Transferring your data from CEMC Fairchild Storage with Globus

Data you collect on the Fairchild Glacios is made available for transfer through CEMC Fairchild Storage, a Globus data transfer node. Use Globus to move it to wherever you need it.

At a glance


Globus collection	CEMC Fairchild Storage
Name your collections	`<date>_<sunetid>_<project>`
Example	`20260824_davidfm_apoferritin`
How long data is kept	30 days from collecting
Access	Granted during microscope training
Help	#cemc-compute on Slack

1. Naming your collections (read this first)

Your collections are sorted into your own directory based on the name you give each collection at the microscope. Get this step right and your collection will automatically appear in Globus. If the name does not match the pattern below, your collection will not appear in your directory and CEMC staff help will be needed to rename it.

On the Glacios, this is the collection file name you specify on the Z: drive in EPU.

Use this pattern:

<date>_<sunetid>_<project>

For example:

20260824_davidfm_apoferritin

Four rules:

Separate the parts with underscores. Not hyphens, not dots, not spaces.
Date first. YYYYMMDD is preferred. Other all-numeric dates may work too. Dates that spell out the month will fail (aug2026).
Your SUNetID second. This is the most important part of the collection name. It is what identifies the collection as yours, so it must be your actual SUNetID: not your initials, not your name, not your lab’s name.
Project name last. This part can be anything you like. Choose something descriptive of the project you’re working on.

If your SUNetID is not in the second position, the system cannot determine who the collection belongs to. Nothing is lost. The collection stays on the acquisition system, but it is not copied to your directory, and it will not be waiting for you when you go to transfer it. A CEMC staff member will need to rename the collection for you.

2. How your cryo-EM collections reach Globus’ CEMC Fairchild Storage

You do not have to do anything to start this. Copying is automatic.

microscope  →  CEMC Fairchild Storage  →  you

New files usually appear within 5–10 minutes of being written, so you can begin transferring while a session is still running.
A file is only copied once it has finished being written. You will never see a half-written file, and a file that appears in your directory is complete.

3. Getting access

If you have been trained on the microscope, you already have access. New users are added during training, so in most cases there is nothing for you to request.

To check whether you have access:

Log in to Globus at app.globus.org and click File Manager.
Enter CEMC Fairchild Storage in the Collection field. You may be prompted to authenticate.
If you see your SUNetID in the Path field, you are set up.

If you do not have access, Globus will tell you so when you navigate to the collection, or your authentication will fail. Drop a message in #cemc-compute on Slack and we will sort it out.

4. Finding your collections in Globus

Globus is a service for moving large amounts of data between computers. You use it through a web browser: you pick a source, pick a destination, and it handles the transfer in the background, restarting anything that gets interrupted. You do not have to stay logged in or keep your laptop awake, unlike other data transfer methods.

If you have not used Globus at Stanford before, see Stanford’s own Globus documentation. Globus also publishes a File Transfer Tutorial covering the basics of logging in and moving files.

To find your collections:

Go to app.globus.org and log in. Choose Stanford University as your organization and sign in with your SUNetID.
In File Manager, search Globus collections for CEMC Fairchild Storage. You may be prompted to authenticate again with your Stanford University identity.
Open it. You will land in your own directory automatically.

If you go up one folder you may see other researchers’ directories listed. You cannot open them, and they cannot open yours. This is expected behavior. See section 5.2 if you need to share data with someone.

5. Transferring your data out

5.1 CEMC Fairchild Storage is a staging point

Your data lands here on its way somewhere else: your lab’s storage, Sherlock, Oak, or your own machine. Plan to move it off promptly. It is kept for 30 days per CEMC policy (section 6).

You cannot share data with collaborators from CEMC Fairchild Storage. Transfer it to a location that supports sharing, and share it from there.

5.3 Transfer to another Globus collection

This is the usual route, and the fastest. Sherlock, Oak, and most university and national computing facilities are already Globus collections.

In File Manager, put CEMC Fairchild Storage on one side and your destination on the other, select what you want to move, and click Start.

5.4 Transfer to your own computer

Install Globus Connect Personal, which turns your own machine into a Globus collection you can transfer to. It is free and available for Windows, macOS, and Linux from the Globus website.

Once it is installed and running, your computer appears in File Manager like any other Globus collection.

One difference from the other routes: your computer has to stay on, awake, and connected for the transfer to progress. Globus still manages it in the background and will resume where it left off if your computer falls asleep, but it cannot move data to a machine that is asleep or shut down.

5.5 Downloading a single file in the browser

Globus lets you download individual files directly from File Manager. This is handy for grabbing one micrograph or a log file to look at.

It is not a way to move a whole collection. It is one file at a time, with no way to resume if it fails. For anything larger than a few files, use one of the methods above.

5.6 What to expect from a large transfer

Symlinks are expanded. If your collection contains symbolic links, Globus copies the contents of whatever each link points at, rather than recreating the link. Several links to the same file become several full copies, so a transfer can be larger at the destination than it appeared at the source.

Lots of small files are slow. Globus handles each file separately, so thousands of small files take much longer than the same total size in a few large ones. A transfer that looks stuck may simply be working through a large number of files. Check the transfer’s progress in Activity before canceling it.

Let it run. Transfers continue whether or not your browser is open. Globus retries automatically after network problems and emails you when the transfer finishes or fails. You can watch progress at any time under Activity.

Encryption is applied to every transfer automatically. There is nothing for you to configure.

6. How long your data is kept

Data on CEMC Fairchild Storage is retained for 30 days. After that it is purged irrevocably, so transfer anything you want to keep before the 30 days are up.

Full details are in the CEMC storage policy.

7. Troubleshooting

My collection has not appeared. Check the name of the collection first, as this is the most common cause. If your SUNetID is not the second part of the name, separated by underscores, it will not have been copied. Message #cemc-compute on Slack and we will rename the collection for you.

If the name is correct and the session finished less than 10 minutes ago, wait a little longer.

I cannot find CEMC Fairchild Storage in Globus, or I get “permission denied”. You probably do not have access yet, or you signed in with a different identity. Make sure you logged in through Stanford University with your SUNetID, then see section 3.

A file I transferred is 0 bytes. This usually means the file could not be read at the source, rather than the file being genuinely empty. Let us know in #cemc-compute which file it was.

My transfer failed or looks stuck. Check Activity in Globus for the error message. Transfers with many small files can look stalled while still making progress. Globus retries network problems on its own, so give it time before canceling. If it has genuinely failed, the error message is the useful thing to post in #cemc-compute.

8. Getting help

Reach out to #cemc-compute on Slack.

When reporting a problem, please include:

the name of the collection
the date of the session
the Globus task ID, if a transfer was involved (find it under Activity)