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I'm looking for an easy way (a command or series of commands, probably involving find) to find duplicate files in two directories, and replace the files in one directory with hardlinks of the files in the other directory.

Here's the situation: This is a file server which multiple people store audio files on, each user having their own folder. Sometimes multiple people have copies of the exact same audio files. Right now, these are duplicates. I'd like to make it so they're hardlinks, to save hard drive space.

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12  
One problem you may run into with hardlinks is if somebody decides to do something to one of their music files that you've hard-linked they could inadvertently be affecting other people's access to their music. –  Steven D Oct 13 '10 at 2:48
3  
another problem is that two different files containing "Some Really Great Tune", even if taken from the same source with the same encoder will very likely not be bit-for-bit identical. –  msw Oct 13 '10 at 2:57
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better sollution might be to have a public music folder... –  Stefan Oct 13 '10 at 7:08
    
Use symlinks then: Copy the MP3 Files to a central repo and symlink them into the user's folder, "deleting" a file would just mean deleting the symlink. (But Stefan's idea of the public music folder is better) –  tante Oct 13 '10 at 7:52
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15 Answers 15

up vote 21 down vote accepted

There is a perl script at http://cpansearch.perl.org/src/ANDK/Perl-Repository-APC-2.002/eg/trimtrees.pl which does exactly what you want:

Traverse all directories named on the command line, compute MD5 checksums and find files with identical MD5. IF they are equal, do a real comparison if they are really equal, replace the second of two files with a hard link to the first one.

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Sounds perfect, thanks!! I'll try it and accept if it works as described! –  Josh Oct 12 '10 at 20:09
2  
This did exactly what I asked for. However I believe that ZFS with dedup will eventually be the way to do, since I did find that the files had slight differences so only a few could be hardlinked. –  Josh Dec 8 '10 at 20:13

Use the fdupes tool:

fdupes -r /path/to/folder gives you a list of duplicates in the directory (-r makes it recursive). The output looks like this:


filename1
filename2

filename3
filename4
filename5


with filename1 and filename2 being identical and filename3, filename4 and filename5 also being identical.

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8  
In Debian, you can use the -L option to replace duplicate files with hardlinks (source) –  Michaël Witrant Jul 21 '11 at 15:16
    
Ubuntu Note: As of September 2013, it hasn't had a stable release (it is on 1.50-PR2-3), so the update doesn't appear in ubuntu yet. –  Stuart Axon Aug 28 '13 at 14:19
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I just tried installing fdupes_1.50-PR2-4 on both Ubuntu and Debian, neither has the -L flag. Luckily building from github.com/tobiasschulz/fdupes was super easy. –  neu242 Aug 30 '13 at 15:07

Since your main target is to save disk space, there is another solution: de-duplication (and probably compression) on file system level. Compared with the hard-link solution, it does not have the problem of inadvertently affecting other linked files.

ZFS has dedup (block-level, not file-level) since pool version 23 and compression since long time ago. If you are using linux, you may try zfs-fuse, or if you use BSD, it is natively supported.

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This is probably the way I'll go eventually, however, does BSD's ZFS implementation do dedup? I thought it did not. –  Josh Dec 8 '10 at 20:14
    
In addition, the HAMMER filesystem on DragonFlyBSD has deduplication support. –  hhaamu Jul 15 '12 at 17:48
    
I used zfs-fuse for a backup partition because of its deduplication and it took days, literally days to copy less than 1TB of data onto it. I can't begin to imagine how zfs-fuse would perform as a home partition or something. –  Christian Jun 14 '13 at 15:04
    
ZFS dedup is the friend of nobody. Where ZFS recommends 1Gb ram per 1Tb usable disk space, you're friggin' nuts if you try to use dedup with less than 32Gb ram per 1Tb usable disk space. That means that for a 1Tb mirror, if you don't have 32 Gb ram, you are likely to encounter memory bomb conditions sooner or later that will halt the machine due to lack of ram. Been there, done that, still recovering from the PTSD. –  killermist Sep 22 at 18:51

This is one of the functions provided by "fslint" -- http://en.flossmanuals.net/FSlint/Introduction

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3  
The -m will hardlink duplicates together, -d will delete all but one, and -t will dry run, printing what it would do –  Azendale Oct 29 '12 at 5:57
    
On Ubuntu here is what to do: sudo apt-get install fslint /usr/share/fslint/fslint/findup -m /your/directory/tree (directory /usr/share/fslint/fslint/ is not in $PATH by default) –  Jocelyn Sep 8 '13 at 15:38

I use hardlink from http://jak-linux.org/projects/hardlink/

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1  
Nice hint, I am using on a regular base code.google.com/p/hardlinkpy but this was not updated for a while... –  meduz Apr 11 '12 at 19:09
    
This appears to be similar to the original hardlink on Fedora/RHEL/etc. –  Jack Douglas Jun 21 '12 at 8:43

To find duplicate files you can use duff.

Duff is a Unix command-line utility for quickly finding duplicates in a given set of files.

Simply run:

duff -r target-folder

To create hardlinks to those files automaticly, you will need to parse the output of duff with bash or some other scripting language.

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Helpful, thanks! –  Josh Oct 12 '10 at 20:08

I've used many of the hardlinking tools for Linux mentioned here. I too am stuck with ext4 fs, on Ubuntu, and have been using its cp -l and -s for hard/softlinking. But lately noticed the lightweight copy in the cp man page, which would imply to spare the redundant disk space until one side gets modified:

   --reflink[=WHEN]
          control clone/CoW copies. See below

       When  --reflink[=always]  is specified, perform a lightweight copy, where the 
data blocks are copied only when modified.  If this is not possible the
       copy fails, or if --reflink=auto is specified, fall back to a standard copy.
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I think I will update my cp alias to always include the --reflink=auto parameter now –  Marcos Mar 14 '12 at 14:08
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Does ext4 really support --reflink? –  Jack Douglas Jun 21 '12 at 8:42
4  
This is supported on btrfs and OCFS2. It is only possible on copy-on-write filesystems, which ext4 is not. btrfs is really shaping up. I love using it because of reflink and snapshots, makes you less scared to do mass operations on big trees of files. –  clacke Jul 3 '12 at 18:57

rdfind does exactly what you ask for (and in the order johny why lists). Makes it possible to delete duplicates, replace them with either soft or hard links. Combined with symlinks you can also make the symlink either absolute or relative. You can even pick checksum algorithm (md5 or sha1).

Since it is compiled it is faster than most scripted solutions: time on a 15 GiB folder with 2600 files on my Mac Mini from 2009 returns this

9.99s user 3.61s system 66% cpu 20.543 total

(using md5).

Available in most package handlers (e.g. MacPorts for Mac OS X).

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+1 I used rdfind and loved it. It has a -dryrun true option that will let you know what it would have done. Replacing duplicates with hard links is as simple as -makehardlinks true. It produced a nice log and it let me know how much space was freed up. Plus, according to the author's benchmark, rdfind is faster than duff and fslint. –  Daniel Trebbien Dec 29 '13 at 20:49

On modern Linux these days there's https://github.com/g2p/bedup which de-duplicates on a btrfs filesystem, but 1) without as much of the scan overhead, 2) files can diverge easily again afterwards.

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I made a Perl script that does something similar to what you're talking about:

http://pastebin.com/U7mFHZU7

Basically, it just traverses a directory, calculating the SHA1sum of the files in it, hashing it and linking matches together. It's come in handy on many, many occasions.

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2  
I hope to get around to trying this soon... why not upload it on CPAN... App::relink or something –  xenoterracide Feb 7 '11 at 11:12

Since I'm not a fan of Perl, here's a bash version:

#!/bin/bash

DIR="/path/to/big/files"

find $DIR -type f -exec md5sum {} \; | sort > /tmp/sums-sorted.txt

OLDSUM=""
IFS=$'\n'
for i in `cat /tmp/sums-sorted.txt`; do
 NEWSUM=`echo "$i" | sed 's/ .*//'`
 NEWFILE=`echo "$i" | sed 's/^[^ ]* *//'`
 if [ "$OLDSUM" == "$NEWSUM" ]; then
  echo ln -f "$OLDFILE" "$NEWFILE"
 else
  OLDSUM="$NEWSUM"
  OLDFILE="$NEWFILE"
 fi
done

This finds all files with the same checksum (whether they're big, small, or already hardlinks), and hardlinks them together.

This can be greatly optimized for repeated runs with additional find flags (eg. size) and a file cache (so you don't have to redo the checksums each time). If anyone's interested in the smarter, longer version, I can post it.

NOTE: As has been mentioned before, hardlinks work as long as the files never need modification, or to be moved across filesystems.

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How can I change your script, so that instead of hardlinking it, it will just delete the duplicate files and will add an entry to a CSV file the deleted file -> Lined File. . ??? –  MR.GEWA Jan 12 '13 at 12:17
    
Sure. The hard link line: echo ln -f "$OLDFILE" "$NEWFILE" Just replaces the duplicate file with a hard link, so you could change it rm the $NEWFILE instead. –  seren Jan 13 '13 at 4:15
    
and how on next line, write in some text file somehow $OLDFILE-> NEWFILE ??? –  MR.GEWA Jan 13 '13 at 13:12
    
Ahh, right. Yes, add a line after the rm such as: echo "$NEWFILE" >> /var/log/deleted_duplicate_files.log –  seren Jan 14 '13 at 19:28
    
thanks @seren so much! –  MR.GEWA Jan 15 '13 at 15:03

If you want to replace duplicates by Hard Links on mac or any UNIX based system, you can try SmartDupe http://sourceforge.net/projects/smartdupe/ am developing it

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2  
Can you expand on how “smart” it is? –  Stéphane Gimenez Nov 4 '12 at 13:25

Seems to me that checking the filename first could speed things up. If two files lack the same filename then in many cases I would not consider them to be duplicates. Seems that the quickest method would be to compare, in order:

  • filename
  • size
  • md5 checksum
  • byte contents

Do any methods do this? Look at duff, fdupes, rmlint, fslint, etc.

The following method was top-voted on commandlinefu.com: Find Duplicate Files (based on size first, then MD5 hash)

Can filename comparison be added as a first step, size as a second step?

find -not -empty -type f -printf "%s\n" | sort -rn | uniq -d | \
  xargs -I{} -n1 find -type f -size {}c -print0 | xargs -0 md5sum | \
  sort | uniq -w32 --all-repeated=separate
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aptitude show hardlink

Description: Hardlinks multiple copies of the same file Hardlink is a tool which detects multiple copies of the same file and replaces them with hardlinks.

The idea has been taken from http://code.google.com/p/hardlinkpy/, but the code has been written from scratch and licensed under the MIT license. Homepage: http://jak-linux.org/projects/hardlink/

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If you'll do hardlinks, pay attention on rights on that file. Notice, owner, group, mode, extended attributes, time and ACL (if you use this) is stored in INODE. Only file names are different because this is stored in directory structure, and other points to INODE properties. This cause, all file names linked to the same inode, have the same access rights. You should prevent modification that file, because any user can damage file to other. It is simple. It is enough, any user put other file in the same name. Inode number is then saved, and original file content is destroyed (replaced) for all hardlinked names.

Better way is deduplication on filesystem layer. You can use BTRFS (very popular last time), OCFS or like this. Look at the page: https://en.wikipedia.org/wiki/Comparison_of_file_systems , specialy at the table Features and column data deduplication. You can click it and sort :)

Specially look at ZFS filesystem. This is available as FUSE, but in this way it's very slow. If you want native support, look at the page http://zfsonlinux.org/ . Then you must patch kernel, and next install zfs tools for managament. I don't understand, why linux doesn't support as drivers, it is way for many other operating systems / kernels.

File systems supports deduplication by 2 ways, deduplicate files, or blocks. ZFS supports block. This means, the same contents that repeats in the same file can be deduplicated. Other way is time when data are deduplicated, this can be online (zfs) or offline (btrfs).

Notice, deduplication consumes RAM. This is, why writing files to ZFS volume mounted with FUSE, cause dramatically slow performance. This is described in documentation. But you can online set on/off deduplication on volume. If you see any data should be deduplicated, you simply set deduplication on, rewrite some file to any temporary and finally replace. after this you can off deduplication and restore full performance. Of course, you can add to storage any cache disks. This can be very fast rotate disks or SSD disks. Of course this can be very small disks. In real work this is replacement for RAM :)

Under linux you should take care for ZFS because not all work as it should, specialy when you manage filesystem, make snapshot etc. but if you do configuration and don't change it, all works properly. Other way, you should change linux to opensolaris, it natively supports ZFS :) What is very nice with ZFS is, this works both as filesystem, and volumen manager similar to LVM. You do not need it when you use ZFS. See documentation if you want know more.

Notice difference between ZFS and BTRFS. ZFS is older and more mature, unfortunately only under Solaris and OpenSolaris (unfortunately strangled by oracle). BTRFS is younger, but last time very good supported. I recommend fresh kernel. ZFS has online deduplication, that cause slow down writes, because all is calculated online. BTRFS support off-line dedupliaction. Then this saves performance, but when host has nothing to do, you run periodically tool for make deduplication. And BTRFS is natively created under linux. Maybe this is better FS for You :)

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Thanks! We actually switched to using ZFS last year. –  Josh Jun 25 at 6:21

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