Ubuntu Manpage: duperemove - Find duplicate extents and print them to stdout

Provided by: duperemove_0.11.2-3build2_amd64

NAME

       duperemove - Find duplicate extents and print them to stdout

SYNOPSIS

       duperemove [options] files...

DESCRIPTION

       duperemove  is  a  simple tool for finding duplicated extents and submitting them for deduplication. When
       given a list of files it will hash the contents of their extents and compare those hashes to each  other,
       finding  and categorizing extents that match each other. When given the -d option, duperemove will submit
       those extents for deduplication using the Linux kernel extent-same ioctl.

       duperemove can store the hashes it computes in a hashfile. If given an existing hashfile, duperemove will
       only compute hashes for those files which have changed since the last run.  Thus you can  run  duperemove
       repeatedly  on  your  data  as  it  changes,  without  having to re-checksum unchanged data.  For more on
       hashfiles see the --hashfile option below as well as the Examples section.

       duperemove can also take input from the fdupes program, see the --fdupes option below.

GENERAL

       Duperemove has two major modes of operation one of which is a subset of the other.

   Readonly / Non-deduplicating Mode
       When run without -d (the default) duperemove will print out one or more tables of matching extents it has
       determined would be ideal candidates for deduplication. As a result, readonly mode is useful  for  seeing
       what duperemove might do when run with -d.

       Generally,  duperemove  does  not  concern  itself  with  the underlying representation of the extents it
       processes. Some of them could be compressed, undergoing I/O, or even have already been  deduplicated.  In
       dedupe mode, the kernel handles those details and therefore we try not to replicate that work.

   Deduping Mode
       This  functions  similarly  to  readonly mode with the exception that the duplicated extents found in our
       "read, hash, and compare" step will actually be submitted for deduplication. Extents  that  have  already
       been  deduped  will  be  skipped.  An  estimate  of the total data deduplicated will be printed after the
       operation is complete. This estimate is calculated by comparing the total amount of shared bytes in  each
       file before and after the dedupe.

OPTIONS

files can refer to a list of regular files and directories or be a hyphen (-) to read them from standard
input. If a directory is specified, all regular files within it will also be scanned. Duperemove can
also be told to recursively scan directories with the '-r' switch.

-r Enable recursive dir traversal.

-d De-dupe the results - only works on btrfs and xfs.

-A Opens files readonly when deduping. Primarily for use by privileged users on readonly snapshots.

-h Print numbers in human-readable format.

-q Quiet mode. Duperemove will only print errors and a short summary of any dedupe.

--hashfile=hashfile
Use a file for storage of hashes instead of memory. This option drastically reduces the memory
footprint of duperemove and is recommended when your data set is more than a few files large.
Hashfiles are also reusable, allowing you to further reduce the amount of hashing done on
subsequent dedupe runs.

If hashfile does not exist it will be created. If it exists, duperemove will check the file paths
stored inside of it for changes. Files which have changed will be rescanned and their updated
hashes will be written to the hashfile. Deleted files will be removed from the hashfile.

New files are only added to the hashfile if they are discoverable via the files argument. For
that reason you probably want to provide the same files list and -r arguments on each run of
duperemove. The file discovery algorithm is efficient and will only visit each file once, even if
it is already in the hashfile.

Adding a new path to a hashfile is as simple as adding it to the files argument.

When deduping from a hashfile, duperemove will avoid deduping files which have not changed since
the last dedupe.

-L Print all files in the hashfile and exit. Requires the --hashfile option. Will print additional
information about each file when run with -v.

-R [file]
Remove file from the db and exit. Can be specified multiple times. Duperemove will read the list
from standard input if a hyphen (-) is provided. Requires the --hashfile option.

Note: If you are piping filenames from another duperemove instance it is advisable to do so into a
temporary file first as running duperemove simultaneously on the same hashfile may corrupt that
hashfile.

--fdupes
Run in fdupes mode. With this option you can pipe the output of fdupes to duperemove to dedupe any
duplicate files found. When receiving a file list in this manner, duperemove will skip the hashing
phase.

-v Be verbose.

--skip-zeroes
Read data blocks and skip any zeroed blocks, useful for speedup duperemove, but can prevent
deduplication of zeroed files.

-b size
Use the specified block size for reading file extents. Defaults to 128K.

--io-threads=N
Use N threads for I/O. This is used by the file hashing and dedupe stages. Default is
automatically detected based on number of host cpus.

--cpu-threads=N
Use N threads for CPU bound tasks. This is used by the duplicate extent finding stage. Default is
automatically detected based on number of host cpus.

Note: Hyperthreading can adversely affect performance of the extent finding stage. If duperemove
detects an Intel CPU with hyperthreading it will use half the number of cores reported by the
system for cpu bound tasks.

--dedupe-options=options
Comma separated list of options which alter how we dedupe. Prepend 'no' to an option in order to
turn it off.

[no]partial
Duperemove can often find more dedupe by comparing portions of extents to each other. This
can be a lengthy, CPU intensive task so it is turned off by default.

The code behind this option is under active development and as a result the semantics of
the partial argument may change.

[no]same
Defaults to off. Allow dedupe of extents within the same file.

[no]fiemap
Defaults to on. Duperemove uses the fiemap ioctl during the dedupe stage to optimize out
already deduped extents as well as to provide an estimate of the space saved after dedupe
operations are complete.

Unfortunately, some versions of Btrfs exhibit extremely poor performance in fiemap as the
number of references on a file extent goes up. If you are experiencing the dedupe phase
slowing down or 'locking up' this option may give you a significant amount of performance
back.

Note: This does not turn off all usage of fiemap, to disable fiemap during the file scan
stage, you will also want to use the --lookup-extents=no option.

[no]block
Deprecated.

--help Prints help text.

--lookup-extents=[yes|no]
Defaults to yes. Allows duperemove to skip checksumming some blocks by checking their extent
state.

--read-hashes=hashfile
This option is primarily for testing. See the --hashfile option if you want to use hashfiles.

Read hashes from a hashfile. A file list is not required with this option. Dedupe can be done if
duperemove is run from the same base directory as is stored in the hash file (basically duperemove
has to be able to find the files).

--write-hashes=hashfile
This option is primarily for testing. See the --hashfile option if you want to use hashfiles.

Write hashes to a hashfile. These can be read in at a later date and deduped from.

--debug
Print debug messages, forces -v if selected.

--hash-threads=N
Deprecated, see --io-threads above.

--hash=alg
You can choose between murmur3 and xxhash. The default is murmur3 as it is very fast and can
generate 128 bit digests for a very small chance of collision. Xxhash may be faster but generates
only 64 bit digests. Both hashes are fast enough that the default should work well for the
overwhelming majority of users.

--exclude=PATTERN
You an exclude certain files and folders from the deduplication process. This might be benefical
for skipping subvolume snapshot mounts, for instance. You need to provide full path for exclusion.
For example providing just a file name with a wildcard i.e duperemove --exclude file-* won't ever
match because internally duperemove works with absolute paths. Another thing to keep in mind is
that shells usually expand glob pattern so the passed in pattern ought to also be quoted. Taking
everything into consideration the correct way to pass an exclusion pattern is duperemove --exclude
"/path/to/dir/file*" /path/to/dir

EXAMPLES

Simple Usage
Dedupe the files in directory /foo, recurse into all subdirectories. You only want to use this for small
data sets.

duperemove -dr /foo

Use duperemove with fdupes to dedupe identical files below directory foo.

fdupes -r /foo | duperemove --fdupes

Using Hashfiles
Duperemove can optionally store the hashes it calculates in a hashfile. Hashfiles have two primary
advantages - memory usage and re-usability. When using a hashfile, duperemove will stream computed hashes
to it, instead of main memory.

If Duperemove is run with an existing hashfile, it will only scan those files which have changed since
the last time the hashfile was updated. The files argument controls which directories duperemove will
scan for newly added files. In the simplest usage, you rerun duperemove with the same parameters and it
will only scan changed or newly added files - see the first example below.

Dedupe the files in directory foo, storing hashes in foo.hash. We can run this command multiple times and
duperemove will only checksum and dedupe changed or newly added files.

duperemove -dr --hashfile=foo.hash foo/

Don't scan for new files, only update changed or deleted files, then dedupe.

duperemove -dr --hashfile=foo.hash

Add directory bar to our hashfile and discover any files that were recently added to foo.

duperemove -dr --hashfile=foo.hash foo/ bar/

List the files tracked by foo.hash.

duperemove -L --hashfile=foo.hash

FAQ

Is there an upper limit to the amount of data duperemove can process?
Duperemove v0.11 is fast at reading and cataloging data. Dedupe runs will be memory limited unless the
'--hashfile' option is used. '--hashfile' allows duperemove to temporarily store duplicated hashes to
disk, thus removing the large memory overhead and allowing for a far larger amount of data to be scanned
and deduped. Realistically though you will be limited by the speed of your disks and cpu. In those
situations where resources are limited you may have success by breaking up the input data set into
smaller pieces.

When using a hashfile, duperemove will only store duplicate hashes in memory. During normal operation
then the hash tree will make up the largest portion of duperemove memory usage. As of Duperemove v0.11
hash entries are 88 bytes in size. If you know the number of duplicate blocks in your data set you can
get a rough approximation of memory usage by multiplying with the hash entry size.

Actual performance numbers are dependent on hardware - up to date testing information is kept on the
duperemove wiki (see below for the link).

How large of a hashfile will duperemove create?
Hashfiles are essentially sqlite3 database files with several tables, the largest of which are the files
and extents tables. Each extents table entry is about 72 bytes though that may grow as features are
added. The size of a files table entry depends on the file path but a good estimate is around 270 bytes
per file. The number of extents in a data set is directly proportional to file fragmentation level.

If you know the total number of extents and files in your data set then you can calculate the hashfile
size as:

Hashfile Size = Num Hashes X 72 + Num Files X 270

Using a real world example of 1TB (8388608 128K blocks) of data over 1000 files:

8388608 * 72 + 270 * 1000 = 755244720 or about 720MB for 1TB spread over 1000 files.

Note that none of this takes database overhead into account.

Is is safe to interrupt the program (Ctrl-C)?
Yes, Duperemove uses a transactional database engine and organizes db changes to take advantage of those
features. The result is that you should be able to ctrl-c the program at any point and re-run without
experiencing corruption of your hashfile.

I got two identical files, why are they not deduped?
Duperemove by default works on extent granularity. What this means is if there are two files which are
logically identical (have the same content) but are laid out on disk with different extent structure they
won't be deduped. For example if 2 files are 128k each and their content are identical but one of them
consists of a single 128k extent and the other of 2 x 64k extents then they won't be deduped. This
behavior is dependent on the current implementation and is subject to change as duperemove is being
improved.

How can I find out my space savings after a dedupe?
Duperemove will print out an estimate of the saved space after a dedupe operation for you.

You can get a more accurate picture by running 'btrfs fi df' before and after each duperemove run.

Be careful about using the 'df' tool on btrfs - it is common for space reporting to be 'behind' while
delayed updates get processed, so an immediate df after deduping might not show any savings.

Why is the total deduped data report an estimate?
At the moment duperemove can detect that some underlying extents are shared with other files, but it can
not resolve which files those extents are shared with.

Imagine duperemove is examing a series of files and it notes a shared data region in one of them. That
data could be shared with a file outside of the series. Since duperemove can't resolve that information
it will account the shared data against our dedupe operation while in reality, the kernel might
deduplicate it further for us.

Why are my files showing dedupe but my disk space is not shrinking?
This is a little complicated, but it comes down to a feature in Btrfs called _bookending_. The Btrfs wiki
explains this in detail: http://en.wikipedia.org/wiki/Btrfs#Extents.

Essentially though, the underlying representation of an extent in Btrfs can not be split (with small
exception). So sometimes we can end up in a situation where a file extent gets partially deduped (and the
extents marked as shared) but the underlying extent item is not freed or truncated.

Is duperemove safe for my data?
Yes. To be specific, duperemove does not deduplicate the data itself. It simply finds candidates for
dedupe and submits them to the Linux kernel extent-same ioctl. In order to ensure data integrity, the
kernel locks out other access to the file and does a byte-by-byte compare before proceeding with the
dedupe.

What is the cost of deduplication?
Deduplication will lead to increased fragmentation. The blocksize chosen can have an effect on this.
Larger blocksizes will fragment less but may not save you as much space. Conversely, smaller block sizes
may save more space at the cost of increased fragmentation.

NOTES

       Deduplication is currently only supported by the btrfs and xfs filesystem.

       The Duperemove project page can be found at https://github.com/markfasheh/duperemove

       There is also a wiki at https://github.com/markfasheh/duperemove/wiki