Globus CLI

output:

Usage: globus [OPTIONS] COMMAND [ARGS]...

Options:

  -v, --verbose                  Control level of output

  -h, --help                     Show this message and exit.

...

Note: You may recieve this error in Markov/Rider. RHEL 8 uses openssl-1.1.1, and  RHEL 9 uses openssl-3.0.x.

ImportError: urllib3 v2.0 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with 'OpenSSL 1.0.2k  26 Jan 2017'. See: https://github.com/urllib3/urllib3/issues/2168

Downgrade urllib3 as showed:

pip3 install "urllib3<2" --user

More Help about the commands:

.local/bin/globus endpoint activate --help

output:

Usage: globus endpoint activate [OPTIONS] ENDPOINT_ID

  Activate an endpoint using Autoactivation, Myproxy, Delegate Proxy, or Web

  activation. Note that --web, --delegate-proxy, and --myproxy activation

...

--myproxy                       Use myproxy activation. Mutually exclusive

Login to authenticate globus services. It needs to be done only once

./globus login --no-local-server

output: 

Please authenticate with Globus here:

------------------------------------

https://auth.globus.org/v2/oauth2/authorize?...Aall

------------------------------------

Enter the resulting Authorization Code here: <Enter the code you get after authentication using the above url>

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

(Note: copy and paste the above url to the browser and proceed to get the authentication code that you can enter at the prompt to login in successfully)

Search Globus Endpoints

Search the HPC Globus server endpoint

./globus endpoint search 'cwru'

output:

ID                                         | Owner                 | Display Name              

------------------------------------ | --------------------- | --------------------------

...

c7f8a02a-d4c8-11e9-939f-02ff96a5aa76 | cwru@globusid.org                     | cwru#dtn2

cd86e0c0-d56c-11e9-98e2-0a63aa6b37da | cwru@globusid.org                     | cwru#dtn3    

Search your endpoints with the filter

./globus endpoint search --filter-scope my-endpoints

ID                                   | Owner                  | Display Name

------------------------------------ | ---------------------- | --------------------------

c2bce39e-0192-11e6-a71b-22000bf2d559 | XXXX@globusid.org      | XXXX#dtn3

...

Check the home directory associated with the endpoint ID

./globus ls 'a75f9880-f348-11e8-8cc5-xxxxxxxxxxxx'

output:

Custom Office Templates/

MobaXterm/

My Music/

...

Transferring Files

Note: During the file transfer, if you receive the message requiring you to activate the endpoint, it is better to activate/authenticate it using the Globus web interface  endpoints tab.

Define two endpoint variables ep1 (e.g. sanjayagajurel) and ep2 (e.g. cwru#hpctransfer)

ep1=a75f9880-f348-11e8-8cc5-xxxxxxxxx

ep2=d98c8071-6d04-11e5-ba46-xxxxx

Transfer a single file:

Transfer a file "file.err" from hpctransfer end point to PC endpoint (sanjayagajurel) with a label "CLI test transfer"

./globus transfer $ep2:~/file.err $ep1:~/file.err --label "CLI test transfer"  

output:

Message: The transfer has been accepted and a task has been created and queued for execution

Task ID: e1a574cc-f354-11e8-8cc6-0a1d4c5c824a

(Note the Task ID)

Check the status of the transfer using the Task ID

./globus task show 'e1a574cc-f354-11e8-8cc6-xxxxxxx'

output:

Label:                   CLI test transfer

Task ID:                 

Is Paused:               False

Type:                    TRANSFER

Files:                   1

Status:                  SUCCEEDED

...

Transfer a directory:

./globus transfer $ep2:~/test $ep1:~/test --recursive --label "CLI test directory transfer"  

(Note the --recursive flag & directory name should match)

Transfer batch of files including directories:

Include all the files and directories to be transferred in a input file "in.txt"

test.log test.log

test.out test.out

test test -r # test is a directory and hence recursive flag -r or --recursive

Transfer

./globus transfer $ep2:~/ $ep1:~/ --batch --label "CLI batch transfer" < in.txt

If the endpoint is deactivated, you may get authentication error. So, activate it using:

.local/bin/globus endpoint activate --myproxy <endpoint-globusID>

It will prompt you for the credentials. For HPC endpoints, you need to enter SSO credentials.

Forced Logged Out:

If you want to login as another user

./globus login --no-local-server --force

Globus CLI - Batch Job

Case Study - Continuously syncing newly generated files

Use the job script template below to create your job script. For advanced automation, refer to https://github.com/globus/automation-examples/blob/master/

#!/bin/bash

#SBATCH --time=<duration-of-transfer>                                                                                                                                                                                                                         # set the duration of transfer e.g. 12:00:00 for 12 hrs

# Load the python module

module load python2

#Set Endpoint Task ID for source endpoint ep1 and destination endpoint ep2

ep1=<Task ID for the source endpoint>                                                                                                                                                                                                                         # e.g. e09e6568-6d04-11e5-ba46-xxxxxxx

ep2=<Task ID for the destination endpoint)                                                                                                                                                                                                                     # e.g. 0409ae6e-a356-11e9-a379-xxxxxxx

# Infinite Loop until the job terminates after the expiry of the walltime (e.g. 10 hrs)

while true; do

~/.local/bin/globus transfer "$ep1:/<path-to-source-directory>/<directory>/" "$ep2:~/<path-to-source-directory>/<directory>/"  --recursive -s 'checksum' --label "CLI delme directory transfer"                                                                      # <directory> should have same name for src and dest

# wait or sleep for <wait-time>  another globus transfer command

sleep <wait-time-for-another-transfer>                                                              # e.g 120 for 2 minutes of wait time

done

Now, submit the job

sbatch <your-job-script>

Check the output once the job starts running

cat slurm-<jobID>.out

output:

Message: The transfer has been accepted and a task has been created and queued for execution

Task ID: 8c59a5e0-2276-11ea-ab46-xxxxxxx

Message: The transfer has been accepted and a task has been created and queued for execution

Task ID: d518036c-2276-11ea-9708-xxxxxx

While in progress, the transfer status can be viewed in the Globus web interface's activity tab. If several transfers are happening simultaneously, each can be referenced by the Task ID.

If you get the error message or want to terminate the job in the middle, issue:

scancel <jobID>

Debugging Globus Transfer

$ globus transfer "$ep1:/alignedJPG/" "$ep2:/mnt/vstor/cryoem/test/delme/alignedJPG/" --recursive -s 'checksum' --label "CLI delme directory transfer" --dry-run

Source Path  | Dest Path                              | Recursive

------------ | -------------------------------------- | ---------

/alignedJPG/ | /mnt/vstor/cryoem/test/delme/alignedJPG/ |         1

# or, with JSON output ("-F json" or "--format json")

$ globus transfer "$ep1:/alignedJPG/" "$ep2:/mnt/vstor/cryoem/test/delme/alignedJPG/" --recursive -s 'checksum' --label "CLI delme directory transfer" --dry-run -F json

{

  "DATA": [

    {

      "DATA_TYPE": "transfer_item",

      "destination_path": "/mnt/vstor/cryoem/test/delme/alignedJPG/",

      "recursive": true,

      "source_path": "/alignedJPG/"

    }

  ],

  "DATA_TYPE": "transfer",

  "delete_destination_extra": false,

  "destination_endpoint": "ddb59af0-6d04-11e5-ba46-22000b92c6ec",

  "encrypt_data": false,

  "label": "CLI delme directory transfer",

  "preserve_timestamp": false,

  "recursive_symlinks": "ignore",

  "skip_activation_check": false,

  "source_endpoint": "ddb59aef-6d04-11e5-ba46-22000b92c6ec",

  "submission_id": "728ae6a5-5284-11ea-ab5b-0a7959ea6081",

  "sync_level": 3,

  "verify_checksum": true

}

Troubleshooting

Issue:

The endpoint could not be auto-activated and must be activated before it can be used.

This endpoint supports the following activation methods: web, delegate proxy, myproxy

For web activation use:

Solution: activate the endpoint from Globus portal using your credentials.

Issue: while using CLI command e.g. ~/.local/bin/globus transfer $ep1:/alignedJPG $ep2:/mnt/vstor/cryoem/test/alignedJPG --recursive -s 'checksum' --label "CLI delme directory transfer", transfer stuck with the warning "warning: is a directory;"

And after using suggested quotes as showed: 

~/.local/bin/globus transfer "$ep1:/alignedJPG/" "$ep2:/mnt/vstor/cryoem/test/alignedJPG/" --recursive -s 'checksum' --label "CLI delme directory transfer", error message was: 

Globus CLI Error: A Transfer API Error Occurred.

HTTP status: 400

request_id: z863CkFhr

code: ClientError.BadRequest

message: The recursive option should be used when transfering directories

Solution: Some strange characters were being sent to the CLI as showed:

/mnt/vstor/cryoem/test/delme/alignedJPG%C2%A0--recursive

Hence, retyping the command not copying/pasting helped.

~/.local/bin/globus transfer "$ep1:/alignedJPG/" "$ep2:/mnt/vstor/cryoem/test/alignedJPG/" --recursive -s 'checksum' --label "CLI delme directory transfer"