$USER@bit-of-a-byte ~ $ cat /var/log/collegi-pixelmon-developer-log.log

Collegi Pixelmon - Developer Log

The following post is an extreme rough draft. In fact, it isn’t even actually a post. These are my development notes from my refactoring of the collegi data infrastructure. As such, they’re arranged in no real sensible order besides having been written chronologically. Additionally, these have not been proofread, grammar checked, copyedited, or spell checked, as i write them in an IDE and not an actual text editor. As such, please don’t judge my writing ability off of them. More importantly, however, these do not have the standardized links that i provide to new concepts or commands in my blog posts, as embedding links to things I already know or have access to in a developer log that on average no one else sees just seems silly.

So, if you have questions, use google, and expect these to be updated over time.

The logs as of this posting run from 10/13/2016 to 10/16/2016, so over three days of work. There is a -LOT- more to be done.

They are broken down into the following format. Each list is a set of specific actions I took, and sometimes the list ends up with notes in it because, again, no one generally sees these, but under the task list is the space reserved for notes on the above list. Then a new task list is declared, then notes, then tasks, and so on and so forth. Generally each new task heading would signify a new blog post, talking about the tasks and the notes, so keep that in mind.

These were requested by Kan, a player on our server. Enjoy!


  • Made a backup of the repository as it stood on 2016-10-13 in the event anything breaks too badly during this.
  • Removed all existing submodules from the git repository. Committed the removal.
  • Ran the previous backup script to make sure that 10/13 was backed up. This included new additions to git annex.
  • Forced git annex to drop the old SHA256E key-value backend files that were made obsolete by the conversion to SHA512E key-value backend.

Notes 1: During this time, and while watching the way the version 1.0 backup script ran, I noticed there is a significant performance penalty for moving the location of the local mirror. Borg uses the entire path as the file name, so any deviation in the path spec causes it to treat the files as brand new. Note that this does not cause any issues with de-duplication, but the process of adding these files causes a massive performance hit. This made me start thinking about including the local mirror in the git annex so that as long as the annex was kept in tact in regards to metadata, the paths would remain the same as all additions to Borg would take place from the same root directory.

The problem with this would be the fact that annex keeps everything as symlinks. As such, I am looking into the unlock feature of version six repositories.

Notes 2: Dropping unused from a local area goes -much- faster than dropping from remote. Who knew, right? :tongue:


  • git-Annex drop completed, but Finder isn’t showing a reduction in used drive space, but I think this is more an error on the side of finder than something with git annex, as du -h showed the directory was down to the size it should have been. Once I manage to get this finder thing figured out, I’ll move on to the next part.
  • Finder is taking too bloody long to figure its shit out, so I moved on to the next step in cleaning up the repository. I’m rewriting the commit history to completely remove files I don’t need from the actual git repo. In theory this shouldn’t touch git-annex at all, but that remains to be seen.
  • Ran BFG Repo Cleaner on the following directories and files:
    • collegi.web
    • collegi.pack
    • collegi.git
    • .DS_Store
    • .gitmodules
    • collegi.logs (Just for a moment, and we made backups.)
    • collegi.configs
  • Ran filter branch to purge any empty commits left after the above.
  • Expired original ref-logs, repacked archive.

Notes 3: At this point we had gone from 230 commits to 102 commits. We were also left with the original envisioning of what this repo would be, which was a simple git annex to push files to Backblaze b2 from the Borg repository. Now to verify that all of our data is still 100% ok.


  • Ran git fsck
  • Ran git annex fsck

Notes 4: Wow this is going to take a long fucking time. Who woulda thunk it.

Notes 5: So apparently the current version of git-annex is using the old mixed hashing method, which is a format that “we would like to stop using” according to the wiki. Might need to migrate. Need to figure out how.

Notes 6: From the wiki: “Initial benchmarks suggest that going from xX/yY/KEY/OBJ to xX/yY/OBJ directories would improve speed 3x.” It’s worth migrating.


  • Run git annex uninit
  • Reading through the git-annex-init man page to see what else we should change now since we’re already migrating. Post Uninit we’re going to have to run a full borg data consistancy check.

Notes 7: Ugh. The document I found was actually an theoretical one, and while it is true that git-annex does use the new hashing format in bare repositories there is no actual way to move to the new one in a regular repo. So I am running an uninit for basically no reason. The only good thing about this that I can think of is that I will be able to reform the final git-annex repo in a much saner fashion. The bad news is that I have lost the log files, unless git-annex is going to bring those back for me. I am annoyed.

Notes 8: Good news! I just remembered that I had made a rsynced backup of the repository before I started fucking with it. So I didn’t actually lose the log files, I just went ahead and pulled them out of the git-annex backup.


  • After the git annex had uninitialized, I decided that if I was going to do this whole damn thing over again I was going to do it right.
  • Started a new borg repository in new-collegi. Pulled out contents from the original borg repository, using backups to restore any files that got hit in the above clusterfuck, then recompressed with maximum LZMA compression.
  • During this period I also standardized how the borg create paths would work. The server would exist within a collegi.mirror directory, and the entire directory would be added to borg upon each run of the backup script. This effectively means we never have to worry about the LZMA penalty discussed below again after the first re-add, unless we do major server restructuring, because paths will remain stable between commits.

Notes 9: The initial speed penalty for using LZMA is absolutely jaw dropping. One borg create took eight hours to complete. Eight. However, I quickly noticed that due to Borg’s de-duplication mechanism, the add times got faster the more data I added, and gzip-9 to lzma-9 did actually yield some improvement. It also reduces the incentive for me to do this fucking disaster again, because of how much it absolutely fucking sucks.

Notes 10: As an example of what I mean by the above, the initial adding of 1.8.9 took six hours with LZMA-9. When the map was changed from NewSeed over to Collegi, it took another four hours just to update the paths and what not, even though the data hadn’t updated, just the paths have changed. (This is indicated by the fact that the total repository size barely increased, all the size that changed could be explained by new metadata.) However, when the paths are kept the same, adding 100GB of data takes 13 to 15 minutes. So, the benefit of LZMA-9 is worth the initial startup, imho.

Notes 11: borg extracting from the GZIP-9 archives takes about 40 minutes, and that’s from highly de-duplicated and GZIP-9 archives. What this means is that pulling from an lzma-9 is probably going to take about an hour, depending on just how de-duplicated the archive is (as in, how many different chunk files contain parts needed to reassemble the original content).

Notes 12: Have hit the series of backups where things have moved into the Users path, and I’m restructuring them. It made me think about how I will handle the mirror directory in the future. I think I am going to do a few new things with respect to the new setup. The mirror directory will be a part of the git-annex repository, so there will be a new folder inside it called collegi.mirror or something similar, and then I can move the new backup script to be ran from the root directory, which will be beneficial. That way everything is neatly packaged. the issue becomes mirroring this, because uploading that much constantly changing data to backblaze would be literally stupid, and not at all within our budget. What I will likely do is initialize a “bare repository” on my time machine drive, and mirror the entirity of the git-annex repository to that.

Mandatory Break Notes

  • You need to run borg info to make sure the latest creation thingy is the proper size, and a borg check might not be a bad idea either as you fell asleep and closed the mac during work on the repo.
  • Cleaned the time machine volume of the repeated backups of the new repository because it doesn’t make any sense to have 20 versions of it.
  • Moved the repo to the time machine drive as temporary storage using rsync.


  • Restarted the transfer process starting on the 8th of October

Notes 13: Not a huge shock but running some of these commands across USB 2.0 can add anywhere from 10 to 30 minutes. Doing them cross device gets even worse, with some transactions taking almost an hour.

Notes 14: I’ve been going back and forth on what filesystem I would like to deploy since I am redoing the collegi drive as a whole. Now the interesting thing to note here is that by the time I get this thing fully ready to deploy, the drive I have here may not be the drive it ends up on, but this is as good of a testbed as any. I’m really thinking I will go with apfs. Most of the gripes I have with it are easily resolved through borg and git annex.

Notes 15: In a highly amusing turn of events, it is bigger in lzma 9 than it was with gzip 9. weird.

Notes 16: While it would likely be prudent to go back to the previous compression method, the benefits that I have made to the directory structure while redoing the borg repository are worth the few extra gigabytes of overhead especially concerning with Backblaze B2 it barely costs a penny.


  • Use JHFSX for the new drive. I would have really liked to use APFS but I am still worried about the data loss considering there is almost a year till it will ship. JHFSX is reasonable enough for right now, while still being safe to unplug.
  • I went round and round on using encryption on the new drive. did it.
  • using rsync to bring the data to its final resting location.
  • OK started setting things up
  • Defined gitlab as the metadata backup again
  • created a bare repository on skaia
  • set up prefered content so skaia requires everything in the main repo
  • set the main repo to require a –force to drop content via preferred content
  • Set the backend to SHA512E
  • began the long process of adding the data to the git-annex
  • Set up bin directory to not be tracked by git-annex but instead by git
  • added backblaze remote, not encrypted, with a proper prefix
  • started to sync to backblaze
  • noticed an issue with how the sync was going to gitlab, will correct.
    • corrected the issue