Data management and transfer

This section covers best practice and tools for data management on Tursa as well as information on the storgae available on the system.

Information

If you have any questions on data management and transfer please do not hesitate to contact the DiRAC service desk at dirac-support@epcc.ed.ac.uk.

Useful resources and links

Harry Mangalam's guide on How to transfer large amounts of data via network. This provides lots of useful advice on transferring data.

Data management

We strongly recommend that you give some thought to how you use the various data storage facilities that are part of the Tursa service. This will not only allow you to use the machine more effectively but also to ensure that your valuable data is protected.

Here are the main points you should consider:

Not all data are created equal, understand your data. Know what data you have. What is your critical data that needs to be copied to a secure location? Which data do you need in a different location to analyse? Which data would it be easier to regenerate rather than transfer? You should create a brief data management plan laying this out as this will allow you to understand which tools to use and when.
Minimise the data you are transferring. Transferring large amounts of data is costly in both researcher time and actual time. Make sure you are only transferring the data you need to transfer.
Minimise the number of files you are transferring. Each individual file has a static overhead in data transfers so it is efficient to bundle multiple files together into a single large archive file for transfer.
Does compression help or hinder? Many tools have the option to use compression (e.g. rsync, tar, zip) and generally encourage you to use them to reduce data volumes. However, in some cases, the time spent compressing the data can take longer than actually transferring the uncompressed data; particularly when transferring data between two locations that both have large data transfer bandwidth available.
Be aware of encryption overheads. When transferring data using scp (and rsync over scp) your data will be encrypted introducing a static overhead per file. This issue can be minimised by reducing the number files to be transferred by creating archives. You can also change the encryption algorithm to one that involves minimal encryption. The fastest performing cipher that is commonly available in SSH at the moment is generally aes128-ctr as most common processors provide a hardware implementation.

Tursa storage

Tursa has two different storage systems available:

Parallel Lustre file system - for working, high-performance storage
Tape storage - for storing large amounts of data that are not currently required for jobs on the system

Parallel Lustre file system

The Tursa storage is provided by a parallel Lustre file system that provides your home directories and working storage. When you log in you will be placed in your home directory.

Warning

The Lustre file system is backed up for disaster recovery purposes only (e.g. loss of the whole file system) so it is not possible to recover individual files if they are deleted by mistake or otherwise lost.

The home directory for each user is located at:

/home/[project code]/[group code]/[username]

where

[project code] is the code for your project (e.g., x01);
[group code] is the code for your project group, if your project has groups, (e.g. x01-a) or the same as the project code, if not;
[username] is your login name.

Each project is allocated a portion of the total storage available, and the project PI will be able to sub-divide this quota among the groups and users within the project. As is standard practice on UNIX and Linux systems, the environment variable $HOME is automatically set to point to your home directory.

Quotas on the Lustre file system

All projects are assigned a quota on the Lustre file systems. The project PI or manager can split this quota up between users or groups of users if they wish.

You can view any Lustre file system quotas that apply to your account by logging into SAFE and navigating to the page for your Tursa login account.

Log into SAFE
Use the "Login accounts" menu and select your Tursa login account
The "Login account details" table lists any user or group quotas that are linked with your account. (If there is no quota shown for a row then you have an unlimited quota for that item, but you may still may be limited by another quota.)

Tip

Quota and usage data on SAFE is updated a few times a day so may not be exactly up to date with the situation on the systems themselves.

You can also examine up to date quotas and usage on the Tursa Lustre file system itself using the lfs quota command. To do this:

To check your user quota, you would use the command:

[dc-user1@tursa-login2 ~]$ lfs quota -hu ${USER} .
Disk quotas for usr dc-user1 (uid 20358):
  Filesystem    used   quota   limit   grace   files   quota   limit   grace
           .  15.52G      0k  97.66T       -  107369       0       0       -
uid 20358 is using default file quota setting

the limit of 0k here indicate that no user quota is set for this user

To check your project quota, you would use the command:

[dc-user1@tursa-login2 ~]$ lfs quota -hp $(id -g) .
Disk quotas for prj 50010 (pid 50010):
      Filesystem    used   quota   limit   grace   files   quota   limit   grace
               .  15.52G      0k    990G       -  107378       0       0       -
pid 50010 is using default file quota setting

the limit of 990G here indicate that you have a project quota of 990 GiB (shared with all users in the project).

Tape storage

The tape storage can be made available to any Tursa user on request and can be used to store data from the Lustre parallel file system.

Managing and transferring data to/from the Tursa tape storage is done via the Miria web interface via an SSH tunnel to the Tursa login nodes.

Important

All data on the tape storage is shared project data rather than data associated with individual user accounts. Any data you move to tape will be visible to all users in the same project as you who have access to the tape storage.

Requesting access to the tape storage

If you want to use the Tursa tape storage, you should contact the DiRAC Service Desk with the username and project ID you want to use to access the storage.

Data locations

In order to move data to the tape storage it must exist in a specific directory on the Tursa Lustre file system. You will need to move or copy the data to this location before it can be moved to tape and when you restore data from tape it will be placed in this location.

There is one directory per project on Tursa. The directory has the path:

/mnt/lustre/tursafs1/archive/[project code]

So, for example, the directory for project dp001 would be:

/mnt/lustre/tursafs1/archive/dp001

Setup the SSH tunnel for Miria

Once your tape storage access has been setup and you have moved data to the archive directory, you will need to connect to the Miria web interface in a web browser on your local system by setting up an SSH tunnel to the Tursa login nodes.

You do this by logging into Tursa in the usual way (with your SSH key and password) and adding the -L 9080:10.144.20.95:443 option to the ssh command.

For example, if your username is dc-user1, you would setup the tunnel by logging into Tursa with (assuming your SSH key is in the default location):

ssh -L 9080:10.144.20.95:443 dc-user1@tursa.dirac.ed.ac.uk

Enter your SSH key passphrase and password in the usual way.

Note

You will need to setup the SSH tunnel each time you want to access the Miria interface.

Access the Miria interface

Once you have setup the SSH tunnel, you should be able to access the Miria interface in a web browser on your local system. Open a new tab and enter the URL:

http://localhost:9080/webapp-en/login

You should see an interface asking you for a username and password. Use the username and password that you use to log into Tursa to log into the tape storage interface.

Transfer data from Tursa Lustre to tape

You use the "Easy Move" option from the left-hand menu to transfer data.

Click on "Easy Move"
Click on the "Find a source" menu and select the disk with your project ID (e.g. "dp001")
Click on the "Find a target" menu and select the archive with your project ID (e.g. "dp001")
Use the file explorer to select the files/directories you wish to move to tape
Click the "Add" button
Scroll to the bottom of the page and select "Validate basket" and confirm you wish to proceed

Your transfer request will be added to the queue. You can check on progress by selecting the "Activity" option in the left hand menu.

Restore data from tape to Tursa Lustre

You use the "Easy Move" option from the left-hand menu to transfer data.

Click on "Easy Move"
Select the "Repository" icon next to the "Find a source" menu
Click on the "Find a source" menu and select the archive with your project ID (e.g. "dp001")
Select the "Platform" icon next to the "Find a source" menu
Click on the "Find a target" menu and select the disk with your project ID (e.g. "dp001")
Use the source file explorer to select the files/directories you wish to restore
Use the target file explorer to select the location oon disk to restore the data
Click the "Add" button
Scroll to the bottom of the page and select "Validate basket" and confirm you wish to proceed

Your transfer request will be added to the queue. You can check on progress by selecting the "Activity" option in the left hand menu.

Bug

If you restore a file rather than a directory, the Miria tool will give the file the name NULL once it is restored, you should use the mv command to rename the file to the correct name once it has been restored.

How you share data with other Tursa users depends on whether or not they belong to the same project as you. Each project has two shared folders that can be used for sharing data.

Each project has an inner shared folder.

/home/[project code]/[project code]/shared

This folder has read/write permissions for all project members. You can place any data you wish to share with other project members in this directory. For example, if your project code is x01 the inner shared folder would be located at /home/x01/x01/shared.

Each project also has an outer shared folder.:

/home/[project code]/shared

It is writable by all project members and readable by any user on the system. You can place any data you wish to share with other Tursa users who are not members of your project in this directory. For example, if your project code is x01 the outer shared folder would be located at /home/x01/shared.

Permissions

You should check the permissions of any files that you place in the shared area, especially if those files were created in your own Tursa account Files of the latter type are likely to be readable by you only.

The chmod command below shows how to make sure that a file placed in the outer shared folder is also readable by all Tursa users.

chmod a+r /home/x01/shared/your-shared-file.txt

Similarly, for the inner shared folder, chmod can be called such that read permission is granted to all users within the x01 project.

chmod g+r /home/x01/x01/shared/your-shared-file.txt

If you're sharing a set of files stored within a folder hierarchy the chmod is slightly more complicated.

chmod -R a+Xr /home/x01/shared/my-shared-folder
chmod -R g+Xr /home/x01/x01/shared/my-shared-folder

The -R option ensures that the read permission is enabled recursively and the +X guarantees that the user(s) you're sharing the folder with can access the subdirectories below my-shared-folder.

Archiving and data transfer

Data transfer speed may be limited by many different factors so the best data transfer mechanism to use depends on the type of data being transferred and where the data is going.

Disk speed - The Tursa file system is highly parallel, consisting of a very large number of high performance disk drives. This allows it to support a very high data bandwidth. Unless the remote system has a similar parallel file-system you may find your transfer speed limited by disk performance.
Meta-data performance - Meta-data operations such as opening and closing files or listing the owner or size of a file are much less parallel than read/write operations. If your data consists of a very large number of small files you may find your transfer speed is limited by meta-data operations. Meta-data operations performed by other users of the system will interact strongly with those you perform so reducing the number of such operations you use, may reduce variability in your IO timings.
Network speed - Data transfer performance can be limited by network speed. More importantly it is limited by the slowest section of the network between source and destination.
Firewall speed - Most modern networks are protected by some form of firewall that filters out malicious traffic. This filtering has some overhead and can result in a reduction in data transfer performance. The needs of a general purpose network that hosts email/web-servers and desktop machines are quite different from a research network that needs to support high volume data transfers. If you are trying to transfer data to or from a host on a general purpose network you may find the firewall for that network will limit the transfer rate you can achieve.

The method you use to transfer data to/from Tursa will depend on how much you want to transfer and where to. The methods we cover in this guide are:

scp/sftp/rsync - These are the simplest methods of transferring data and can be used up to moderate amounts of data. If you are transferring data to your workstation/laptop then this is the method you will use.

Before discussing specific data transfer methods, we cover archiving which is an essential process for transferring data efficiently.

Archiving

If you have related data that consists of a large number of small files it is strongly recommended to pack the files into a larger "archive" file for ease of transfer and manipulation. A single large file makes more efficient use of the file system and is easier to move and copy and transfer because significantly fewer meta-data operations are required. Archive files can be created using tools like tar and zip.

tar

The tar command packs files into a "tape archive" format. The command has general form:

tar [options] [file(s)]

Common options include:

-c create a new archive
-v verbosely list files processed
-W verify the archive after writing
-l confirm all file hard links are included in the archive
-f use an archive file (for historical reasons, tar writes its output to stdout by default rather than a file).

Putting these together:

tar -cvWlf mydata.tar mydata

will create and verify an archive.

To extract files from a tar file, the option -x is used. For example:

tar -xf mydata.tar

will recover the contents of mydata.tar to the current working directory.

To verify an existing tar file against a set of data, the -d (diff) option can be used. By default, no output will be given if a verification succeeds and an example of a failed verification follows:

$> tar -df mydata.tar mydata/*
mydata/damaged_file: Mod time differs
mydata/damaged_file: Size differs

Note

tar files do not store checksums with their data, requiring the original data to be present during verification.

Tip

Further information on using tar can be found in the tar manual (accessed via man tar or at man tar).

zip

The zip file format is widely used for archiving files and is supported by most major operating systems. The utility to create zip files can be run from the command line as:

zip [options] mydata.zip [file(s)]

Common options are:

-r used to zip up a directory
-# where "#" represents a digit ranging from 0 to 9 to specify compression level, 0 being the least and 9 the most. Default compression is -6 but we recommend using -0 to speed up the archiving process.

Together:

zip -0r mydata.zip mydata

will create an archive.

Note

Unlike tar, zip files do not preserve hard links. File data will be copied on archive creation, e.g. an uncompressed zip archive of a 100MB file and a hard link to that file will be approximately 200MB in size. This makes zip an unsuitable format if you wish to precisely reproduce the file system layout.

The corresponding unzip command is used to extract data from the archive. The simplest use case is:

unzip mydata.zip

which recovers the contents of the archive to the current working directory.

Files in a zip archive are stored with a CRC checksum to help detect data loss. unzip provides options for verifying this checksum against the stored files. The relevant flag is -t and is used as follows:

$> unzip -t mydata.zip
Archive:  mydata.zip
    testing: mydata/                 OK
    testing: mydata/file             OK
No errors detected in compressed data of mydata.zip.

Tip

Further information on using zip can be found in the zip manual (accessed via man zip or at man zip).

Data transfer via SSH

The easiest way of transferring data to/from Tursa is to use one of the standard programs based on the SSH protocol such as scp, sftp or rsync. These all use the same underlying mechanism (SSH) as you normally use to log-in to Tursa. So, once the the command has been executed via the command line, you will be prompted for your password for the specified account on the remote machine (Tursa in this case).

To avoid having to type in your password multiple times you can set up a SSH key pair and use an SSH agent as documented in the User Guide at connecting.

SSH data transfer performance considerations

The SSH protocol encrypts all traffic it sends. This means that file transfer using SSH consumes a relatively large amount of CPU time at both ends of the transfer (for encryption and decryption). The Tursa login nodes have fairly fast processors that can sustain about 100 MB/s transfer. The encryption algorithm used is negotiated between the SSH client and the SSH server. There are command line flags that allow you to specify a preference for which encryption algorithm should be used. You may be able to improve transfer speeds by requesting a different algorithm than the default. The aes128-ctr or aes256-ctr algorithms are well supported and fast as they are implemented in hardware. These are not usually the default choice when using scp so you will need to manually specify them.

A single SSH based transfer will usually not be able to saturate the available network bandwidth or the available disk bandwidth so you may see an overall improvement by running several data transfer operations in parallel. To reduce metadata interactions it is a good idea to overlap transfers of files from different directories.

In addition, you should consider the following when transferring data:

Only transfer those files that are required. Consider which data you really need to keep.
Combine lots of small files into a single tar archive, to reduce the overheads associated in initiating many separate data transfers (over SSH, each file counts as an individual transfer).
Compress data before transferring it, e.g. using gzip.

scp

The scp command creates a copy of a file, or if given the -r flag, a directory either from a local machine onto a remote machine or from a remote machine onto a local machine.

For example, to transfer files to Tursa from a local machine:

scp [options] source user@tursa.dirac.ed.ac.uk:[destination]

(Remember to replace user with your Tursa username in the example above.)

In the above example, the [destination] is optional, as when left out scp will copy the source into your home directory. Also, the source should be the absolute path of the file/directory being copied or the command should be executed in the directory containing the source file/directory.

If you want to request a different encryption algorithm add the -c [algorithm-name] flag to the scp options. For example, to use the (usually faster) arcfour encryption algorithm you would use:

scp [options] -c aes128-ctr source user@tursa.dirac.ed.ac.uk:[destination]

(Remember to replace user with your Tursa username in the example above.)

rsync

The rsync command can also transfer data between hosts using a ssh connection. It creates a copy of a file or, if given the -r flag, a directory at the given destination, similar to scp above.

Given the -a option rsync can also make exact copies (including permissions), this is referred to as mirroring. In this case the rsync command is executed with ssh to create the copy on a remote machine.

To transfer files to Tursa using rsync with ssh the command has the form:

rsync [options] -e ssh source user@tursa.dirac.ed.ac.uk:[destination]

(Remember to replace user with your Tursa username in the example above.)

In the above example, the [destination] is optional, as when left out rsync will copy the source into your home directory. Also the source should be the absolute path of the file/directory being copied or the command should be executed in the directory containing the source file/directory.

Additional flags can be specified for the underlying ssh command by using a quoted string as the argument of the -e flag. e.g.

rsync [options] -e "ssh -c arcfour" source user@tursa.dirac.ed.ac.uk:[destination]

(Remember to replace user with your Tursa username in the example above.)

Tip

Further information on using rsync can be found in the rsync manual (accessed via man rsync or at man rsync).

SSH data transfer example: laptop/workstation to Tursa

Here we have a short example demonstrating transfer of data directly from a laptop/workstation to Tursa.

Note

This guide assumes you are using a command line interface to transfer data. This means the terminal on Linux or macOS, MobaXterm local terminal on Windows or Powershell.

Before we can transfer of data to Tursa we need to make sure we have an SSH key setup to access Tursa from the system we are transferring data from. If you are using the same system that you use to log into Tursa then you should be all set. If you want to use a different system you will need to generate a new SSH key there (or use SSH key forwarding) to allow you to connect to Tursa.

Tip

Remember that you will need to use both a key and your password to transfer data to Tursa.

Once we know our keys are setup correctly, we are now ready to transfer data directly between the two machines. We begin by combining our important research data in to a single archive file using the following command:

tar -czf all_my_files.tar.gz file1.txt file2.txt file3.txt

We then initiate the data transfer from our system to Tursa, here using rsync to allow the transfer to be recommenced without needing to start again, in the event of a loss of connection or other failure. For example, using the SSH key in the file ~/.ssh/id_RSA_A2 on our local system:

rsync -Pv -e"ssh -c aes128-gcm@openssh.com -i $HOME/.ssh/id_RSA_A2" ./all_my_files.tar.gz otbz19@tursa.dirac.ed.ac.uk:/home/z19/z19/otbz19/

Note the use of the -P flag to allow partial transfer -- the same command could be used to restart the transfer after a loss of connection. The -e flag allows specification of the ssh command - we have used this to add the location of the identity file. The -c option specifies the cipher to be used as aes128-gcm which has been found to increase performance. Unfortunately the ~ shortcut is not correctly expanded, so we have specified the full path. We move our research archive to our project work directory on Tursa.

Note

Remember to replace otbz19 with your username on Tursa.

If we were unconcerned about being able to restart an interrupted transfer, we could instead use the scp command,

scp -c aes128-gcm@openssh.com -i ~/.ssh/id_RSA_A2 all_my_files.tar.gz otbz19@transfer.dyn.tursa.ac.uk:/home/z19/z19/otbz19/

but rsync is recommended for larger transfers.

Data management and transfer

Useful resources and links

Data management

Tursa storage

Parallel Lustre file system

Quotas on the Lustre file system

Tape storage

Requesting access to the tape storage

Data locations

Setup the SSH tunnel for Miria

Access the Miria interface

Transfer data from Tursa Lustre to tape

Restore data from tape to Tursa Lustre

Sharing data with other Tursa users

Sharing data with Tursa users in your project

Sharing data with all Tursa users

Permissions

Archiving and data transfer

Archiving

tar

zip

Data transfer via SSH

SSH data transfer performance considerations

scp

rsync

SSH data transfer example: laptop/workstation to Tursa