The Open Enclave provides several ways for transferring files to/from the NFS home directories, NFS project directories, Lustre project directories, and Lustre scratch directories. DTNs (Data Transfer Nodes) furnish this capability. At the time of this writing, there are four DTNs available to Open Enclave users. Table 1.1 shows these nodes.
|Data Transfer Node|
These DTNs are setup for NetID authentication, Duo TFA, and authentication through an InCommon Credential so users can login to this node and perform data transfer functions.
To connect to these DTNs, use ssh in a terminal. More information on ssh usage can be found in the Access and Login document. Replace the hostname of the login node with the hostname of the DTN to which you wish to connect, then authenticate with your UT NetID, password, and Duo TFA.
The Open Enclave supports several data transfer protocols including SCP, SFTP, GSISCP, and Globus. SCP and SFTP are both ssh utilities available for transferring files but perform slower than Globus. At the time of this writing, Globus offers the fastest data transfers on the Open Enclave. Still, SCP and SFTP are useful for small transfers. GSISCP is used for unattended data transfers.
SCP and SFTP are both ssh utilities available for transferring files on the Open Enclave. However, they perform slower than Globus. At the time of this writing, Globus offers the fastest data transfers on the Open Enclave. Still, SCP and SFTP are useful for quick, small transfers. For larger file transfers, please use Globus.
SCP and SFTP are available to Linux and MacOS systems by default. Windows 10 users with the most recent updates can use these utilities within Command Prompt or PowerShell. Windows 7 and 8 users must use a third-party utility to use SCP and SFTP. For more information on ssh in Windows, see the Access and Login document. For Windows 7 and 8 users, the third-party utilities FileZilla and WinSCP are reviewed later in this document.
The general syntax of SCP is given below. In general, SCP is useful when transferring a file on your system to the Open Enclave. The <source> argument is the pathname of the file on your system that you wish to copy. The <destination> (in this case, datamover1) argument is the hostname of the datamover you wish to use. Additionally, the <directory> argument specifies the absolute pathname within the destination to place the file.
scp <source> <NetID>@datamover1.acf.utk.edu:<directory>
If you wanted to copy a file from your system and place it on the ACF, you could use
For SFTP, you specify the hostname of the system to which you intend to connect. For example, to securely transfer files between your local system and the Open Enclave, use the syntax below in a terminal on your local system. Ensure that you enter SFTP from the directory that contains the file(s) you wish to copy to the Open Enclave. You can use the pwd command to determine your current directory before entering SFTP.
Once you authenticate with your UT NetID, password, and Duo TFA, you will enter SFTP’s interactive mode. Use the
put <file> command to upload a file to the Open Enclave. For example, to upload a file named JobScript.sh to the Open Enclave from your local machine, use
put JobScript.sh. This syntax assumes that the JobScript.sh file is in the directory from which you entered SFTP.
To retrieve files from the Open Enclave, use the
get <file> command. To download a file named ResearchResults.txt from the Open Enclave to your local machine, use
get ResearchResults.txt. SFTP will place the file in the directory from which you entered the utility. To change directories on the Open Enclave, use the
cd <directory> command. Use the
lcd <directory> command to change the directory on your local system. Once you are done with SFTP, use the
exit commands to exit it. Other commands are available with the SFTP utility. Type
help within SFTP to read more about them.
The Globus web interface allows you to conveniently perform data transfers to and from Open Enclave resources. At the time of this writing, Globus is the fastest and most efficient data transfer method available on the Open Enclave. Before you can use Globus, you must create an InCommon Credential and associate it with your account. To perform this task, please consult the User Portal documentation. After you associate your InCommon Credential with your account, continue through this document to use Globus. You should also review the official Globus documentation for more information on how to use the tool.
Credential information is updated on the datamovers every hour. If you are unable to use Globus, please wait approximately an hour for the datamovers to obtain your information. Generally, if you see your InCommon credential appear in the User Portal, you should be able to use Globus.
To access the Globus interface in your browser, navigate to the Globus website. Login using the existing organizational login option. Verify that the University of Tennessee is selected, then select “Continue.” Authenticate with your UT NetID, password, and Duo TFA. You will then see the interface depicted in Figure 3.1. If you experience issues logging in, verify that your InCommon credential was configured per the steps given in the Configuring your InCommon Credential section.
Before you can initiate file transfers between your local machine and the Open Enclave, you must configure endpoints. One endpoint will reference your local system while the other will reference one of the Open Enclave DTNs. Further instructions on these endpoints will be provided below.
To configure the endpoints in the Globus interface, select the “Endpoints” tab on the left-side of the page. You will then see a page similar to Figure 3.2. At the top-right of the page, select “Create new endpoint.” On the endpoint type selection page, choose “Globus Connect Personal.”
On the next page, name the endpoint. The name you choose is unimportant; however, it should be something memorable. After you name the endpoint, generate a setup key for the Globus Connect Personal client software. The option to generate the key is listed under Step 2 in Figure 3.3. Copy this key. Finally, download and install the Globus Connect Personal client software. When prompted, enter the setup key you copied to configure your local machine as an endpoint. Refer to Figure 3.3 for a screenshot of the endpoint creation page.
Once you configure your local machine as a Globus endpoint, return to the “File Manager” tab on the left-side of the page. Make sure you select the double panels option in the top-right of the page (Figure 3.9 highlights this option). This will display your local machine’s filesystem in addition to the datamover’s. Once both panels are displayed, click on “Collection” in the left panel. Type the name of your endpoint in the search bar or find it under “My Collections.”
After your endpoint has been selected, you will return to the File Manager. In the right panel, click on “Collection.” Search for one of the four Open Enclave datamovers. The hostnames of these DTNs are given below.
Once both endpoints are configured, you can transfer data between the two. You can select individual files and directories for these transfers. When you select the data you wish to transfer, press the “Start” button below the endpoint from which you will transfer data. Additionally, you can navigate throughout the filesystem hierarchy in either endpoint using the Globus interface. Other options are available for your transfers, but they are usually unnecessary for most transfers. Figure 3.4 shows what the Globus interface should look like when both endpoints are selected.
Unattended data transfers are possible on the Open Enclave with gsissh and its associated tools. You may find these transfers useful in situations where massive amounts of data must be transferred overnight or a job requires input or output data without your intervention. To use gsissh, follow the steps in the User Portal document to create and associate an InCommon credential with your account, then navigate to the CILogon website and select the University of Tennessee as your identity provider. After you authenticate to the UT CAS, follow these steps to supply a password for your credential and upload it to the Open Enclave.
mkdir ~/.globusto create the directory. Execute
cd .globusto enter this directory.
wget <copied-url>where <copied-url> is the download link to your InCommon Credential. You should be able to paste the link with the key combination Ctrl + V on Windows and Linux systems or Command + V on MacOS systems. Verify that you are in the .globus directory with pwd before you execute wget. Figure 4.3 shows the output of a successful wget download.
[user-x@acf-login8 .globus]$ wget https://polo1.cilogon.org/pkcs12/36E8DB8887F08ACC5/usercred.p12 --2020-01-16 16:08:58-- https://polo1.cilogon.org/pkcs12/36E8DB8887F08ACC5/usercred.p12 Resolving polo1.cilogon.org (polo1.cilogon.org)... 220.127.116.11 Connecting to polo1.cilogon.org (polo1.cilogon.org)|18.104.22.168|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 2837 (2.8K) [application/x-pkcs12] Saving to: ‘usercred.p12’ 100%[==========================================>] 2,837 --.-K/s in 0s 2020-01-16 16:08:58 (156 MB/s) - ‘usercred.p12’ saved [2837/2837]
chmod 600 usercred.p12to change the permissions of the InCommon Credential file. Execute
ls -lon the .globus directory to verify that the usercred.p12 file has read and write permissions for the user owner. Figure 4.4 shows the permissions that should apply to the credential file.
[user-x@acf-login8 .globus]$ ls -l total 4 -rw-------. 1 user-x testgrp 2837 Jan 16 16:08 usercred.p12
After you have successfully downloaded and modified the usercred.p12 file, execute
grid-proxy-init to use the InCommon Credential for authentication. Enter the password you set in the first step of the credential configuration process. Figure 4.5 shows what should appear if the certificate initialization was successful.
[user-x@acf-login8 ~]$ grid-proxy-init Enter GRID pass phrase for this identity: Your identity: /DC=org/DC=cilogon/C=US/O=University of Tennessee/CN=User X A12345678 Creating proxy ...................... Done Your proxy is valid until: Fri Jan 17 04:30:39 2020
Figure 4.5 – Using grid-proxy-init to Initialize a Credential
In some cases, you may require the credential to be valid for an extended period. Execute
grid-proxy-init -valid hh:mm to specify the amount of time the credential should remain valid. For example, to make the credential last for three days, execute
grid-proxy-init -valid 72:00. If successful, the output of the certificate initialization will show the date when the certificate will expire. In Figure 4.5, the certificate expires twelve hours from the time it was initialized. This is the default expiration timer.
Once your credential is initialized, gsiscp will work without prompting you for a password or Duo TFA. You will receive a password prompt, but gsissh will automatically override the prompt to allow the transfer. The syntax for gsiscp is
gsiscp <source> <destination:directory>. For instance, to transfer a gzipped tar archive named MedJobResults.tar.gz in your Open Enclave home directory to a remote system, execute
gsiscp ~/MedJobResults.tar.gz remotestorage.local:~/Documents. To transfer a zip archive named fluid_dynamics_results.zip from your home directory on the Open Enclave to a remote datamover, execute
gsiscp ~/fluid_dynamics_results.zip remote_datamover1:~/
FileZilla will work with file transfers to the Open Enclave. Please only use the DTNs listed in Table 1.1 at the beginning of this document.
To use the FileZilla client with your NetID, password, and Duo TFA, follow these steps.
WinSCP can perform file transfers to and from the Open Enclave. Please use the DTNs listed in Table 1.1 at the beginning of this document.
To use the WinSCP client with your NetID, password, and Duo TFA, follow these steps.
Before you initiate any data transfers from the Open Enclave to another storage resource, consider preparing the data you wish to transfer by archiving and compressing it. When you archive data, several files and directories can be added to the same location. When you compress data, you reduce its total size. Both methods reduce the total amount of data that must be sent across the network and make it easier for you to organize the data you wish to transfer. At the time of this writing, the tar and zip utilities are the best methods for data archiving and compression for Open Enclave users across Linux, MacOS, and Windows.
The tar (tape archiver) utility uses simple command syntax and allows large amounts of data to be aggregated into the same archive. Linux, MacOS, and updated Windows 10 systems can use tar. Older Windows systems will be limited to the zip utility.
To create a tar archive, execute
tar czvf <archive-name> <dir-to-archive>. Replace the <archive-name> argument with the name of the new archive. Be sure to follow the name with the .tar.gz extension, as in my_archive.tar.gz. Replace the <dir-to-archive> argument with the directory you wish to place within the archive. If the directory you intend to archive is not within your working directory, specify the relative or absolute path to it. By default, tar will recursively place the directory and its contents into the new archive. Figure 2.1 shows the successful creation of a tar archive.
[user@acf-login5 ~]$ tar czvf new_archive.tar.gz Documents Documents/ Documents/IntroUnix.pdf Documents/JobSubData.zip Documents/MATLAB/ Documents/Scripts.zip Documents/PyLists.py
Figure 2.1 – Creating a tar Archive
After the archive is created, execute
ls -l to verify that the archive exists. You can view its contents with the
tar tvf <archive-name> command. You may then transfer the archive using one of the data transfer methods described in this document. In general, Globus is the best method. Please refer to the Globus section to learn how to configure it for your system. On the remote system, execute
tar xvf <archive-name> to extract the contents of the archive. The files will be extracted into your working directory.
On older Windows systems, the zip utility should be used to archive and compress your data on the Open Enclave.
To create a zip archive on the Open Enclave, execute
zip -r <archive-name>.zip <dir-to-archive>. Be sure that the directory you wish to archive is in your working directory. Otherwise, specify the relative or absolute path to the directory you wish to archive. Replace the <archive-name> argument with the name of the new zip archive. You may or may not include the .zip file extension to the archive’s name; if you do not, the zip utility will add it automatically. Replace the <dir-to-archive> argument with the directory you wish to place in the zip archive. The -r option ensures that the directory and its contents are archived and compressed. Figure 2.2 shows the successful creation of a zip archive.
[user@acf-login5 ~]$ zip -r Documents Documents adding: Documents/ (stored 0%) adding: Documents/IntroUnix.pdf (deflated 4%) adding: Documents/MATLAB/ (stored 0%) adding: Documents/PyLists.py (deflated 61%)
Figure 2.2 – Creating a zip Archive
After the zip archive has been created, execute
ls -l in the directory from which you created it to ensure the archive exists. It will appear with the name you gave to the archive followed by the .zip extension.
With the zip archive created and verified, transfer it to your system using one of the data transfer methods described in this document. In most cases, Globus is the most convenient method. Please refer to the Globus section to learn how to configure it for use on your system. Once you transfer the zip archive to your system, open the File Explorer and navigate to the directory in which you placed the archive. Right-click on the archive and select the “Extract All…” option in the submenu. Figure 2.3 shows where to locate this option. Specify the directory in which the contents should be extracted, then select “Extract.” You may then open the archive and peruse its contents.