Difference between revisions of "Transfer Data"

Latest revision as of 23:13, 29 March 2024

Overview

This document describes transferring data between a local computer (client) and HiPerGator (HPG). For file sharing on the cluster see Sharing Files

Note: ResVault users: find more info in this page

Tools

There are a variety of command-line, GUI, and even web-based tools available for transferring data to or from HiPerGator. Command-line tools include, for example, 'cp, mv, scp, rsync, sftp, wget, curl, or ncftp (from the ncftp environment module]'. GUI tools like Cyberduck, WinSCP, BitVise SFTP and similar tools can be used on your local computer. Globus data transfer tool is available via a web interface in addition to command-line and GUI versions that can be run on your local computer. Please visit the HPG how-to video series on Data Transfer for more details.

Transferring Data within HiPerGator

Login servers on HiPergator (hpg.rc.ufl.edu) can be used for rsync, copying files with cp or mv depending on the group configuration and permissions or filesystem ACLs (extended permissions). There is a shared directory at /blue/GROUP/share for groups that prefer to share their data between group members. See also: Shared Work and Storage Management, Sharing Within A Cluster

Transferring Data Outside of HiPerGator

Between a local computer and HiPerGator

Open OnDemand

Open OnDemand has file management tools to transfer files (less than 20Gb at the time). See Open OnDemand for details

Globus

If your data files are large (hundreds of megabytes or gigabytes) then try Globus first.

Samba

Samba is a Linux server that provides remote filesystem access using SMB/CIFS protocol. See Samba Main Wiki Page for more info.

SFTP/Rsync

For smaller file sizes, or if Globus is not an option, use SFTP/rsync/scp by connecting to the 'hpg.rc.ufl.edu' or 'sftp.rc.ufl.edu'. Set port to 22 if you have to specify it. Use your gatorlink credentials to connect. Make sure MFA (multi-factor authentication) is taken into account to avoid having to go through MFA for every file transferred. You can also use terminal interfaces like BitVise, which include an GUI SFTP function embedded.

Note: If you are using Cyberduck on a MacOS computer and notice that it is using the old password resulting in a security lockout uncheck 'Use Keychain' in 'Preferences > General'.

Rclone

Rclone is a command-line data transfer tool that support transferring data from or to dozens of cloud storage providers and remote locations. Please see https://rclone.org/docs/ for information on a specific storage provider.

JupyterHub

The easiest way to upload data using JypyterHub is by using the Upload Files button included in the File Browser (Ctrl+Shift+F) menu.

From HiPerGator to a remote system/site

If you are logged into HiPerGator and need to transfer data to or from a remote system or a site use the login nodes. Transfers can also be made from within developmental sessions. You can use ftp (lftp command), sftp, scp, rsync, or Globus to transfer data out.

Downloading Data from an External Server or Third-Party Website

Terminal: wget or curl

In most file managing websites, the "Download" buttons have the option to right-click and select an option similar to "Copy link address".

Once the link address is copied in the clipboard, you can paste it in your HPG terminal following your "wget" or "curl" commands, such as: $ wget https://github.com/author/software/main.zip"

Internet Browser from HPG Host

Another option is to use the Firefox or Chrome browsers via Open OnDemand or an X11-based SSH session.

Start a X11 forwading-enabled SSH session or a terminal on a HiPerGator Desktop session on Open OnDemand:

1. From a HPG node, launch the module ubuntu, which contains a version of the Google Chrome browser.

   - $ module load ubuntu
   - $ chrome (or firefox)
   The Internet browser should launch.

2. Navigate and login to the third-party service, such as Dropbox or Google Drive using your gatorlink account.

3. Edit the browser's download settings to change the Download location (path) to your preferred /blue directory.

4. Navigate to the target directory in your Drive account using the browser and select files or folders to download.

  The files should download directly to your selected /blue path.

Download data to personal computer first

Alternatively, users can download files to their local computers and upload them into HPG using one of the methods described in the "Between a local computer and HiPerGator" section above.

Providing access to your data

If you need to share data with another RC user or publicly for collaboration, view instructions at Providing Access To Data

@@ Line 1: / Line 1: @@
-[[Category:How-To]][[Category:Transfer Data]]
+[[Category:Essentials]][[Category:Transfer Data]][[Category:Data]]
+{|align=right
+  |__TOC__
+  |}
 ==Overview==
-This document describes transferring data between a local computer (client) and HiPerGator (HPG).
+This document describes transferring data between a local computer (client) and HiPerGator (HPG). For file sharing on the cluster see [https://help.rc.ufl.edu/doc/Sharing_Files Sharing Files]
-=Tools=
+* Note: ResVault users: [https://help.rc.ufl.edu/doc/How_To_ResVault#How_to_Transfer_Data_from.2Fto_RV find more info in this page]
-There are a variety of command-line, GUI, and even web-based tools available for transferring data to or from HiPerGator. Command-line tools include, for example, 'cp, mv, scp, [[Rsync|rsync]], sftp, wget, curl, or ncftp (from the ncftp environment module]'. GUI tools like Cyberduck, WinSCP, BitVise SFTP and similar tools can be used on your local computer. [[Globus|Globus data transfer tool]] is available via a web interface in addition to command-line and GUI versions that can be run on your local computer.
-=Transfers within HiPerGator=
+==Tools==
-Login servers on HiPergator (hpg.rc.ufl.edu) can be used for [[Rsync|rsync]], copying files with cp or mv depending on the permissions or filesystem ACLs (extended permissions).
+There are a variety of command-line, GUI, and even web-based tools available for transferring data to or from HiPerGator. Command-line tools include, for example, 'cp, mv, scp, [[Rsync|rsync]], sftp, wget, curl, or ncftp (from the ncftp environment module]'. GUI tools like Cyberduck, WinSCP, BitVise SFTP and similar tools can be used on your local computer. [[Globus|Globus data transfer tool]] is available via a web interface in addition to command-line and GUI versions that can be run on your local computer. [https://help.rc.ufl.edu/doc/Training_Videos#data%20transfer Please visit the HPG how-to video series on Data Transfer for more details.]
-==Transfers between a local computer and HiPerGator==
+==Transferring Data within HiPerGator==
-===Globus===
+Login servers on HiPergator (hpg.rc.ufl.edu) can be used for [[Rsync|rsync]], copying files with cp or mv depending on the group configuration and permissions or filesystem ACLs (extended permissions). There is a shared directory at /blue/GROUP/share for groups that prefer to share their data between group members. See also: [https://help.rc.ufl.edu/doc/Storage#Shared_Work_and_Storage_Management Shared Work and Storage Management], [[Sharing Within A Cluster]]
+==Transferring Data Outside of HiPerGator==
+===Between a local computer and HiPerGator===
+====Open OnDemand====
+Open OnDemand has file management tools to transfer files (less than 20Gb at the time). See [https://help.rc.ufl.edu/doc/Open_OnDemand Open OnDemand] for details
+====Globus====
 If your data files are large (hundreds of megabytes or gigabytes) then try [[Globus]] first.
-===SFTP/Rsync===
+====Samba====
-For smaller file sizes, or if Globus is not an option, use SFTP/[[Rsync|rsync]]/scp by connecting to the '<code>hpg.rc.ufl.edu</code>' or '<code>sftp.rc.ufl.edu</code>'. Set port to 22 if you have to specify it. Use your gatorlink credentials to connect. Make sure [[Authentication_With_MFA#Using_MFA_with_GUI_SFTP_Programs|MFA (multi-factor authentication)]] is taken into account to avoid having to go through MFA for every file transferred.
+Samba is a Linux server that provides remote filesystem access using SMB/CIFS protocol. See [https://help.rc.ufl.edu/doc/Samba_Access Samba Main Wiki Page] for more info.
+====SFTP/Rsync====
+For smaller file sizes, or if Globus is not an option, use SFTP/[[Rsync|rsync]]/scp by connecting to the '<code>hpg.rc.ufl.edu</code>' or '<code>sftp.rc.ufl.edu</code>'. Set port to 22 if you have to specify it. Use your gatorlink credentials to connect. Make sure [[Authentication_With_MFA#Using_MFA_with_GUI_SFTP_Programs|MFA (multi-factor authentication)]] is taken into account to avoid having to go through MFA for every file transferred. You can also use terminal interfaces like [https://www.bitvise.com/ BitVise], which include an GUI SFTP function embedded.
 ;Note: If you are using [https://cyberduck.io/ Cyberduck] on a MacOS computer and notice that it is using the old password resulting in a security lockout uncheck 'Use Keychain' in 'Preferences > General'.
-==Transferring data from HiPerGator to a remote system/site==
+====Rclone====
+[[Rclone]] is a command-line data transfer tool that support transferring data from or to dozens of cloud storage providers and remote locations. Please see [https://rclone.org/docs/ https://rclone.org/docs/] for information on a specific storage provider.
+====JupyterHub====
+The easiest way to upload data using JypyterHub is by using the Upload Files button included in the File Browser (Ctrl+Shift+F) menu.<br>
+[[File:Jupyterhub upload.png|frameless]]
+===From HiPerGator to a remote system/site===
 If you are logged into HiPerGator and need to transfer data to or from a remote system or a site use the login nodes. Transfers can also be made from within [[Development_and_Testing|developmental sessions]]. You can use ftp (lftp command), sftp, scp, rsync, or Globus to transfer data out.
+==Downloading Data from an External Server or Third-Party Website==
+====Terminal: wget or curl====
+[[File:Copy Link Address.jpg|thumb]]In most file managing websites, the "Download" buttons have the option to right-click and select an option similar to "Copy link address".
+Once the link address is copied in the clipboard, you can paste it in your HPG terminal following your "wget" or "curl" commands, such as:
+<code>$ wget https://github.com/author/software/main.zip"</code>
+====Internet Browser from HPG Host====
+Another option is to use the Firefox or Chrome browsers via [[Open OnDemand]] or an X11-based SSH session.
+Start a X11 forwading-enabled SSH session or a terminal on a HiPerGator Desktop session on Open OnDemand:
+. From a HPG node, launch the module ubuntu, which contains a version of the Google Chrome browser.
+    - $ module load ubuntu
+    - $ chrome (or firefox)
+    The Internet browser should launch.
+. Navigate and login to the third-party service, such as Dropbox or Google Drive using your gatorlink account.
+. Edit the browser's download settings to change the Download location (path) to your preferred /blue directory.
+. Navigate to the target directory in your Drive account using the browser and select files or folders to download.
+   The files should download directly to your selected /blue path.
+====Download data to personal computer first====
+Alternatively, users can download files to their local computers and upload them into HPG using one of the methods described in the "Between a local computer and HiPerGator" section above.
 ==Providing access to your data==
-===Within HiPerGator===
+If you need to share data with another RC user or publicly for collaboration, view instructions at [[Providing Access To Data]]
-If you need to share data with another RC user there are two common options to select from.
-* First, a [[Globus|Globus Shared Collection]] can be created on any directory you own. Either read, write, or read/write access can be granted to any Globus user and revoked at any time.
-* Second, you can submit a [https://support.rc.ufl.edu support request] to have the receiving user added to your group. You may also have to change permissions on the respective directory tree to make the source directory and the files within readable by the receiving user by running 'chmod g+rx <directory>' command on the minimal set of directories that will allow access to the group starting from the source directory and 'chmod g+r *' inside the source directory to make the files readable by the group.
-* In some cases it is possible to set up a filesystem ACL (access control list) to provide more complicated permission structure for a directory tree or file(s) without changing file ownership or linux permissions. We'd be happy to review your request to see whether setting an ACL may help in a particular case.
-===Outside of HiPerGator===
-If you need to serve data to the outside either publicly or with password protection for collaborations you can:
-* Set up a shared end-point in [[Globus]] as shown above.  Either read, write, or read/write access to the SEP can be granted to any Globus user and revoked at will by you. Note that the data does not necessarily have to be in /blue. Log into [http://globus.org Globus]; go to the 'Groups' menu and select 'Search For Groups'. Search for 'University of Florida Research Computing' and request to be added to the group. Once added, you will be able to install [https://www.globus.org/globus-connect-personal Globus Connect Personal] and create a Personal Shared End-Point (PSEP) on your local computer, which will work the same way a SEP works on HiPerGator giving you the flexibility to transfer data either way with any other Globus user.
-* Submit a [https://support.rc.ufl.edu support request] and we'll help you get set up with serving static data from [https://data.rc.ufl.edu https://data.rc.ufl.edu]
-* If you want to create your own application for data sharing you can purchase a unit service for our PubApps web application infrastructure.