Transfers from ARCHER2

This article explains how to transfer data between ARCHER2 and JASMIN. It covers:

  • The choice of available tools / routes
  • Example of how to use the currently-recommended method

Choice of available Tools/Routes

See  JASMIN external connections and Data Transfer Tools  for general details.

Users transferring data between ARCHER2 and JASMIN are often transferring relatively large sets of data, so it is important to choose the most appropriate route, method and tools to ensure you get the most efficient and reliable transfer experience. This can vary depending on system and network conditions.

If you want to try  all the options available, you will need:

  • high-performance data transfer access on JASMIN
  • a login account at ARCHER2
  • (only for certificate-based GridFTP) to have registered the subject of your JASMIN-issued short-term credential with ARCHER support.

Check the examples in the linked documentation articles and ensure that you use them between the hosts used in the examples. Not all services connect over all routes to/from all hosts!

NOTE:

  • Enquiries about access to or use of ARCHER2 should be directed to ARCHER2 support (support@archer2.ac.uk)
  • Enquiries about access to or use of JASMIN should be directed to JASMIN support (use beacon, below-right or support@jasmin.ac.uk)

Table 1, below, shows recommended combinations of hosts & tools for transfers between RDF and JASMIN.

Note that (until 

scp/rsync/sftp
Simple transfer using easy method to general purpose xfer nodes. Convenient.
source dest notes
login.archer2.ac.uk xfer1.jasmin.ac.uk over 10G JANET, but to virtual machine at JASMIN end
login.archer2.ac.uk xfer2.jasmin.ac.uk same
GridFTP over SSH  

2nd choice method

GridFTP performance with convenience of SSH.  Requires persistent ssh agent on local machine where you have your JASMIN key.
login.archer2.ac.uk hpxfer1.jasmin.ac.uk over 10G JANET
login.archer2.ac.uk hpxfer2.jasmin.ac.uk over 10G JANET
hpxfer2 is configured for longer distances but can be useful if hpxfer1 is busy
GridFTP using certificate auth
(now working again!)

1st choice method

Fully-featured GridFTP. Suitable for person-not-present transfers & long-running ARCHER2 workflows.
login.archer2.ac.uk gridftp1.jasmin.ac.uk over 10G JANET.
Dedicated GridFTP server.
No need for persistent SSH agent at ARCHER2 end

Table 1: comparison of current methods and routes for transferring data between RDF and JASMIN.

1st choice method: example

The now-recommended method for transfers between ARCHER2 and JASMIN is using globus-url-copy with the concurrency option, as described below, but using certificate-based authentication rather than SSH. This will work for person-not-present transfers, so is suitable for long-running processes on ARCHER2 which need to spawn a transfer to JASMIN at intervals up to a month from initiation.

1. Load your SSH key for ARCHER2 on your local machine, then log in to ARCHER2.

This method does not require you to use your JASMIN SSH key. It involves:

  • obtaining tools to communicate with JASMIN's short-lived credentials service
  • using the service to obtain a credential (it should last for 30 days, but a new one can be obtained at any time)
  • using the credential to initiate a transfer (this what you would need to repeat for each transfer)

A fuller explanation of the process is given in this document:

Once you have done these steps, you should be able to initiate new a transfer as follows:

$ ./onlineca-get-cert-wget.sh -U https://slcs.jasmin.ac.uk/certificate/ -l USERNAME -o ./cred.jasmin
$ chmod 600 cred.jasmin

Note that the path ./ is used for the script onlineca-get-cert-wget.sh, but you should use the path to wherever you saved it. Alternatively, if you make yourself a bin directory and add that to your PATH, then you don't need to specify the path.

2. Load the gct module (to make the current globus-url-copy command available in your path on ARCHER2)

$ module load gct
$ which globus-url-copy
/work/y07/shared/gct/v6.2.20201212/bin/globus-url-copy

3. Transfer a single file to your home directory on JASMIN (limited space, but to check things work)

$ globus-url-copy -vb <file> -cred cred.jasmin src/data gsiftp://gridftp1.jasmin.ac.uk/~/ <file>

Note that we specify the credentials file cred.jasmin and use the protocol gsiftp:// with no need to specify the username in the connection string (we've used the path /~/ to signify "my home directory" as the destination path). Note also that the hostname in this case, gridftp1.jasmin.ac.uk is a host that you can ONLY connect to directly using gsiftp: it does not permit SSH connections.

In all other aspects, the transfer is the same as for the SSH method (see "2nd choice method" below), so the commands below are very similar: we're just using the gsiftp method instead of sshftp (both are ways of using the gridftp transfer protocol)

4. Recursively transfer a directory of files, using the concurrency option for multiple parallel transfers

$ globus-url-copy -vb -cd -r -cc 4 -cred cred.jasmin src/data/ gsiftp://gridftp1.jasmin.ac.uk/path/dest/data/

NOTE: The -cc option initiates the parallel transfer of several files at a time, which achieves good overall transfer rates for recursive directory transfers. This is different from using the -p N -fast options which use parallel network streams to parallelism the transfer of each file.

The  -p N -fast options (for parallel-streamed transfers) are not currently working to all JASMIN storage locations, so use at your own risk until further notice. The transfer should work OK out of ARCHER2 (check by writing a single file to /dev/null at the JASMIN end) but currently will not work properly when writing to the SOF storage (/gws/nopw/j04 or /gws/nopw/j07, or /work/xfc/vol[1-3], though other paths should work OK). This is a known issue at the JASMIN end, thought to be related to network configuration, which is still under investigation. Single-stream transfers (omitting the -p N -fast options) should work fine.

Here, the options used are (see man globus-url-copy for full details):

-vb | -verbose-perf 
       During the transfer, display the number of bytes transferred
       and the transfer rate per second.  Show urls being transferred
-concurrency | -cc
      Number of concurrent ftp connections to use for multiple transfers.
-cd | -create-dest
       Create destination directory if needed
-r | -recurse
       Copy files in subdirectories

Experiment with different concurrency options (4 is a good start, more than 16 would start to "hog" resources so please consider

5. Use the sync option to synchronise 2 directories between source and target file systems:

$ globus-url-copy -vb -cd -r -cc 4 -sync -cred cred.jasmin src/data/ gsiftp://gridftp11.jasmin.ac.uk/path/dest/data/

where  src/data/ and /path/dest/data/ are source and destination paths, respectively (include trailing slash).

Options are as before but with:

-sync
       Only transfer files where the destination does not exist or differs
       from the source.  -sync-level controls how to determine if files
       differ

Note that the default sync level is 2, see level descriptions below, which only compares time stamps. If you want to include a file integrity check using checksums, you need to use -sync-level 3 but there may be a performance cost.

-sync-level 
	Choose criteria for determining if files differ when performing a
       sync transfer.  Level 0 will only transfer if the destination does
       not exist.  Level 1 will transfer if the size of the destination
       does not match the size of the source.  Level 2 will transfer if
       the timestamp of the destination is older than the timestamp of the
       source, or the sizes do not match.  Level 3 will perform a checksum of
       the source and destination and transfer if the checksums do not match,
       or the sizes do not match.  The default sync level is 2.

So a full sync including comparison of checksums would be:

$ globus-url-copy -vb -cd -r -cc 4 -sync -sync-level 3 -cred cred.jasmin src/data/ gsiftp://gridftp1.jasmin.ac.uk/path/dest/data/

2nd choice method: example

The next-best method for transfers between ARCHER2 and JASMIN is using globus-url-copy with SSH authentication, as described below:

1. Load your SSH keys for both JASMIN and ARCHER2 on your local machine, then log in to ARCHER2.

You will need to have loaded into your SSH agent:

  • The SSH key associated with your JASMIN account
  • The SSH key associated with your ARCHER2 account, if you have one (it is recommended to use a different one than for JASMIN, if so)

You also need to ensure that you connect with the -A option for agent forwarding, to enable the JASMIN key to be available for the onward authentication with the JASMIN server.

Note that you do not (and should not) copy your JASMIN private key to ARCHER2. It should stay on your local machine. This does mean that you need an ssh-agent running on your local machine, so this method may not work for long-running continuous processes that need to spawn transfers.

$ ssh-add <jasmin ssh key> #(path to your JASMIN ssh key file on your local machine)
$ ssh-add <archer2 ssh key> #(path to your ARCHER2 ssh key if you have one, on on your local machine)
$ ssh-add -l # check both keys are loaded (are both key signatures listed in the output?)
$ ssh -A <archer2-username>@login.archer2.ac.uk
(you are prompted for your password by the ARCHER2 system, whether or not you use an SSH key with your ARCHER2 account)

2. Load the gct module (to make the current globus-url-copy command available in the path)

$ module load gct
$ which globus-url-copy
/work/y07/shared/gct/v6.2.20201212/bin/globus-url-copy

3. Transfer a single file to your home directory on JASMIN (limited space, but to check things work)

$ globus-url-copy -vb <file> sshftp://<jasmin-username>@hpxfer1.jasmin.ac.uk/~/<file>

Obviously, replace <file> with the path to the file you want to transfer.

From here on, the commands are the same as described above in the "1st choice method" but simply replace

-cred cred.jasmin gsiftp://gridftp1.jasmin.ac.uk

with

sshftp://<jasmin-username>@hpxfer1.jasmin.ac.uk