Getting Started on Globus
November 02 2017
File transfer using Globus on Your Home Computer, Clusters, and Jetstream
File transfer to a Jetstream instance can be done through several ways. For small files, such as a simple two-line text file, copy pasting the content is probably just as quick as transferring the file. When you get to larger or multiple files, such as a directory (folder) or bigger file, you can transfer it using:
scp, rsync(if you are comfortable with commandline), WinSCP ,FileZilla (windows users) or CyberDuck(windows and OS).
However, when you have really large files, such as raw sequence data, it can be a bit tedious to transfer files via command line, not to mention problematic if your internet connection drops out. In these cases, Globus is a favorable alternative. Globus allows you to transfer gigabytes or terabytes of data securely and quickly.
To transfer files between two points, you need to make sure the two points have active Globus endpoints. Endpoints are the two points you want to transfer data to and from. Both must have Globus set up according to the endpoint type. Setting Globus up on your computer is free (see below), but clusters, academic, or commercial endpoints are required to pay for a subscription. For more information about subscription type and their features, see the subscription information here.
Setting up Globus endpoint on your personal computer
It is likely you will need to transfer files between your preferred cluster and your home computer at some point. To set up Globus on your home computer,
You have access to Globus plus features with an XSEDE account (required for Jetstream – if you don’t have one, go here and fill out the form. It does not take long. See here for more detail on getting started on XSEDE and Jetstream). Globus plus allows you to transfer files between two personal computers or between Jetstream image to
Go to subsection “Globus Plus”. Under “Select another organization” select option XSEDE Plus Sponsor.
Under the Subgroups tab, find a link to XSEDE Global Plus Users. Select Join group.
Once your request to join the group is approved (usually takes ~hour), you will receive an email to your primary identity (email account) listed under Accounts. As soon as you are accepted, you will be able to transfer between two Globus personal endpoints (i.e. your computer and your Jetstream VM)!
More information and tutorials on
Globus endpoints on HPC clusters
If your company/institution has a Globus endpoint installed (this is a paid subscription), you should be able to search for
Look for the endpoint on
1. Log in at https://www.globus.org/
You should see this page after logging in, if not click on “Transfer”.
2. Click on
globus endpoint on Jetstream VMs
These are basically the instructions for the set up of Globus on any Linux machine. However, an example on Jetstream with
Log into the VM (terminal in WebDesktop, Webshell or ssh- your preference). If you are new to command line, “Welcome to the Dark Side!”. You can access the WebDesktop (red) and Webshell (black) with the following links when you click on an active image in your Jetstream Atmosphere Portal. In this case, you will want to use the Web Shell.
NOTE: If the beta is still listed as such, please use that. The old version does not have support for copy and paste. If there is no longer a beta listed, it is likely that the new system has fully replaced the old and you can just use the only
You can also run these commands via putty (Windows), ssh command on terminal (LINUX/MAC), you can
If you are working on the Webshell, the main weirdness you will run into is using copy or paste from your computer to Webshell and vice-versa. Here is the trick, on the WebShell:
Windows (shift+ctl+alt)/Mac (shift+ctrl+cmd) -> This brings up a
- To paste from your computer to the VM, you will have to paste the text here. Then, exit the sidebar with shift+ctl+cmd, and paste into the shell with shift+ctl+alt/shift+ctrl+v(mac).
- To paste from the VM to your computer, highlight the text, bring up the
side bar, and make sure the text is in the common clip board, then paste as normal.
- To paste from the VM to the VM, you can just
hightlightthe text and paste as normal (not going across computers).
Once you are in a terminal of your choosing, follow these steps:
1. In your home directory, or wherever you install files, download
2. Unzip the
3. Make a new ssh-key for the instance:
This command will create a public and private key at current working directory under the name “js”. Type in a passphrase here- acts as 2 step verification process.
Once done, you will see a pattern as shown below.
4. Move the “js.pub” and “js” to ./ssh
mv js.* ~/.ssh/
5. Add new key (public) to
- Click on Account
- In accounts, click on “ manage SSH and X.509 keys.”
IF YOU DO NOT SEE THE ABOVE OPTION: Look at the linked identities under Account. If you do not see an account ending in “globusid.org”, you will need to get one. A
globusidis required to add keys. You are able to log in witha gmail/institutional email, and may not have a globusid.
globusid, follow this link.
Once you have signed up, you should link your account to your main account (listed under globus.org, Accounts).
The option “ manage SSH and X.509 keys” should show up now.
- Then select “add a new key”
- Fill in the information and copy paste public key to the body
- Click on “Add Key”
6. Back to Jetstream instance, in the terminal go to
7. Log into globusonline.org with your ssh key from your instance (you need to use your username):
ssh -i ~/.ssh/js firstname.lastname@example.org
8. Now setup endpoint on globusonline.org for your instance
endpoint-add -n name_of_the_endpoint --
This command will give you an Endpoint ID and Setup ID for the instance, which you WILL NEED in the next set of commands. Copy paste them to a text editor if needed. Sign out of the ssh with "exit", then in the
./globusconnect -setup Setup_ID
./globusconnect -start &
ssh -i ~/.ssh/js email@example.com endpoint-activate Endpoint_ID
Globus connect endpoint is now
9. Verification step to see if the
10. Transfer files using
11. To stop
DONE! You are all set!
- I have logged in to
globusbut can't find IU#dc2 endpoint to transfer files to IU computers?
Here is the trick you need to login to
- you need to have your google account (firstname.lastname@example.org),
xsedeaccount (email@example.com), IU ID (firstname.lastname@example.org) or other accounts all listed under accounts.
logoutand log back in using your Google credentials
- Search for the endpoint IU#dc2 and you should be able to connect to this endpoint.
If you have any questions mail us at email@example.com