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I know that copying or transferring what was originally a sparse file without using a utility that understands sparse files will cause the 'holes' to be filled out. Is there a method or utility to turn what was once a sparse file back to sparse?

For Example:
create sparse file:

% dd if=/dev/zero of=TEST bs=1 count=0 seek=1G
# do some op that pads out the holes
% scp TEST localhost:~/TEST2
% ls -lhs TEST*
   0 -rw-rw-r--. 1 tony tony 1.0G Oct 16 13:35 TEST
1.1G -rw-rw-r--. 1 tony tony 1.0G Oct 16 13:37 TEST2

Is there some way to:

% resparse TEST2
to get:
   0 -rw-rw-r--. 1 tony tony 1.0G Oct 16 13:35 TEST
  0G -rw-rw-r--. 1 tony tony 1.0G Oct 16 13:37 TEST2
share|improve this question
Sorry, I had to pretty up the original ques... – user25849 Oct 16 '12 at 17:41
The only thing that can do this from all I've seen is a GNU 'cp', as in '% cp --sparse=always formerly-sparse-file newly-sparse-file' The detractor is it will not do it 'in-place'. – user25849 Oct 16 '12 at 19:21
If you want to copy a sparse file and let the copy be sparse, use rsync -aS. – Gilles Oct 16 '12 at 22:05

Edit 2015

as of util-linux 2.25, the fallocate utility on Linux has a -d/--dig-hole option for that.

fallocate -d the-file

Would dig a hole for every block full of zeros in the file

On older systems, you can do it by hand:

Linux has a FALLOC_FL_PUNCH_HOLE option to fallocate that can do this. I found a script on github with an example:

Using FALLOC_FL_PUNCH_HOLE from Python

I modified it a bit to do what you asked -- punch holes in regions of files that are filled with zeros. Here it is:

Using FALLOC_FL_PUNCH_HOLE from Python to punch holes in files

usage: punch.py [-h] [-v VERBOSE] FILE [FILE ...]

Punch out the empty areas in a file, making it sparse

positional arguments:
  FILE                  file(s) to modify in-place

optional arguments:
  -h, --help            show this help message and exit
  -v VERBOSE, --verbose VERBOSE
                        be verbose


# create a file with some data, a hole, and some more data
$ dd if=/dev/urandom of=test1 bs=4096 count=1 seek=0
$ dd if=/dev/urandom of=test1 bs=4096 count=1 seek=2

# see that it has holes
$ du --block-size=1 --apparent-size test1
12288   test1
$ du --block-size=1 test1
8192    test1

# copy it, ignoring the hole
$ cat test1 > test2
$ du --block-size=1 --apparent-size test2
12288   test2
$ du --block-size=1 test2
12288    test2

# punch holes again
$ ./punch.py test2
$ du --block-size=1 --apparent-size test2
12288   test2
$ du --block-size=1 test2
8192    test2

# verify
$ cmp test1 test2 && echo "files are the same"
files are the same

Note that punch.py only finds blocks of 4096 bytes to punch out, so it might not make a file exactly as sparse as it was when you started. It could be made smarter, of course. Also, it's only lightly tested, so be careful and make backups before trusting it!

share|improve this answer
I like this the best because it doesn't require rewriting the whole file again. – Peter Jul 24 '14 at 9:13
In util-linux 2.26.2 it's -d/--dig-holes. – Karl Richter Dec 24 '15 at 17:41

If you want to make a file sparse you can do that directly with dd.

dd if=./zeropadded.iso of=./isnowsparse.iso conv=sparse

From the dd(1) manual:

          sparse   If one or more output blocks would consist solely of
                   NUL bytes, try to seek the output file by the required
                   space instead of filling them with NULs, resulting in a
                   sparse file.

So, note that it will seek ahead only if the entire block is empty. For maximum sparseness use bs=1.

share|improve this answer
Any block size less than bs=512 doesn't really make sense, as disks are block devices. (bs=4096 in newer drives) – lapo Jan 22 '14 at 11:06

Short of tar-ing it up with a -S flag (assuming GNU tar), and re-executing the scp... no. No utility I'm aware of would have a way of knowing where the "holes" were.

share|improve this answer
GNU cp will resparse a file: From the man page: Specify --sparse=always to create a sparse DEST file whenever the SOURCE file contains a long enough sequence of zero bytes. – user25849 Oct 16 '12 at 19:45
Awesome. Learn something every day - when was that flag introduced? Pays to read man-pages of "well known" programs once in a while ;D – tink Oct 16 '12 at 20:09

I've had good luck with this:

cd whatever
rsync -avxWSHAXI . .

The -I forces rsync to update all files, regardless of whether it thinks they've changed or not; the -S causes the new files to be sparsified. -a makes it happen recursively so you can sparsify whole directory trees in one command.

It's not as good as a bespoke tool which hunts out holes and destroys them with FALLOC_FL_PUNCH_HOLE, but it's better than having to duplicate entire directory trees.

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