Transfer Data

You can transfer data between your computer and our storage systems in several ways. You can mount Bucket as a shared folder; you can use ssh to copy data from the terminal; use Datashare to transfer data to other users on deigo; and you can use Rsync for fast, reliable transfer lf large data sets.

Access Bucket as a shared remote folder from your desktop
Use ssh and sftp to copy data on the command line
Quickly transfer data to other users with Datashare

Fast, reliable transfer using Rsync
Mount a remote directory using sshfs

Using remote folders

You can access and move data from your desktop by using bucket as a remote shared folder on your desktop. The details differ by operating system, but you mount it as a shared drive using the Samba protocol.

Please check the IT help pages for more information on how to mount remote shared folders on your operating system:

Windows
Mac OSX
Linux
 

Copy Files Using scp

The "scp" command, for "Secure CoPy", is the main way to copy files to and from Deigo. If you want to copy a file myfile.txt to Deigo, you would open a terminal (or a MobaXTerm window) on your own computer and do:

$ scp myfile.txt username@deigo.oist.jp:    

This command works like the regular cp command. The big difference is that we can tell it to copy to remote machines. The colon at end of the address tells scp that it's a remote machine, not a file name. If you forget the colon you will copy myfile.txt to a new file with name "username@deigo.oist.jp" which is not quite what you wanted.

If you set up aliases like described in "Connect to the Clusters" you can use the alias here too:

$ scp myfile.txt deigo:

The default remote target directory is your home. You can add a path after the colon (and note that tab completion works remotely under Linux):

$ scp myfile.txt deigo:/bucket/MyUnit/

Everything before the colon in deigo: specifies the remote computer. Everything after the colon is the directory or file on the remote machine. You can use shell wildcards to specify multiple files, and you can copy from the remote machine to your local machine as well:

$ scp deigo:some_directory/* .

This would copy all the files in directory some_directory in your home on Deigo to the current directory on your local computer. If you add the -r option, you can copy recursively, that is, copy all files in all subdirectories. The below command will copy somedir and all its data:

$ scp -r deigo:somedir .

Browse interactively using sftp

sftp (do not confuse it with ftps, another protocol) is a simple protocol to browse and copy files interactively over ssh. You can use it on the command line:

$ sftp <your oist-id>@deigo.oist.jp

The most common commands are:

Use the "help" command to see a list of commands.

The command line client works, but if you run Linux you can also use sftp through your file browser.

On Linux you can use the Nautilus file browser (default on most desktops) to connect and browse, copy and move files via sftp. Select "connect to server" or just press ctrl-l. Then enter sftp://deigo.oist.jp, enter your OIST ID and password, and you will be able to browse and handle your remote files.

By default you can just see your home directory. To get to, say, Bucket, you need to edit the location. Press ctrl-l. Your location will look like "sftp://deigo.oist.jp/". Add "bucket" to the end, like "sftp://deigo.oist.jp/bucket", to browse /bucket instead. You can add a bookmark to reconnect easily if you like.

Windows and OSX does not support sftp by default, but there are a number of sftp clients for free download that will let you access Deigo in a file browser in much the same way.

Datashare

The Deigo login nodes have a directory (storage system) called Datashare, mounted as /datashare. It's meant for quick, temporary sharing of data to workshop participants, or for members of different units that need to transfer data to each other.

If you copy data to Datashare it will automatically become readable to anybody. Any data there will also be deleted after about one day if you forget to delete it yourself.

If you want to transfer a file to somebody else, follow these steps:

1. From a login node, copy the data to /datashare.
2. Ask the recipients to log in and copy the data from /datashare to their own bucket or home.
3. Once they've done this, delete the data.

Note: All data here is publicly readable. Don't use Datashare to transfer restricted or confidential data!

Advanced file access

Rsync

rsync is an advanced program for synchronizing directories and copying large number of files locally or over a network using ssh.

Before the copy, rsync compares the source and destination. Only the files that have changed, and (normally) only the changes to each file are actually transferred.

• If you use rsync to keep two directories in sync between your local and remote machines, only the changes since the last sync will be transferred. This greatly reduces the amount of time you need to synchronize them.

• If rsync is interrupted - because you lost the connection, or because you had to leave and turn off the computer for instance - it will pick up again where it left off instead of starting over. This makes rsync a very dependable way to copy data over slow or unreliable network connections.

It is quite a complicated program with many options, so we refer you to the main documentation. Here are a couple of common examples:

$ rsync -av --no-group --no-perms mydir/ deigo:target-dir/

This sends the content of "mydir" into "target-dir". Note the "/" at the end; rsync takes this to mean you want to copy the contents inside. You end up with "target-dir/".

The flag "-a" is short for "archive". It will copy all file attributes as well, such as creation and modification dates, links, permissions, ownership and so on. "-v" means to be verbose and print out what rsync is doing. "--no-group" and "--no-perms" makes sure we don't copy ownership and permissions, as they are different on the remote system.

$ rsync -av --no-group --no-perms mydir deigo:target-dir/

This sends "mydir" itself and its contents into "target-dir". Without a "/" at the end, rsync will copy the directory itself, so you get "target-dir/mydir/"

$ rsync -av --no-group --no-perms --partial mybigfiles/ deigo:target-dir/

For very large files (gigabytes or more), resending the entire file if it got interrupted would waste a lot of time. The "--partial" option tells rsync not to delete partial files, but to pick up where it left off.
 

$ rsync -av --no-group --no-perms --del --exclude=*bk deigo:datadir localdir 

Synchronize everything in "datadir" on Deigo with "localdir" on the local machine. Delete any files in "localdir" that are not in "datadir" (that is, if they were deleted in "datadir" they'll be deleted locally as well). Exclude any file that ends in "bk".

sshfs

"sshfs" is a "pseudo-filesystem" that you can use on Linux and OSX. It will connect a remote and a local directory, much like mounting a remote filesystem. In the background it uses sftp to actually transfer the data, but it lets you treat your remote directory as a part of your regular filesystem.

First you need to get sshfs. On Linux it is available from your distributions package manager. On OSX you may need to install it through one of the open source distribution systems. Once you installed it, the format for starting it is:

$ sshfs [options] deigo:datadir localdir/

This will mount "datadir" on Deigo onto "localdir" on your local computer. "localdir" needs to be an empty directory. Ideally you would make a specific subdirectory, one for each remote, in a "mount" directory:

$ mkdir -p mount/deigo

If there's no activity, ssh will normally close the connection after some time. That is very inconvenient when you use it as a file system. Also, sshfs will by default not try to reconnect if it loses connection. Finally, your user ID is different on the local and remote machine, and we want to make sure any files are presented with the right ownership.

You will want to use three options for sshfs: "reconnect" to make it reconnect; "idmap=user" to resolve user identity differences; and "ServerAliveInterval=30" to keep the connection alive and to detect if it disconnects, by pinging the server every 30 seconds.

Let's say I want to mount my /bucket/UnitU/mydata/ directory on Deigo, and mount it locally on mount/deigo. I would do this as:

$ sshfs -o reconnect,idmap=user,ServerAliveInterval=30 deigo:/bucket/UnitU/mydata mount/deigo

That command is a mouthful, so you may want to put this in a small shell script.

You can unmount it again with "fusermount":

$ fusermount -u mount/deigo

Issues

sshfs is very convenient: you can mount any directory you can reash with ssh, in a safe, encrypted manner, and treat as a local directory without using a VPN or any other extras. But it has a few drawbacks.

The main issue is that it does not deal well with disconnections. Any access to the directory while it's disconnected will hang, waiting for a remote reply. You can try it for yourself. Mount a directory on deigo as above, disable wifi, then try listing the directory:

$ ls mount/deigo

After a few seconds, the command will suddenly hang, and can't be stopped. In fact, any software that directly or indirectly tries to access that directory will now freeze.

Since we added the "ServerAliveInterval" option above, sshfs will eventually give up trying and let the applications run again, but it will still take up to a minute or so. For this reason, sshfs is really better suited for your workstation than for a laptop that often loses the connection as you move about.

To forcibly stop sshfs, you can force unmount the file system (you may need to do it as root):

$ sudo umount --force mount/deigo

You may need to repeat the command a few times before it really takes effect.

You can also look for the actual ssh process and kill it:

$ ps ax|grep "ssh.*sftp"
26854 pts/23 S  0:00 ssh -x -a [...] -oServerAliveInterval=30 [...] deigo -s sftp
$ kill -9 26854

Just be careful that you don't kill the wrong ssh process by mistake.

Finally, if sshfs has disconnected, the OS may still mistakenly see the remote as mounted, so you can't remount. Then you can do a "lazy" unmount (where it doesn't wait for a reponse from the server) to make the OS release the mount point:

$ fusermount -uz mount/deigo