Fossil

The Problem

Fossil has a delta compression feature which removes redundant information from a file relative to its parent on check-in.¹ That delta is then zlib-compressed before being stored in the Fossil repository database file.

Storing pre-compressed data files in a Fossil repository defeats both of these space-saving measures:

1. Binary data compression algorithms turn the file data into pseudorandom noise.²

   Typical data compression algorithms are not hash functions, where the goal is that a change to each bit in the input has a statistically even chance of changing every bit in the output, but because they do approach that pathological condition, pre-compressed data tends to defeat Fossil’s delta compression algorithm, there being so little correlation between two different outputs from the binary data compression algorithm.

2. An ideal lossless binary data compression algorithm cannot be applied more than once to make the data even smaller, since random noise is incompressible. The consequence for our purposes here is that pre-compressed data doesn’t benefit from Fossil’s zlib compression.

You might then ask, what does it matter if the space savings comes from the application file format (e.g. JPEG, DOCX, Zip, etc.) or from Fossil itself? It really doesn’t, as far as point 2 above goes, but point 1 causes the Fossil repository to balloon out of proportion to the size of the input data change on each checkin. This article will illustrate that problem, quantify it, and give a solution to it.

Affected File Formats

In this article’s core experiment, we use 2D image file formats, but this article’s advice also applies to many other file types. For just a few examples out of what must be thousands:

• Microsoft Office: The OOXML document format used from Office 2003 onward (.docx, .xlsx, .pptx, etc.) are Zip files containing an XML document file and several collateral files.

• Libre Office: For the purposes of this article, its OpenDocument Format is designed the same basic way as OOXML.

• Java: A Java .jar file is a Zip file containing JVM .class files, manifest files, and more.

• Windows Installer: An *.msi file is a proprietary database format that contains, among other things, Microsoft Cabinet-compressed files, which in turn may hold Windows executables, which may themselves be compressed.

• SVG, PDF, TIFF, etc.: Many file formats are available in both compressed and uncompressed forms. You should use the uncompressed form with Fossil wherever practical, as we will show below.

Demonstration

The companion image-format-vs-repo-size.ipynb file (download, preview) is a JupyterLab notebook implementing the following experiment:

1. Create a new minimum-size Fossil repository. Save this initial size.

2. Use ImageMagick via Wand to generate a JPEG file of a particular size — currently 256 px² — filled with Gaussian noise to make data compression more difficult than with a solid-color image.

3. Check that image into the new Fossil repo, and remember that size.

4. Change a random pixel in the image to a random RGB value, save that image, check it in, and remember the new Fossil repo size.

5. Iterate on step 4 some number of times — currently 10 — and remember the Fossil repo size at each step.

6. Repeat the above steps for BMP, TIFF,³ and PNG.

7. Create a bar chart showing how the Fossil repository size changes with each checkin.

We chose to use JupyterLab for this because it makes it easy for you to modify the notebook to try different things. Want to see how the results change with a different image size? Easy, change the size value in the second cell of the notebook. Want to try more image formats? You can put anything ImageMagick can recognize into the formats list. Want to find the break-even point for images like those in your own repository? Easily done with a small amount of code.

Results

Running the notebook gives a bar chart something like⁴ this:

There are a few key things we want to draw your attention to in that chart:

• BMP and uncompressed TIFF are nearly identical in size for all checkins, and the repository growth rate is negligible past the first commit.⁵ We owe this economy to Fossil’s delta compression feature: it is encoding each of those single-pixel changes in a very small amount of repository space.

• The JPEG and PNG bars increase by large amounts on most checkins even though each checkin also encodes only a single-pixel change.

• The size of the first checkin in the BMP and TIFF cases is roughly the same as that for the PNG case, because both PNG and Fossil use the zlib binary data compression algorithm. This shows that for repos where the image files are committed only once, there is virtually no penalty to using BMP or TIFF over PNG. The file sizes likely differ only because of differences in zlib settings between the cases.

• Because JPEG’s lossy nature allows it to start smaller and have smaller size increases than PNG, the crossover point with BMP/TIFF isn’t until 7-9 checkins in typical runs of this Monte Carlo experiment. Given a choice among these four file formats and a willingness to use lossy image compression, a rational tradeoff is to choose JPEG for repositories where each image will change fewer than that number of times.

Automated Recompression

Since programs that produce and consume binary-compressed data files often make it either difficult or impossible to work with the uncompressed form, we want an automated method for producing the uncompressed form to make Fossil happy while still having the compressed form to keep our content creation applications happy. This Makefile should⁶ do that for BMP, PNG, SVG, and XLSX files:

    .SUFFIXES: .bmp .png .svg .svgz

    .svgz.svg:
        gzip -dc < $< > $@

    .svg.svgz:
        gzip -9c < $< > $@

    .bmp.png:
        convert -quality 95 $< $@

    .png.bmp:
        convert $< $@

    SS_FILES := $(wildcard spreadsheet/*)


    all: $(SS_FILES) illus.svg image.bmp doc-big.pdf

    reconstitute: illus.svgz image.png
        ( cd spreadsheet ; zip -9 ../spreadsheet.xlsx) * )
        qpdf doc-big.pdf doc-small.pdf


    $(SS_FILES): spreadsheet.xlsx
        unzip $@ -d $<

    doc-big.pdf: doc-small.pdf
        qpdf --stream-data=uncompress $@ $<

This Makefile allows you to treat the compressed version as the process input, but to actually check in only the changes against the uncompressed version by typing “make” before “fossil ci”. This is not actually an extra step in practice, since if you’ve got a Makefile-based project, you should be building (and testing!) it before checking each change in anyway!

Because this technique is based on dependency rules, only the necessary files are generated on each make command.

You only have to run “make reconstitute” once after opening a fresh Fossil checkout to produce those compressed sources. After that, you work with the compressed files in your content creation programs. Your build system might include some kind of bootstrapping or auto-configuration step that you could attach this to, so that it doesn’t need to be run by hand.

This Makefile illustrates two primary strategies:

Input and Output File Formats Differ by Extension

In the case of SVG and the bitmap image formats, the file name extension differs between the cases, so we can use make suffix rules to get the behavior we want. The top half of the Makefile just tells make how to map from *.svg to *.svgz and vice versa, and the same for *.bmp to/from *.png.

Input and Output Use the Same Extension

We don’t have that luxury for Excel and PDF files, each for a different reason:

• Excel: Excel has no way to work with the unpacked Zip file contents at all, so we have to unpack it into a subdirectory, which is what we check into Fossil. On making a fresh Fossil checkout, we have to pack that subdirectory’s contents back up into an *.xlsx file with “make reconstitute” so we can edit it with Excel again.

• PDF: All PDF readers can display an uncompressed PDF file, but many PDF-producing programs have no option for uncompressed output. Since the file name extension is the same either way, we treat the compressed PDF as the source to the process, yielding an automatically-uncompressed PDF for the benefit of Fossil. Unlike with the Excel case, there is no simple “file base name to directory name” mapping, so we just created the -big to -small name scheme here.

Footnotes and Digressions

1. This problem is not Fossil-specific. Several other programs also do delta compression, so they’ll also be affected by this problem: rsync, Unison, Git, etc. You should take this article’s advice when using all such programs, not just Fossil.

   When using file copying and synchronization programs without delta compression, on the other hand, it’s best to use the most highly-compressed file format you can tolerate, since they copy the whole file any time any bit of it changes.

2. In fact, a good way to gauge the effectiveness of a given compression scheme is to run its output through the same sort of tests we use to gauge how “random” a given PRNG is. Another way to look at it is that if there is a discernible pattern in the output of a compression scheme, that constitutes information (in the technical sense of that word) that could be further compressed.

3. We're using uncompressed TIFF here, not LZW- or Zip-compressed TIFF, either of which would give similar results to PNG, which is always zlib-compressed.

4. The raw data changes somewhat from one run to the next due to the use of random noise in the image to make the zlib/PNG compression more difficult, and the random pixel changes. Those test design choices make this a Monte Carlo experiment. We’ve found that the overall character of the results doesn’t change from one run to the next.

5. It’s not clear to me why there is a one-time jump in size for BMP and TIFF past the first commit. I suspect it is due to the SQLite indices being initialized for the first time.

   Page size inflation might have something to do with it as well, though we tried to control that by rebuilding the initial DB with a minimal page size. If you re-run the program often enough, you will sometimes see the BMP or TIFF bar jump higher than the other, again likely due to one of the repos crossing a page boundary.

   Another curious artifact in the data is that the BMP is slightly larger than for the TIFF. This goes against expectation because a low-tech format like BMP should have a small edge in this test because TIFF metadata includes the option for multiple timestamps, UUIDs, etc., which bloat the checkin size by creating many small deltas.

6. The Makefile above is not battle-tested. Please report bugs and needed extensions on the forum.