2014-07-07 transferring (lots of) files to a remote server + saving space

I have recently been asked how to transfer lots of file from a backup server to a local disk. The context is that

  1. the backup is an archive to be put on an external hard drive and then in a closet for future use,
  2. the transfer line is not quite reliable and transfers may stop (for instance if it is mounted as a samba / windows / applefile share)

rsync

The solution is to use the beloved rsync tool:

In its most simple form, you use this command in the termina:

rsync -av  $INPUT  $OUTPUT

Where -avstands for "keep file attributes and be (not too) verbose", $INPUT is the folder containing the files to be backed up, $OUTPUT is the destination folder. Be careful to avoid a trailing slash in $INPUT, unless you want the files that reside within the folder to be transferred instead of the folder itself.

One huge advantage is that $INPUT or $OUTPUT can contain a remote server in the form of myname@remoteserver:/path/to/my/folder.

An additional, useful option is --dry-run to try the command without moving the files. Also --progress gives a bit more info.

Let's try it:

In [2]:
%%bash
rsync -av  --progress --dry-run perrinet.l@frioul.int.univ-amu.fr:/riou/work/invibe/ARCHIVES/backups_perrinet/12_backups/alex /Volumes/3tera/backups/12_backups/
receiving incremental file list
alex/
alex/bruitlolo_090319.mat
alex/lolo.mat
alex/lolo2.mat
alex/lolocenter.mat
alex/lolofrozenpixel.mat
alex/worloloofr.mat
alex/.AppleDouble/
alex/.AppleDouble/.Parent
alex/.AppleDouble/bruitlolo_090319.mat
alex/.AppleDouble/lolo.mat
alex/.AppleDouble/lolo2.mat
alex/.AppleDouble/lolocenter.mat
alex/.AppleDouble/lolofrozenpixel.mat
alex/.AppleDouble/worloloofr.mat

sent 58 bytes  received 422 bytes  960.00 bytes/sec
total size is 2,772,534,329  speedup is 5,776,113.19 (DRY RUN)

All good! We could connect to the server and the folder names were apparently correct. Let's use another option to exclude some files:

In [4]:
%%bash
INPUT=perrinet.l@frioul.int.univ-amu.fr:/riou/work/invibe/ARCHIVES/backups_perrinet/12_backups/alex
OUTPUT=/Volumes/3tera/backups/12_backups/
rsync -av --dry-run  --progress --exclude .AppleDouble $INPUT $OUTPUT
receiving incremental file list
alex/
alex/bruitlolo_090319.mat
alex/lolo.mat
alex/lolo2.mat
alex/lolocenter.mat
alex/lolofrozenpixel.mat
alex/worloloofr.mat

sent 51 bytes  received 222 bytes  546.00 bytes/sec
total size is 2,772,529,142  speedup is 10,155,784.40 (DRY RUN)

Let's now do it for real:

In [5]:
%%bash
INPUT=perrinet.l@frioul.int.univ-amu.fr:/riou/work/invibe/ARCHIVES/backups_perrinet/12_backups/alex
OUTPUT=/Volumes/3tera/backups/12_backups/
rsync -av  --progress --exclude .AppleDouble $INPUT $OUTPUT
receiving incremental file list
alex/
alex/bruitlolo_090319.mat
    986,581,489 100%   63.21MB/s    0:00:14 (xfr#1, to-chk=5/7)
alex/lolo.mat
        248,942 100%  248.83kB/s    0:00:00 (xfr#2, to-chk=4/7)
alex/lolo2.mat
    522,599,574 100%   49.22MB/s    0:00:10 (xfr#3, to-chk=3/7)
alex/lolocenter.mat
        458,267 100%  438.75kB/s    0:00:01 (xfr#4, to-chk=2/7)
alex/lolofrozenpixel.mat
     65,216,914 100%   47.08MB/s    0:00:01 (xfr#5, to-chk=1/7)
alex/worloloofr.mat
  1,197,423,956 100%   54.14MB/s    0:00:21 (xfr#6, to-chk=0/7)

sent 147 bytes  received 2,772,868,036 bytes  58,376,172.27 bytes/sec
total size is 2,772,529,142  speedup is 1.00

Everything went fine, with a file transfer speed of ~58Mb/s. The good sync with rsync is that if you do that once again (or if the transfer was interrupted) you only transfer the files you need and not the whole thing. So for instance, if we do the same command again, we get:

In [7]:
%%bash
INPUT=perrinet.l@frioul.int.univ-amu.fr:/riou/work/invibe/ARCHIVES/backups_perrinet/12_backups/alex
OUTPUT=/Volumes/3tera/backups/12_backups/
rsync -av  --progress --exclude .AppleDouble $INPUT $OUTPUT
receiving incremental file list

sent 30 bytes  received 201 bytes  154.00 bytes/sec
total size is 2,772,529,142  speedup is 12,002,290.66

That is a speedup of more than $10^7$, but that does not make sense, it's just very quick :-)

Hardlinking

And now, what about saving space? On a hard drive, files exist physically on the plates as streeams of bits --- zeros and ones--- but a curcial point is that they may be chunked in different pieces (imagine placing a big file on a disk which is fragmented may cause problems similar to when you have to re-order your desk...). A solution on most filesystems is that they contain a file allocation tables containing (1) all the filenames and the name of the folder in which they sit (2) a pointer to the chunks on the physical disk where the actual data is.

So we can take advantage of that on a backup: a somewhat obscure habit is to take a folder my_work, copy it and then rename my_work_new. Strange habit, but let's stick with that and take advantage of the previous remark. Such technique is used in many backup mechanisms (such as the Time Machine used on Mac Os X) and allows to copy a whole folder with a different name but without taking more space on the disk (google incremental backups for more info on this).

As a matter of fact, it is possible to have two files with different names but pointing to the same data chunks, it is a harlink. If a program would detect files that are exactly the same, for instance if we used the copy-and-paste procedure described above, this would greatly reduce the actual physical space. Many such programs exist and one easy piece of software is available on https://hardlinkpy.googlecode.com/. It just consists of a python script, so the install is obvious:

In [13]:
%%bash
wget https://hardlinkpy.googlecode.com/hg-history/1be1ba7ea38917e6b52c189ef625b05b4e7e4d52/hardlink.py
--2014-07-07 11:47:55--  https://hardlinkpy.googlecode.com/hg-history/1be1ba7ea38917e6b52c189ef625b05b4e7e4d52/hardlink.py
Resolving hardlinkpy.googlecode.com (hardlinkpy.googlecode.com)... 173.194.70.82, 2a00:1450:4001:c02::52
Connecting to hardlinkpy.googlecode.com (hardlinkpy.googlecode.com)|173.194.70.82|:443... connected.
HTTP request sent, awaiting response... 
  HTTP/1.1 200 OK
  Accept-Ranges: none
  ETag: "544c8545289d2cbbb3d7b6d76eca8d743bca65bf/hardlink.py"
  Date: Mon, 07 Jul 2014 09:45:13 GMT
  Content-Type: text/plain
  Server: hg_frontend
  X-XSS-Protection: 1; mode=block
  Cache-Control: public,max-age=60
  Age: 0
  Alternate-Protocol: 443:quic
  Transfer-Encoding: chunked
Length: unspecified [text/plain]
Last-modified header missing -- time-stamps turned off.
--2014-07-07 11:47:55--  https://hardlinkpy.googlecode.com/hg-history/1be1ba7ea38917e6b52c189ef625b05b4e7e4d52/hardlink.py
Reusing existing connection to hardlinkpy.googlecode.com:443.
HTTP request sent, awaiting response... 
  HTTP/1.1 200 OK
  Accept-Ranges: none
  ETag: "544c8545289d2cbbb3d7b6d76eca8d743bca65bf/hardlink.py"
  Date: Mon, 07 Jul 2014 09:45:13 GMT
  Content-Type: text/plain
  Server: hg_frontend
  X-XSS-Protection: 1; mode=block
  Cache-Control: public,max-age=60
  Age: 0
  Alternate-Protocol: 443:quic
  Transfer-Encoding: chunked
Length: unspecified [text/plain]
Saving to: 'hardlink.py'

     0K .......... ..........                                   947K=0.02s

2014-07-07 11:47:55 (947 KB/s) - 'hardlink.py' saved [21430]

Now imagine we had copied the folder twice:

In [17]:
%%bash
INPUT=perrinet.l@frioul.int.univ-amu.fr:/riou/work/invibe/ARCHIVES/backups_perrinet/12_backups/alex
OUTPUT=/Volumes/3tera/backups/12_backups/alex_new
rsync -av  --progress --exclude .AppleDouble $INPUT $OUTPUT
receiving incremental file list
created directory /Volumes/3tera/backups/12_backups/alex_new
alex/
alex/bruitlolo_090319.mat
    986,581,489 100%   19.40MB/s    0:00:48 (xfr#1, to-chk=5/7)
alex/lolo.mat
        248,942 100%    1.70MB/s    0:00:00 (xfr#2, to-chk=4/7)
alex/lolo2.mat
    522,599,574 100%   52.06MB/s    0:00:09 (xfr#3, to-chk=3/7)
alex/lolocenter.mat
        458,267 100%  962.42kB/s    0:00:00 (xfr#4, to-chk=2/7)
alex/lolofrozenpixel.mat
     65,216,914 100%   47.12MB/s    0:00:01 (xfr#5, to-chk=1/7)
alex/worloloofr.mat
  1,197,423,956 100%   58.84MB/s    0:00:19 (xfr#6, to-chk=0/7)

sent 147 bytes  received 2,772,868,036 bytes  34,878,845.07 bytes/sec
total size is 2,772,529,142  speedup is 1.00

The program is easy to use: just type python hardlink.py in the terminal to have basic usage:

In [16]:
!python hardlink.py
Usage: hardlink.py [options] directory [ directory ... ]

Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  -f, --filenames-equal
                        Filenames have to be identical
  -n, --dry-run         Do NOT actually hardlink files
  -p, --print-previous  Print previously created hardlinks
  -q, --no-stats        Do not print the statistics
  -t, --timestamp-ignore
                        File modification times do NOT have to be identical
  -c, --content-only    Only file contents have to match
  -v LEVEL, --verbose=LEVEL
                        Verbosity level (default: 1)
  -x REGEX, --exclude=REGEX
                        Regular expression used to exclude files/dirs (may specify multiple times)

Error: Must supply one or more directories

Such that in our case, we want to do this: python hardlink.py /Volumes/3tera/backups/12_backups/ :

In [18]:
!python hardlink.py /Volumes/3tera/backups/12_backups/
Comparing: /Volumes/3tera/backups/12_backups/alex/bruitlolo_090319.mat
     to  : /Volumes/3tera/backups/12_backups/alex_new/alex/bruitlolo_090319.mat
Linked: /Volumes/3tera/backups/12_backups/alex_new/alex/bruitlolo_090319.mat
     to: /Volumes/3tera/backups/12_backups/alex/bruitlolo_090319.mat, saved 986581489
Comparing: /Volumes/3tera/backups/12_backups/alex/lolo.mat
     to  : /Volumes/3tera/backups/12_backups/alex_new/alex/lolo.mat
Linked: /Volumes/3tera/backups/12_backups/alex_new/alex/lolo.mat
     to: /Volumes/3tera/backups/12_backups/alex/lolo.mat, saved 248942
Comparing: /Volumes/3tera/backups/12_backups/alex/lolo2.mat
     to  : /Volumes/3tera/backups/12_backups/alex_new/alex/lolo2.mat
Linked: /Volumes/3tera/backups/12_backups/alex_new/alex/lolo2.mat
     to: /Volumes/3tera/backups/12_backups/alex/lolo2.mat, saved 522599574
Comparing: /Volumes/3tera/backups/12_backups/alex/lolocenter.mat
     to  : /Volumes/3tera/backups/12_backups/alex_new/alex/lolocenter.mat
Linked: /Volumes/3tera/backups/12_backups/alex_new/alex/lolocenter.mat
     to: /Volumes/3tera/backups/12_backups/alex/lolocenter.mat, saved 458267
Comparing: /Volumes/3tera/backups/12_backups/alex/lolofrozenpixel.mat
     to  : /Volumes/3tera/backups/12_backups/alex_new/alex/lolofrozenpixel.mat
Linked: /Volumes/3tera/backups/12_backups/alex_new/alex/lolofrozenpixel.mat
     to: /Volumes/3tera/backups/12_backups/alex/lolofrozenpixel.mat, saved 65216914
Comparing: /Volumes/3tera/backups/12_backups/alex/worloloofr.mat
     to  : /Volumes/3tera/backups/12_backups/alex_new/alex/worloloofr.mat
Linked: /Volumes/3tera/backups/12_backups/alex_new/alex/worloloofr.mat
     to: /Volumes/3tera/backups/12_backups/alex/worloloofr.mat, saved 1197423956


Hard linking Statistics:
Files Hardlinked this run:
Hardlinked: /Volumes/3tera/backups/12_backups/alex_new/alex/bruitlolo_090319.mat
        to: /Volumes/3tera/backups/12_backups/alex/bruitlolo_090319.mat
Hardlinked: /Volumes/3tera/backups/12_backups/alex_new/alex/lolo.mat
        to: /Volumes/3tera/backups/12_backups/alex/lolo.mat
Hardlinked: /Volumes/3tera/backups/12_backups/alex_new/alex/lolo2.mat
        to: /Volumes/3tera/backups/12_backups/alex/lolo2.mat
Hardlinked: /Volumes/3tera/backups/12_backups/alex_new/alex/lolocenter.mat
        to: /Volumes/3tera/backups/12_backups/alex/lolocenter.mat
Hardlinked: /Volumes/3tera/backups/12_backups/alex_new/alex/lolofrozenpixel.mat
        to: /Volumes/3tera/backups/12_backups/alex/lolofrozenpixel.mat
Hardlinked: /Volumes/3tera/backups/12_backups/alex_new/alex/worloloofr.mat
        to: /Volumes/3tera/backups/12_backups/alex/worloloofr.mat

Directories           : 4
Regular files         : 12
Comparisons           : 6
Hardlinked this run   : 6
Total hardlinks       : 6
Bytes saved this run  : 2772529142 (2.582 gibibytes)
Total bytes saved     : 2772529142 (2.582 gibibytes)
Total run time        : 17.3441710472 seconds

Ok, we just saved over 2Go :-)

book keeping

In [24]:
%%writefile 14-07-07-transferring-lots-of-files-to-a-remote-server-saving-space.meta
.. title: 14-07-07 transferring (lots of) files to a remote server + saving space
.. slug: 14-07-07-transferring-lots-of-files-to-a-remote-server-s
.. date: 2014-07-07 10:31:28 UTC+02:00
.. tags: int, hardlink, rsync
.. link: 
.. description: 
.. type: text
Overwriting 14-07-07-transferring-lots-of-files-to-a-remote-server-saving-space.meta
In [25]:
!nikola build
Scanning posts........done!
.  render_posts:cache/posts/14-07-07-transferring-lots-of-files-to-a-remote-server-saving-space.html
.  render_sources:output/posts/14-07-07-transferring-lots-of-files-to-a-remote-server-s.ipynb
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.  render_tags:output/categories/anr-balav1.xml
.  render_tags:output/categories/demo.xml
.  render_tags:output/categories/find.xml
.  render_tags:output/categories/nikola.xml
.  render_tags:output/categories/year09.xml
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.  render_tags:output/categories/year07.xml
.  render_tags:output/categories/blog.xml
.  render_tags:output/categories/craac.xml
.  render_tags:output/categories/cnrs.xml
.  render_tags:output/categories/python.xml
.  render_tags:output/categories/neuralensemble.xml
.  render_tags:output/categories/hardlink.xml
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In [23]:
!nikola deploy
Scanning posts........done!
[2014-07-07T09:57:21Z] INFO: deploy: ==> git add .
[2014-07-07T09:57:21Z] INFO: deploy: ==> git commit --dry-run -am 'Test' |grep -q -v 'nothing to commit' && git commit -am 'Update'; git push
[master 6f3001e] Update
 2 files changed, 126 insertions(+), 9 deletions(-)
Counting objects: 5, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (5/5), done.
Writing objects: 100% (5/5), 1.16 KiB | 0 bytes/s, done.
Total 5 (delta 4), reused 0 (delta 0)
To https://meduz@bitbucket.org/meduz/invibe.git
   154ad20..6f3001e  master -> master
[2014-07-07T09:57:24Z] INFO: deploy: ==> ./deploy.sh
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Removing old file `categories/talks.html'
Transferring file `categories/talks.html'
Removing old file `categories/tropique.html'
Transferring file `categories/tropique.html'
Removing old file `categories/ubuntu.html'
Transferring file `categories/ubuntu.html'
Removing old file `categories/using.html'
Transferring file `categories/using.html'
Removing old file `categories/vim.html'
Transferring file `categories/vim.html'
Removing old file `categories/year07.html'
Transferring file `categories/year07.html'
Removing old file `categories/year08.html'
Transferring file `categories/year08.html'
Removing old file `categories/year09.html'
Transferring file `categories/year09.html'
Removing old file `categories/year10.html'
Transferring file `categories/year10.html'
Removing old file `categories/year12.html'
Transferring file `categories/year12.html'
Mirroring directory `galleries'
Mirroring directory `galleries/demo'
Mirroring directory `listings'
Mirroring directory `posts'
Removing old file `posts/14-06-25-grille-hexagonale.html'
Transferring file `posts/14-06-25-grille-hexagonale.html'
Transferring file `posts/14-07-07-transferring-lots-of-files-to-a-remote-server-s.html'
Transferring file `posts/14-07-07-transferring-lots-of-files-to-a-remote-server-s.ipynb'
Mirroring directory `stories'
[2014-07-07T09:57:42Z] INFO: deploy: Successful deployment

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