Choose a version:
45% The original file has 337784 bytes (329.9k) and is available from the project website.
There you can find the official minified version, too, which brings down the size to 151665 bytes (148.1k, 45%).

After GZIP compression these minified files vary in size:
Boot
  61038 bytes (59.6k)
CDN, direct link
jsdelivr
  61038 bytes (59.6k)
CDN, direct link
cdnhttps
  53630 bytes (52.4k)
CDN, direct link
cdnjs
  53630 bytes (52.4k)
CDN, direct link
unpkg
  53630 bytes (52.4k)
CDN, direct link
gzip -6 (default)
  53506 bytes (52.3k)
local copy
gzip -9
  53368 bytes (52.1k)
local copy
libdeflate -12
  51665 bytes (50.5k)
local copy
7zip -mx=9 -tgzip
  51609 bytes (50.4k)
local copy
pigz -11 -n
  51359 bytes (50.2k)
local copy
kzip -s0 -rn -b8
  51324 bytes (50.1k)
local copy
Zopfli
  51267 bytes (50.1k)
local copy
Zopfli (defluff)
  51266 bytes (50.1k)
local copy

perma-link to the smallest file on my server:
http://minime.stephan-brumme.com/files/d3/d3-3.5.13.min.js

You will automatically get the smallest D3 3.5.13 file, ETag caching is available and
if your browser doesn't support GZIP decompression then the uncompressed version will be sent.

Currently best Zopfli settings

Save 2363 bytes by using my D3 3.5.13 Zopfli version instead of the best available CDN (4.61% smaller than unpkg, 51267 vs. 53630 bytes):
You can use my super-compressed files for whatever purpose you like as long as you respect the library's original license agreement.
There are no restrictions from my side - but please avoid hot-linking if you run a high-traffic website.

These command-line settings yielded the best compression ratio so far (Linux version of zopfli-krzymod):
zopfli --i1000000 --mb8 --mls128 --bsr7 --lazy --ohh

(found January 22, 2016)
Description Value Parameter
iterations 1000000  --i1000000
maximum blocks 8  --mb8
maximum length score 128  --mls128
block splitting recursion 7  --bsr7
lazy matching in LZ77 yes  --lazy
optimized Huffman headers yes  --ohh
initial random W for iterations 1  --rw1
initial random Z for iterations 2  --rz2

Even Smaller Files Thanks To Defluff

Zopfli's output can be further optimized by the defluff tool.
In this particular case, defluff saves 1 more byte (51266 bytes).

Verify file integrity

After decompression, my uncompressed files are identical to the original ones:

MD5:
curl --silent --compressed https://raw.githubusercontent.com/mbostock/d3/v3.5.13/d3.min.js --location | md5sum
383c75d864642a4f88e4b7166d7f7a1c  -
curl --silent --compressed http://minime.stephan-brumme.com/files/d3/d3-3.5.13.min.zopfli.js.gz | md5sum
383c75d864642a4f88e4b7166d7f7a1c  -

SHA1:
curl --silent --compressed https://raw.githubusercontent.com/mbostock/d3/v3.5.13/d3.min.js --location | sha1sum
bdb8d3bc798e7bf4547d33db5af17b636f4552a3  -
curl --silent --compressed http://minime.stephan-brumme.com/files/d3/d3-3.5.13.min.zopfli.js.gz | sha1sum
bdb8d3bc798e7bf4547d33db5af17b636f4552a3  -

All listed CDNs deliver identical contents:
CDN Size (compressed) MD5 (uncompressed) Timestamp
Boot 61038 bytes 383c75d864642a4f88e4b7166d7f7a1c (invalid)
jsdelivr 61038 bytes 383c75d864642a4f88e4b7166d7f7a1c (invalid)
cdnhttps 53630 bytes 383c75d864642a4f88e4b7166d7f7a1c November 22, 2016 @ 16:32
cdnjs 53630 bytes 383c75d864642a4f88e4b7166d7f7a1c (invalid)
unpkg 53630 bytes 383c75d864642a4f88e4b7166d7f7a1c July 11, 2016 @ 16:30

Note: only the MD5 hashes are shown to keep things simple.

Other Versions

Available D3 versions at minime.stephan-brumme.com:

4.9.1, 4.9.0, 4.8.0, 4.7.4, 4.7.3, 4.7.2, 4.7.1, 4.7.0, 4.6.0, 4.5.0, 4.4.4, 4.4.3, 4.4.2, 4.4.1, 4.4.0, 4.3.0, 4.2.8, 4.2.7, 4.2.6, 4.2.5, 4.2.4, 4.2.3, 4.2.2, 4.2.1, 4.2.0, 4.1.1, 4.1.0, 4.0.0,
3.5.17, 3.5.16, 3.5.15, 3.5.14, 3.5.13, 3.5.12, 3.5.11, 3.5.10, 3.5.9, 3.5.8, 3.5.7, 3.5.6, 3.5.5, 3.5.4, 3.5.3, 3.5.2, 3.5.1, 3.5.0, 3.4.13, 3.4.12, 3.4.11, 3.4.10, 3.4.9, 3.4.8, 3.4.6, 3.4.5, 3.4.4, 3.4.3, 3.4.2, 3.4.1, 3.4.0, 3.3.13, 3.3.12, 3.3.11, 3.3.10, 3.3.9, 3.3.8, 3.3.7, 3.3.6, 3.3.5, 3.3.4, 3.3.3, 3.3.2, 3.3.1, 3.3.0, 3.2.8, 3.2.7, 3.2.6, 3.2.5, 3.2.4, 3.2.3, 3.2.2, 3.2.1, 3.2.0, 3.1.10, 3.1.9, 3.1.8, 3.1.7, 3.1.6, 3.1.5, 3.1.4, 3.1.3, 3.1.2, 3.1.1, 3.1.0, 3.0.8, 3.0.7, 3.0.6, 3.0.5, 3.0.4, 3.0.3, 3.0.2, 3.0.1, 3.0.0

The project site contains an overview how well these versions were compressed.
Other interesting projects are AngularJS, BackboneJS, Bootstrap, Dojo, Ember, jQuery, Knockout, lodash, React, Socket.IO, ThreeJS, UnderscoreJS and Vue.

Changelog

Best Zopfli parameters so far:
Size Improvement Parameters Found
51267 bytes -3 bytes zopfli --i1000000 --mls128 --bsr7 --lazy --ohh January 22, 2016 @ 18:45
51270 bytes -6 bytes zopfli --i100000 --mls128 --bsr7 --lazy --ohh January 21, 2016 @ 11:39
51276 bytes -6 bytes zopfli --i10000 --mls128 --bsr7 --lazy --ohh January 21, 2016 @ 08:55
51282 bytes -22 bytes zopfli --i1000 --mls128 --bsr7 --lazy --ohh January 21, 2016 @ 08:41
51304 bytes -11 bytes zopfli --i1000 --mls2 --bsr30 --lazy --ohh January 21, 2016 @ 08:36
51315 bytes -7 bytes zopfli --i1000 --mls32768 --bsr6 --lazy --ohh January 21, 2016 @ 08:35
51322 bytes zopfli --i100 --mls32768 --bsr6 --lazy --ohh January 21, 2016 @ 08:33

If there are multiple parameter sets yielding the same compressed size, only the first one found is shown.

Most recent activity on November 22, 2016 @ 16:32.

Heatmaps

This Zopfli heatmap visualizes how compression changes when modifying the --bsr and --mls parameter.
Cell's contents is the best filesize achieved (in bytes, hover with mouse over cells to see number of iterations).

Good parameters are green, bad are red. The best and worst are bold as well.
The brightness of the blue background color indicates how many iterations were processed:
10,000, 100,000 or 1,000,000.
bsr \ mls
2 4 8 16 32 64 128 256 512 1024 2048 4096 8192 16384 32768
bsr \ mls
2 4 8 16 32 64 128 256 512 1024 2048 4096 8192 16384 32768
51418 51480 51432 51501 51416 51417 51452 51445 51443 51444 51527 51429 51417 51418 51550
51337 51309 51297 51331 51381 51347 51388 51405 51405 51398 51423 51404 51401 51404 51300
51327 51463 51335 51359 51339 51323 51329 51398 51390 51385 51403 51398 51379 51384 51308
51380 51437 51360 51471 51373 51391 51267 51403 51377 51395 51386 51408 51385 51385 51342
51361 51454 51333 51358 51463 51420 51354 51402 51394 51390 51409 51408 51538 51376 51542
51354 51458 51342 51375 51358 51406 51353 51405 51405 51401 51410 51410 51386 51378 51276
51376 51361 51361 51388 51339 51372 51360 51403 51383 51397 51531 51420 51385 51398 51309
51435 51430 51427 51363 51450 51448 51332 51401 51402 51398 51396 51386 51397 51388 51312
51320 51432 51362 51336 51295 51373 51459 51419 51388 51393 51400 51403 51384 51387 51327
51350 51353 51360 51378 51342 51320 51376 51413 51409 51394 51399 51408 51391 51386 51309
51367 51457 51456 51351 51320 51428 51352 51398 51374 51385 51396 51395 51392 51387 51376
51378 51431 51345 51381 51355 51387 51361 51396 51416 51388 51402 51392 51384 51376 51378
51458 51335 51359 51348 51356 51429 51331 51403 51401 51399 51390 51396 51390 51395 51296
51356 51370 51360 51329 51461 51370 51456 51407 51378 51385 51409 51410 51380 51384 51309
51375 51435 51345 51373 51357 51428 51353 51414 51389 51387 51397 51409 51397 51397 51333
51312 51317 51437 51378 51392 51427 51332 51405 51400 51398 51384 51403 51382 51376 51310
51382 51457 51338 51364 51356 51371 51466 51403 51398 51387 51410 51410 51382 51379 51327
51381 51333 51360 51352 51359 51370 51344 51405 51390 51389 51401 51409 51385 51377 51278
51373 51360 51365 51378 51322 51426 51351 51402 51399 51397 51404 51409 51386 51382 51299
51313 51419 51338 51378 51349 51343 51328 51405 51417 51381 51399 51386 51383 51390 51313
51328 51435 51361 51376 51396 51377 51353 51403 51397 51393 51402 51397 51386 51385 51327
51290 51362 51363 51379 51355 51348 51352 51402 51403 51396 51396 51406 51381 51384 51328
51408 51418 51428 51369 51324 51429 51326 51408 51378 51397 51380 51392 51384 51393 51347

Due to the Monte Carlo design of my search algorithm, not all parameters have reached the same number of iterations yet:
Iterations Min. Bytes Reduction Coverage
100 51296 bytes 100%
1,000 51282 bytes -14 bytes 100%
10,000 51276 bytes -6 bytes 100%
100,000 51270 bytes -6 bytes 2.61%
1,000,000 51267 bytes -3 bytes 0.29%
10,000,000

KZIP has far less options available for tuning/optimization. I only played around with the number of blocks (parameter -n):
Blocks Min. Bytes Compared To Best Zopfli Compared To Best KZIP
51576 bytes +309 bytes (+0.60%) +252 bytes
51576 bytes +309 bytes (+0.60%) +252 bytes
51586 bytes +319 bytes (+0.62%) +262 bytes
51517 bytes +250 bytes (+0.49%) +193 bytes
51465 bytes +198 bytes (+0.39%) +141 bytes
51457 bytes +190 bytes (+0.37%) +133 bytes
51362 bytes +95 bytes (+0.19%) +38 bytes
51371 bytes +104 bytes (+0.20%) +47 bytes
51324 bytes +57 bytes (+0.11%)

Non-DEFLATE Algorithms

Archivers based on completely different compression algorithms often produce superior results.
Unfortunately, browsers only support gzip compression at the moment.
Algorithm Program Parameters Size Compared To Best Zopfli
ZPAQ (Wikipedia) zpaq zpaq -method 69 40888 bytes -10379 bytes (-20.24%)
RAR (proprietary) RAR rar a -m5 -md64m -mc63:128t -mt1 43501 bytes -7766 bytes (-15.15%)
PPMd (Wikipedia) 7zip 7za a -mx=9 -m0=ppmd 44568 bytes -6699 bytes (-13.07%)
Brotli (Wikipedia) brotli brotli -q 11 46340 bytes -4927 bytes (-9.61%)
LZMA2 (Wikipedia) xz xz -9 47008 bytes -4259 bytes (-8.31%)
Burrows-Wheeler transform (Wikipedia) bzip2 bzip2 -9 48946 bytes -2321 bytes (-4.53%)
ZSTD (Wikipedia) zstd zstd -19 49555 bytes -1712 bytes (-3.34%)

Detailled Analysis

I wrote a DEFLATE decoder in Javascript. Click the button below to start a client-side analysis of the smallest gzipped files (may take a second):


Notes: pigz is a fast open source multi-threaded implementation of gzip written by one of the original authors of gzip.
However, when using compression level 11, pigz actually switches to the slower Zopfli algorithm and isn't multi-threaded anymore.
KrzyMOD's extensions to Zopfli offer the highest level of configuration and is therefore used for my brute-force search.
Ken Silverman wrote the closed-source KZIP compression program and Jonathon Fowler ported it to Linux.
Defluff was created by Joachim Henke; DeflOpt is a tool by Ben Jos Walbeehm.

website made by Stephan Brumme in 2015 and still improving in 2017.
all timestamps are displayed in central european time. see my changelog.
no flash, not even images or external css files - and everything squeezed into a single html file.
which was handsomely compressed before releasing it into the wild internet - obviously.

please visit my homepage and my blog, too.
email: minime (at) stephan-brumme.com