{"id":11291,"date":"2025-08-01T10:54:28","date_gmt":"2025-08-01T14:54:28","guid":{"rendered":"https:\/\/labs.icahn.mssm.edu\/minervalab\/?page_id=11291"},"modified":"2025-09-15T15:14:05","modified_gmt":"2025-09-15T19:14:05","slug":"file-transfer-globus","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/minervalab\/documentation\/file-transfer-globus\/","title":{"rendered":"File Transfer: Globus"},"content":{"rendered":"

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Scientific Computing and Data<\/a>\u00a0\/\u00a0High Performance Computing<\/a>\u00a0\/\u00a0Documentation<\/a> \/ File Transfer: Globus and Others<\/p>\n

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File Transfer: Globus and Others<\/h1>\n

Icahn School of Medicine at Mount Sinai (ISMMS) maintains high speed network connections with the commercial Internet and Internet2 through NYSERNet.\u00a0 ISMMS currently maintains the following options for file transfer:<\/p>\n

 <\/p>\n

Globus<\/a>
SCP, SFTP, rsync<\/a><\/h3>\n

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<\/a>Globus<\/span><\/h2>\n

Globus is a secure, high-performance data transfer service commonly used by researchers and institutions to move large files between systems (e.g., between your computer and a high-performance computing center, or between universities).<\/p>\n

An advanced secure version of Globus File Manager with High Assurance HIPAA compliance BAA subscription is deployed on Minerva.[\/et_pb_text][et_pb_text _builder_version=”4.16″ header_font=”|600|||||||” header_text_color=”#221f72″ background_size=”initial” background_position=”top_left” background_repeat=”repeat” custom_margin=”10px||20px||false|false” custom_padding=”10px||20px||false|false” global_colors_info=”{}”]<\/p>\n

Globus Web Application<\/span><\/h3>\n

The Globus Web App provides a user-friendly interface for managing data transfers interactively, suitable for users who prefer a graphical interface over command-line operations.<\/p>\n

Authentication with mssm.edu<\/span><\/h4>\n

To manage or share your Minerva files with collaborators, visit https:\/\/app.globus.org\/<\/a> to login. When prompted for authentication, please use your Mount Sinai school email (eg, first.last@mssm.edu) for access. For more information on “Log In and Transfer Files with Globus”, click here<\/a>. If you are sure you have the correct username and password (no VIP), please contact hpchelp@mssm.edu<\/a> for further assistance.<\/p>\n

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Locating Minerva Collections
<\/strong><\/span><\/h4>\n

After login, in the File Manager tab, search Minerva in the collections. Please use the following two collections to access your files under \/sc\/arion<\/code> and your files under home \/hpc\/users<\/code>. Watch the owner id be89659c-xxx.<\/p>\n

\"\"<\/p>\n

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How to Share files with Globus?<\/span><\/h4>\n

Please see step by step instruction for file sharing here<\/a>.<\/p>\n

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Globus CLI (Globus Command Line Interface)<\/span><\/h3>\n

The Globus CLI is a Python-based tool for interacting with Globus services from a terminal, ideal for scripting and automation. It allows users to manage file transfers, collections, and tasks. Globus CLI has been installed under the module python\/3.12.5<\/code>.<\/p>\n

Authentication<\/span><\/h4>\n

Authenticate to access Globus services.<\/p>\n

\n
globus login\r\n<\/code><\/pre>\n<\/blockquote>\n
This generates a URL. Copy it to a browser, log in with your mssm.edu credentials, and consent to CLI access. Paste the resulting authorization code back into the terminal.<\/p>\n
Use globus whoami<\/code> to verify your identity.<\/p>\n
Log out with globus logout<\/code> when done.<\/p>\n
Locating Minerva Collections<\/span><\/h4>\n
Search for Minerva collections.[\/et_pb_text][et_pb_image src=”https:\/\/scpublic.dmz.hpc.mssm.edu\/HPC\/globus\/globus_cli_search_collection.png” align=”center” _builder_version=”4.16″ _module_preset=”default” width=”80%” max_width=”80%” module_alignment=”center” custom_margin=”10px||20px||false|false” custom_padding=”||||false|false” global_colors_info=”{}”][\/et_pb_image][et_pb_text _builder_version=”4.16″ _module_preset=”default” global_colors_info=”{}”]<\/p>\n
In the provided Globus endpoint search results for “Minerva Arion”, the UUID refers to the ID column, which uniquely identifies the endpoint. In this case, the UUID is:<\/p>\n
Save collection Universally Unique Identifiers (UUIDs) as environment variables for ease.<\/p>\n
6621ca70-103f-4670-a5a7-a7d74d7efbb7<\/code><\/p>\n
\n
export ENDPOINT1=uuid1\r\nexport ENDPOINT2=uuid2\r\n<\/code><\/pre>\n<\/blockquote>\n
View directory contents on a collection<\/p>\n
\n
globus ls $ENDPOINT1:\/path\/to\/directory\r\n<\/code><\/pre>\n<\/blockquote>\n
Create a directory.<\/p>\n
\n
globus mkdir $ENDPOINT1:\/path\/to\/new_directory<\/code><\/pre>\n<\/blockquote>\n
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Data Transfer<\/span><\/h4>\n
Transfer files or directories between collections.<\/p>\n
\n
globus transfer $ENDPOINT1:\/path\/to\/source $ENDPOINT2:\/path\/to\/destination --recursive\r\n<\/code><\/pre>\n<\/blockquote>\n
Use --recursive<\/code> for directories, --preserve-mtime<\/code> to maintain timestamps.
\nTransfer multiple files using a text file.<\/p>\n
\n
echo \"\/source\/file1.txt \/dest\/file1.txt\" > batch.txt\r\necho \"\/source\/file2.txt \/dest\/file2.txt\" >> batch.txt\r\nglobus transfer $ENDPOINT1 $ENDPOINT2 --batch batch.txt\r\nTask ID: abc12345-6789-0123-4567-890123456789\r\n<\/code><\/pre>\n<\/blockquote>\n
Here, abc12345-6789-0123-4567-890123456789<\/code> is the <task_id><\/code>.<\/p>\n
Check transfer status.<\/p>\n
\n
globus task show <task_id>\r\n<\/code><\/pre>\n<\/blockquote>\n
For more information on Globus CLI, please review the official documentation https:\/\/docs.globus.org\/cli\/<\/a>.[\/et_pb_text][et_pb_text _builder_version=”4.16″ _module_preset=”default” custom_margin=”20px||40px||false|false” global_colors_info=”{}”]<\/p>\n
Globus API (Application Programming Interface)<\/span><\/h4>\n
The Globus API enables programmatic access to Globus services, ideal for integrating data transfer into custom workflows or applications. It uses RESTful endpoints and OAuth 2.0 for authentication.<\/p>\n
For detailed information on the use of Globus API, please review the official documentation https:\/\/docs.globus.org\/api\/<\/a>.<\/p>\n
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Globus Transfer Protocols and HTTPS Server-Side Size Limit<\/h4>\n
Globus utilizes GridFTP for high-performance and reliable data transfers between endpoints. GridFTP is an extension of the standard FTP protocol optimized for high-bandwidth, wide-area networks, providing features like fault recovery and automated performance tuning.<\/p>\n
In addition to GridFTP, Globus also supports:<\/p>\n