidian.
Tried to click a file in the Obsidian file explorer, the pane changed from showing the no file open screen to show a file called “No File”, and I can now write text in the window, the file does not exist and the text does not get written to disk. The file I clicked on the file pane was left untouched.
Curiously the behavior of Obsidian changed. If I now close the “No File” pane and then split the pane again Obsidian shows the “No File” named file again instead of the screen with the buttons.
The original pane on the screen has a link, I clicked the link and Obsidian reloaded the current file in its empty state.
Running out of ideas to try, I pressed Cmd-R for Force Reload and Obsidian resolved its state and started functioning normally again.
Even after the situation seems resolved and Obsidian is working as normal, the vault folder in Finder shows the cloud icon stuck on “Waiting to Update”.
I have two other Obsidian instances open on different vaults, unfortunately I didn’t test them at the time the error occurred. However the other vaults work as normal without requiring reloading.
On the following day the iCloud cloud icon on the vault folder is still stuck, seems to be permanently stuck.
Obsidian version 0.13.23 (installer version 0.13.23).
macOS BigSur ver. 11.6.1
MacBook Pro 13-inch, M1, 2020, 16Gb, 2Tb
iCloud+, iCloud Drive 200Gb, with Optimize Mac Storage option turned off and 45.61Gb available space.
I have two users on my other MacBook Pro, both use same Obsidian installation but on different vaults, both were loaded but the computer was sleeping at the time of error.
I also have Dropbox, but do not use it with Obsidian. Mentioning it just because it is notorious for misbehaving and has caused problems for me previously.
I do not have Time Machine enabled on this machine, but my other MacBook Pro does take Time Machine backups from all my vaults to QNap NAS. I did not realize to check if Time Machine was active on the other computer during the error. It does that even while sleeping.
I invite you to download and reinstall obsidian from the website version 0.13.30. The new installer contains an updated version of electron, it might affect this issue.
