Globus is the recommended way to move significant amounts of data between NERSC and other sites. Globus addresses many of the common challenges faced by researchers in moving, sharing, and archiving large volumes of data. With Globus, you hand-off data movement tasks to a hosted service that manages the entire operation, monitoring performance and errors, retrying failed transfers, correcting problems automatically whenever possible, and reporting status to keep you informed while you focus on your research. Visit Globus.org for documentation on its easy to use web interface and its versatile REST/API for building scripted tasks and operations.
Globus is available as a free service that any user can access. You can log into Globus web interface with your NERSC credentials (by selecting NERSC in the drop down menu of supported identity providers) or using many of the other supported providers listed that you can authenticate against. NERSC maintains several Globus endpoints that can be activated for individual use by any NERSC user. The list of endpoints are provided in the table below.
|Endpoint Name||Description||Recommended Use|
|NERSC DTN||Multi-node, high performance transfer system with access to all NERSC Global File systems (NGF) as well as Cori Scratch||Almost all data transfers needs into & out of NERSC|
|NERSC HPSS||Single node system connected directly to the NERSC HPSS tape archive||Remote transfers into & out of HPSS|
|NERSC Cori||Originally a dual-node system needed for accessing the Cori scratch file system. The endpoint is the same as NERSC DTN||Use NERSC DTN instead|
|NERSC DTN-JGI||Single node system that was used to access JGI-specific file systems, which are now connected to the NERSC DTN servers.||Use NERSC DTN instead|
|NERSC SHARE||Single node system with read-only access to some NERSC file systems||Shared Globus endpoint|
Be aware that Globus will follow hard links and copy the data to the target directory. Depending on the way the directory or file is transferred, it will also follow soft links. You can find details here: https://docs.globus.org/faq/transfer-sharing/#how_does_globus_handle_symlinks
To transfer files into/out of your laptop or desktop computer, you can install a Globus connect (personal) server to configure an endpoint on your personal device.
Data can be shared at NERSC using Globus Sharing. Currently shared endpoints are read-only, no writing is allowed. To share data, create a "gsharing" directory in your repo's Community directory. Then open a ticket and let us know the directory path you'd like to share (we currently have to manually update the configuration file to allow directories to be shared). Once you hear back from us, go to the Globus endpoint web page and search for the "NERSC SHARE" endpoint. Click on the "Shares" tab and select "Add a Shared Endpoint". This will bring you to a screen where you can give your shared endpoint a name and fill in the path you'd like to share. Currently sharing is limited to /global/cfs/cdirs/<your_repo_name>/gsharing and subdirectories (and the dna file system for JGI users). Once you click "Create Share" it will take you to another screen where you can share this endpoint with specific Globus users or with all Globus users (these users do not have to be NERSC users). You can also make other Globus users administrators, which will mean that they will have the power to add or remove other users from the shared endpoint.
If your files and directories are set to be world readable, they can be shared by any NERSC user if you opt into Globus Sharing. We recommend you set the permissions on your files and directories to be only user and group readable to avoid accidental sharing.
Command Line Globus Transfers at NERSC¶
Globus provides a python based SDK (Software Development Kit) for doing data transfers, managing endpoints, etc. You can access this at NERSC by loading the globus-sdk module (
module load globus-sdk). NERSC has written several scripts using the Globus SDK to help with command line data transfers. These scripts use Globus Applications and tokens to manage authorization and access.
You can use this script for internal transfers between NERSC file systems or for external transfers between two Globus endpoints provided you have the endpoint's UUID (which can be looked up on Globus' Endpoint Page). This script also understands "hpss" (the NERSC HPSS Endpoint), "dtn" (the NERSC DTN Endpoint), or "cori" (the NERSC Cori Endpoint), so you won't need to look up the UUIDs for those endpoints.
nersc> module load globus-sdk nersc> ./transfer_files.py -h transfer_files.py: error: the following arguments are required: -s, -t, -d, -i Globus transfer helper Required arguments: -s SOURCE source endpoint UUID -t TARGET target endpoint UUID -d OUT_DIR target endpoint output directory -i INFILES file containing list of full path of input files Optional arguments: -p, --preserve Preserve time stamps
If you are using Globus to read a large number (>100) of files from NERSC's HPSS Archive, please use this script. It will ensure that the files are read off in in tape order.
Checking the Status of Transfers¶
You can use this script to check on the status of your transfers. If you call it with no arguments it will show you the status of your last 10 Globus transfers. You can also invoke it with a transfer UUID to see just a single transfer or with the
-p flag to get easily parsable output. If a transfer fails, you can use the
-d option to see the reason.
nersc> check_transfers.py --help usage: check_transfers.py [-h] [-i IDS] [-n NUMBER] [-d] [-p] Globus transfer lister optional arguments: -h, --help show this help message and exit -i IDS, --id IDS Transfer ID or comma separated list of transfer IDs to lookup -n NUMBER, --number NUMBER Number of transfer records to retrieve -d, --details Get details on individual transfers -p, --parsable Get easy to parse output: Tranfer ID | Status
Transfer files from NERSC's Community file system to NERSC's Cori Scratch file system¶
This can be used to stage data on Cori scratch before using it in a running job.
First, generate a list of files and directories you wish to transfer. If a directory is included in this list, its contents will be recursively transferred to the target directory.
nersc> ls /global/cfs/cdirs/<myrepo>/<my_dataset_directory> > transfer.txt nersc> ls /global/cfs/cdirs/<myrepo>/<my_other_dataset_directory>/data01.dat >> transfer.txt
module load globus-sdk nersc> transfer_files.py -s dtn -t dtn -d /global/cscratch1/sd/<your_username>/input_directory -i transfer.txt (if this is the first time running the script, you'll see the next two lines) Please go to this URL and login: https://auth.globus.org/v2/oauth2/authorize?client_id=<super_mega_long_string_here> Please enter the code you get after login here: <snipped> Transfer ID is b'XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX' label is <username>_<datestamp>
nersc> module load globus-sdk nersc> check_tranfer.py -i XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX Task(XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX): label: <your_user_name>_2019-11-21_12_21_17, start: 2019-11-21 20:21:18+00:00, done:2019-11-21 20:21:23+00:00 nersc#dtn -> nersc#dtn SUCCEEDED
nersc> module load globus-sdk nersc> check_tranfer.py -i XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX -p XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX | SUCCEEDED
Transfer files from NERSC's HPSS Archive to another location¶
It's important to order your retrievals when reading from HPSS. These command line tools will do this automatically for you.
First, generate a list of files you'd like to transfer:
nersc> hsi -q ls -1 -R name_of_hpss_directory_or_file 2> gtransfer_list.txt
nersc> transfer_files.py -s hpss -t <target_endpoint_UUID> -d /your/destination/path -i gtransfer_list.txt (if this is the first time running the script, you'll see the next two lines) Please go to this URL and login: https://auth.globus.org/v2/oauth2/authorize?client_id=<super_mega_long_string_here> Please enter the code you get after login here: <snipped> Transfer ID is b'XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX' label is <username>_<datestamp>
The first time you run any of these scripts, it will generate and store a Globus token in your NERSC home directory. It does this by creating a one-time Globus web page for you grant permission to generate this token. Paste this web page address into a browser and it will take you to a page where you can grant the native Globus application permission to make transfers on your behalf and check on the status of your transfers. You may get a prompt to log into Globus first if you don't already have an active session. Once you click "Allow" it will generate a one-time code. Paste this code back into the terminal at the prompt and push return. It will use this to generate a token that can be used for this and future Globus interactions on your behalf.
Do not share this Globus token with anyone else. This is the same as sharing your NERSC password and is against NERSC policy.
Connection Errors Between NERSC and other endpoint¶
If you are getting errors that you cannot connect to the NERSC endpoint after you've activated it, please check with your system administrator that they are not blocking the IP of the NERSC host (you can find this information in the error message of the Activity pane on the globus web page). If they are not, please open a ticket with the IP address of the other endpoint and we will investigate further.
Trouble Activating a NERSC Endpoint¶
If you are having trouble activating a NERSC endpoint, please try logging into Iris to clear your authentication failures. If that still doesn't fix the issue, please open a ticket with the error and we'll investigate further.