Data Transfer Tools: Using the Globus Command-Line Interface
This article describes:
- how to transfer data using the Globus Command Line Interface. It covers:
- how an end-user can set up their host (laptop, desktop or home directory on their departmental server) with the Globus Command-Line Interface (CLI)
- examples of common tasks using the CLI
It is not necessary to use the Globus CLI on a JASMIN server: it is a tool that you can use anywhere (for example your own desktop/laptop) to interact with the Globus service, to orchestrate a transfer between 2 endpoints. The CLI is not centrally installed on JASMIN, and does not need to be in the same place as either of the 2 endpoints involved in the transfer. The fact that one of those endpoints is the JASMIN Globus Endpoint does not mean that you need to be on JASMIN to orchestrate the transfer: you could use the CLI on your own laptop/desktop, even if the 2 endpoints were 2 institutional Globus endpoints on opposite sides of the world. You could of course decide to install the CLI in your home directory on JASMIN if that were useful as part of your processing/data transfer workflow.
- Linux environment with normal user privileges, or
- Mac environment with ability to install applications, or
- Windows environment with ability to install applications
- Python environment for that platform, with ability to create virtual environments (to enable installation of additional packages)
- For use of the JASMIN Globus endpoint:
- An active JASMIN user account, with “jasmin-login” and “hpxfer” privileges.
- You may also wish to set up your own Globus endpoint using Globus Connect Personal, though this is not needed for these examples.
Note on access requirements
(only relevant to examples accessing the JASMIN endpoint, but needed if you want to transfer data to/from data using Globus)
Access to the Globus endpoint provided by JASMIN (called the "JASMIN Globus endpoint (jasmin credentials") is controlled by the JASMIN “hpxfer” access role: this is the same role which we use to control access to the servers hpxfer.jasmin.ac.uk. The process of registering asks for a specific IP address. However, if you are just using Globus (rather than logging in via SSH to hpxfer.jasmin.ac.uk), this address is not required, because the IP addresses of the Globus servers are already registered. In this case, a dummy value should be specified: please use that of host
xfer1.jasmin.ac.uk whose IP address is
18.104.22.168. This will be accepted by the registration process.
Please note that if you subsequently need to access
hpxfer[1,2].jasmin.ac.uk for SSH-based transfers (but on these higher-performance machines), you may still need to contact the helpdesk to supply a specific IP address of the source host at your institution. However, you can still access these 2 machines from within JASMIN (via the login nodes) to pull data from external hosts: you only need to supply the IP address if you need to initiate a direct SSH connection from a host at your institution to one of these 2 machines.
- Get a Globus ID if you haven’t already got one
- Set up the Globus CLI on your (end-user) machine
Get a Globus ID
Set up the Globus CLI on your machine
Make a Python virtual environment and activate it:
$ python3 -m venv ./venv $ source ./venv/bin/activate
Download the Globus CLI and install it into the virtual environment (
$ pip install globus-cli
globus login command. The first time you run this, you will be prompted to authorise the Globus CLI to carry out operations on behalf of your Globus ID. The URL will open in your default browser, where you should authenticate with your Globus ID credentials. If you prefer, you can copy/paste the URL from the command-line to a browser of your choice. Either way, you then need to click "Allow" in the browser window, then copy/paste the resulting "Native App Authorization Code" back to the terminal window where you issued the
globus login command:
$ globus login --no-local-server Please authenticate with Globus here: ------------------------------------ https://auth.globus.org/v2/oauth2/authorize?client_id=abc1234-9c3c-4ad42-be31-8d6c87101239014&redirect_uri=https%3A%2F%2Fauth.globus.org%2Fv2%2Fweb%2Fauth-code&scope=openid+profile+email+urn%3Aglobus%3Aauth%3Ascope%3Aauth.globus.org%3Aview_identity_set+urn%3Aglobus%3Aauth%3Ascope%3Atransfer.api.globus.org%3Aall+urn%3Aglobus%3Aauth%3Ascope%3Agroups.api.globus.org%3Aall+urn%3Aglobus%3Aauth%3Ascope%3Asearch.api.globus.org%3Aall&state=_default&response_type=code&access_type=offline&prompt=login ------------------------------------ Enter the resulting Authorization Code here:
You should then see the following:
You have successfully logged in to the Globus CLI! You can check your primary identity with globus whoami For information on which of your identities are in session use globus session show Logout of the Globus CLI with globus logout
You can now use the Globus CLI commands as listed by the following command:
$ globus --help Usage: globus [OPTIONS] COMMAND [ARGS]... Interact with Globus from the command line All `globus` subcommands support `--help` documentation. Use `globus login` to get started! The documentation is also online at https://docs.globus.org/cli/ Options: -v, --verbose Control level of output -h, --help Show this message and exit. -F, --format [unix|json|text] Output format for stdout. Defaults to text --jmespath, --jq TEXT A JMESPath expression to apply to json output. Takes precedence over any specified ' --format' and forces the format to be json processed by this expression --map-http-status TEXT Map HTTP statuses to any of these exit codes: 0,1,50-99. e.g. "404=50,403=51" Commands: bookmark Manage endpoint bookmarks collection Manage your Collections delete Submit a delete task (asynchronous) endpoint Manage Globus endpoint definitions get-identities Lookup Globus Auth Identities group Manage Globus Groups list-commands List all CLI Commands login Log into Globus to get credentials for the Globus CLI logout Logout of the Globus CLI ls List endpoint directory contents mkdir Create a directory on an endpoint rename Rename a file or directory on an endpoint rm Delete a single path; wait for it to complete search Use Globus Search to store and query for data session Manage your CLI auth session task Manage asynchronous tasks transfer Submit a transfer task (asynchronous) update Update the Globus CLI to its latest version version Show the version and exit whoami Show the currently logged-in identity
- Find an endpoint
We will use the
globus endpoint search subcommand. Find help on the particular options for that with
$ globus endpoint search --help Usage: globus endpoint search [OPTIONS] [FILTER_FULLTEXT] Search for Globus endpoints with search filters. If --filter-scope is set to the default of 'all', then FILTER_FULLTEXT is required. If FILTER_FULLTEXT is given, endpoints which have attributes (display name, legacy name, description, organization, department, keywords) that match the search text will be returned. The result size limit is 100 endpoints. Options: --filter-scope [all|administered-by-me|my-endpoints|my-gcp-endpoints|recently-used|in-use|shared-by-me|shared-with-me] The set of endpoints to search over. [default: all] --filter-owner-id TEXT Filter search results to endpoints owned by a specific identity. Can be the Identity ID, or the Identity Username, as in "email@example.com" --limit INTEGER RANGE The maximum number of results to return. [default: 25; 1<=x<=1000] -v, --verbose Control level of output -h, --help Show this message and exit. -F, --format [unix|json|text] Output format for stdout. Defaults to text --jmespath, --jq TEXT A JMESPath expression to apply to json output. Takes precedence over any specified '--format' and forces the format to be json processed by this expression --map-http-status TEXT Map HTTP statuses to any of these exit codes: 0,1,50-99. e.g. "404=50,403=51"
Search for the endpoints matching the search term "tutorial" and owned by the Globus ID "firstname.lastname@example.org":
$ globus endpoint search "tutorial" --filter-owner-id email@example.com ID | Owner | Display Name ------------------------------------ | --------------- | -------------------------- ddb59aef-6d04-11e5-ba46-22000b92c6ec | firstname.lastname@example.org | Globus Tutorial Endpoint 1 ddb59af0-6d04-11e5-ba46-22000b92c6ec | email@example.com | Globus Tutorial Endpoint 2
(The 2 globus tutorial endpoints actually "see" the same filesystem, so we'll just use the first one)
For convenience, let's set environment variables representing the ID of this endpoint:
$ export ep1=ddb59aef-6d04-11e5-ba46-22000b92c6ec $ echo $ep1 ddb59aef-6d04-11e5-ba46-22000b92c6ec
We'll also find another endpoint, this time a public test endpoint which can be used for performance testing:
$ globus endpoint search "star dtn" ID | Owner | Display Name ------------------------------------ | ------------------ | ------------------------------------- 57218f41-3200-11e8-b907-0ac6873fc732 | firstname.lastname@example.org | ESnet Read-Only Test DTN at Starlight
stardtn to the ID of this endpoint:
$ export stardtn=57218f41-3200-11e8-b907-0ac6873fc732
NOTE: None of the endpoints mentioned so far require authentication in order to use them. This makes demonstrating basic functionality simpler, but we'll look at how to activate an endpoint which requires authentication, later.
- Listing files at a path on an endpoint
endpoint ls command to list the contents of the
stardtn endpoint, at the path
<code><div>$ globus ls $stardtn:/data1 500GB-in-large-files/ 50GB-in-medium-files/ 5GB-in-small-files/ 5MB-in-tiny-files/ Climate-Huge/ Climate-Large/ Climate-Medium/ Climate-Small/ bebop/ logs/ write-testing/ 100G.dat 100M.dat 10G.dat 10M.dat 1G.dat 1M.dat 500G.dat 50G.dat 50M.dat
These are files and directories containing dummy data which can be used for test purposes.
- Copy a file from one endpoint to another
Let's transfer the file
1M.dat from the
stardtn endpoint to
$ globus transfer $stardtn:/data1/1M.dat $ep1:/~/1M.dat Message: The transfer has been accepted and a task has been created and queued for execution Task ID: dfb36cd8-7d39-11ec-891f-939ceb6dfaf1
The transfer task is a separate activity and does not require any connection from the CLI client to either of the 2 endpoints: the Globus transfer service manages the transfer for us. We can check on the progress of this transfer task with:
$ globus task show dfb36cd8-7d39-11ec-891f-939ceb6dfaf1 Label: None Task ID: dfb36cd8-7d39-11ec-891f-939ceb6dfaf1 Is Paused: False Type: TRANSFER Directories: 0 Files: 1 Status: SUCCEEDED Request Time: 2022-01-24T17:20:07+00:00 Faults: 0 Total Subtasks: 2 Subtasks Succeeded: 2 Subtasks Pending: 0 Subtasks Retrying: 0 Subtasks Failed: 0 Subtasks Canceled: 0 Subtasks Expired: 0 Subtasks with Skipped Errors: 0 Completion Time: 2022-01-24T17:20:08+00:00 Source Endpoint: ESnet Read-Only Test DTN at Starlight Source Endpoint ID: 57218f41-3200-11e8-b907-0ac6873fc732 Destination Endpoint: Globus Tutorial Endpoint 1 Destination Endpoint ID: ddb59aef-6d04-11e5-ba46-22000b92c6ec Bytes Transferred: 1000000 Bytes Per Second: 587058
We can also list the destination endpoint to check that the file has reached its destination:
$ globus ls $ep1:/~/ 1M.dat
We can also make a subdirectory with
$ globus mkdir $ep1:/~/mydata/ The directory was created successfully
We can move our
1M.dat into that directory with a
globus rename command
$ globus rename $ep1 /~/1M.dat /~/mydata/1M.dat File or directory renamed successfully
We now have a directory
mydata containing files
$ globus ls $ep1:/~/mydata/ 1M.dat
- Recursively copy a directory and its contents, from one endpoint to another
Let's copy a directory on the
stardtn endpoint which contains some small files, to our destination endpoint
ep1 (The Globus tutorial endpoints only provide very limited storage space).
The files we want to copy are at the path
/data1/5MB-in-tiny-files/a/a/ on the
stardtn endpoint, and are small, as their names suggest:
$ globus ls $stardtn:/data1/5MB-in-tiny-files/a/a/ a-a-1KB.dat a-a-2KB.dat a-a-5KB.dat
Copy the parent directory recursively to
$ globus transfer -r $stardtn:/data1/5MB-in-tiny-files/a/a $ep1:/~/star-data Message: The transfer has been accepted and a task has been created and queued for execution Task ID: 4ae9bab0-7d40-11ec-bef3-a18800fa5978
Check destination content:
$ globus ls $ep1 mydata1/ star-data/ $ globus ls $ep1:/~/star-data a-a-1KB.dat a-a-2KB.dat a-a-5KB.dat
We could now delete one of the small files using the
globus delete command:
$ globus delete $ep1:/~/star-data/a-a-2KB.dat Message: The delete has been accepted and a task has been created and queued for execution Task ID: be4d6934-7d40-11ec-891f-939ceb6dfaf1
And list contents again, to verify that it has been deleted:
$ globus ls $ep1:/~/star-data a-a-1KB.dat a-a-5KB.dat
- Sync a source directory to a target (repeatable)
We could now repeat the copying of the source data, but this time using the
--sync-level exists command so that we only copy the data that is now missing from the destination. The full set of sync options is
$ globus transfer -s exists -r $stardtn:/data1/5MB-in-tiny-files/a/a $ep1:/~/star-data Message: The transfer has been accepted and a task has been created and queued for execution Task ID: 759a3cac-7d41-11ec-bef3-a18800fa5978
This should only copy the data that do not already exist at the desination: We end up with the same set of files at the destination:
$ globus ls $ep1:/~/star-data a-a-1KB.dat a-a-2KB.dat a-a-5KB.dat
But we can see that only 2000 bytes were transferred (so we know it only copied that one file, which is what we wanted):
$ globus task show 759a3cac-7d41-11ec-bef3-a18800fa5978 Label: None Task ID: 759a3cac-7d41-11ec-bef3-a18800fa5978 Is Paused: False Type: TRANSFER Directories: 1 Files: 3 Status: SUCCEEDED Request Time: 2022-01-24T18:14:24+00:00 Faults: 0 Total Subtasks: 5 Subtasks Succeeded: 5 Subtasks Pending: 0 Subtasks Retrying: 0 Subtasks Failed: 0 Subtasks Canceled: 0 Subtasks Expired: 0 Subtasks with Skipped Errors: 0 Completion Time: 2022-01-24T18:14:58+00:00 Source Endpoint: ESnet Read-Only Test DTN at Starlight Source Endpoint ID: 57218f41-3200-11e8-b907-0ac6873fc732 Destination Endpoint: Globus Tutorial Endpoint 1 Destination Endpoint ID: ddb59aef-6d04-11e5-ba46-22000b92c6ec Bytes Transferred: 2000 Bytes Per Second: 60
This task could be repeated in a shell script, cron job or even using the Globus timer functionality, for either a source or destination directory that is expected to change.
- Activate an endpoint that requires authentication
Most Globus Connect Server endpoints require activation, which usually involves both authentication (checking identity) and authorization (checking that you have the correct permission to carry out a particular activity).
Let's find, then set up an alias to the JASMIN Globus Endpoint. It is owned by the globus ID
$ globus endpoint search "jasmin" --filter-owner-id email@example.com ID | Owner | Display Name ------------------------------------ | ----------------- | ------------------------------------------- 2b0a1a4c-ee1f-11eb-b467-eb47ba14b5cc | firstname.lastname@example.org | JASMIN Globus Endpoint (jasmin credentials) export epj=2b0a1a4c-ee1f-11eb-b467-eb47ba14b5cc
Let's activate this endpoint, opting to use the MyProxy method, for which we need our JASMIN account credentials. Include
$ globus endpoint activate --myproxy --myproxy-username <username> $epj Myproxy password: Endpoint activated successfully using a credential fetched from a MyProxy server.
Note (1) You can also specify the password in the command using the -P option, to do this in one action, but this is less secure as your password will be visible in your system’ command history
If successful, you can now interact with the JASMIN endpoint, for example listing your home directory:
$ globus ls $epj:/~/ ... (file listing) ...
- Re-activate an endpoint
You can check if an endpoint is activated like this:
$ globus endpoint is-activated $epj 2b0a1a4c-ee1f-11eb-b467-eb47ba14b5cc is activated
This can be used in conjunction with the previous command to re-activate if necessary. Activation normally lasts 72 hrs (although this may increase in future, for the JASMIN endpoint).
An alternative method for activating an endpoint is also available using the --delegate-proxy method, specifying the path to an x509 credential certificate obtained using the JASMIN SLCS service, as described in this article. In this case, the activation command would be
$ globus endpoint activate --delegate-proxy <credential file> $epj Endpoint activated successfully using a proxy credential provided by the client.
Activation can therefore be carried out independently of any transfers (via the CLI or web interface, or by storing a secure but time-limited credential on the file system), so transfers need not be interrupted. Do not store your username or password in the file system to facilitate renewal of your credential, however: this is insecure. The lifetime of the credential (currently 72 hrs but we are working on extending this) should be sufficient that obtaining the credential for activation of the endpoint can be a "one-off" manual task which is carried out before any transfer takes place: it does not need to be part of the transfer workflow itself.
The functionality above can be combined into useful scripts which can perform useful, repeatable tasks such as:
- recursively syncing the contents of directories between 2 endpoints
Globus provide 2 implementations of this here:
Examples of automation using the Globus CLI, specifically:
- cli-sync.sh : bash script using the Globus CLI as demonstrated above
- globus_folder_sync.py : Python code using the Globus Python software development kit (SDK)
- We have not covered the Python SDK here, but this is a useful example of how you could integrate Globus transfer functionality into your own workflows. You would need to install and authorise this first)
Taking the first of these examples, we can adapt it slightly:
1. Select the JASMIN endpoint at the destination, and set the destination path. Modify the corresponding variables in the script to these values:
$ source ~/.globus-cli-venv/bin/activate
$ globus login
$ globus endpoint activate --myproxy --myproxy-username=<username>
$ ./cli-sync.sh Checking for a previous transfer Last transfer f5db7238-8f06-11ec-8fe0-dfc5b31adbac SUCCEEDED, continuing Verified that source is a directory Submitted sync from ddb59aef-6d04-11e5-ba46-22000b92c6ec:/share/godata/ to ddb59af0-6d04-11e5-ba46-22000b92c6ec:/~/sync-demo/ Link: https://app.globus.org/activity/04e277f4-8f07-11ec-811e-493dd0cf73a1/overview Saving sync transfer ID to last-transfer-id.txt
- following the URL to app.globus.org to view the task under "activities", or
$ globus task show <taskid>
7. Experiment by changing the SYNCTYPE. Other options are:
- see here for descriptions of the available sync levels:
You could then consider how to repeat the task automatically. For example:
- scheduling the running of the cli-sync.sh command on your own machine using cron
- Remember: the invocation of the command does NOT need to be done on JASMIN, it can be done wherever you have the CLI installed, for example your local machine.
- Learn about how to use timers with Globus: these can be set up using the web interface or using an additional CLI globus-timer-cli which can be installed into the same
virtualenvas the main globus cli.