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Data Transfer Services

Data Transfer Overview

Transferring data in and out of CHPC resources is a critical portion of many science workflows.  Science workflows may transfer a few small text files between collaborators or sites, or may transfer multiple tera or petabytes of data.  CHPC offers a number of options exist for moving data to and from CHPC storage resources.  In some cases, the data may not need to be moved, as there are options to mount some CHPC file systems from local resources. On this webpage, a description and usage information for four common scenarios is provided:

A good resource for information on data transfer considerations is the ESnet Faster Data site.  Specifically, for setting expectations regarding transfer times, see the page "expected time to transfer data".  For understanding the impacts of dropped packets on network protocols and the corresponding impacts to large science transfers, see the page regarding "tcp for long range data transfers".

Direct mounts of CHPC file systems

Native mounts

NOTE: Direct mounts are NOT allowed for the CHPC PE fileserver(s), e.g., mammoth. sshfs can be used instead.

For usage situations where you do not need a second copy on a local machine, but instead only need to access a file, you can do so by having the CHPC file system in which the file is located mounted on your local machine. CHPC allows mounts of home directories as well as group owned file systems on local machines. In addition we allow mounts of other group owned file systems; however, we do not allow mounts of the general CHPC scratch file systems such as /scratch/kingspeak/serial and /scratch/general/lustre. If the local machine is off campus, you must access via a VPN. Below is information on how to do the mounts for home and group spaces on Windows, Mac and Linux systems. Note that there is also a short training video that covers this topic. In all of the following you must replace <uNID>  with your unid. 

  • For home directories:  The information needed to mount your  home directory space exists in the Account Creation Notification email sent to new users.  Alternately, you can also get this information when on a CHPC resources, by issuing a df or df | grep <uNID> command. As an example if the df command returns  cottonwood-vg2-1-lv1.chpc.utah.edu:/uufs/cottonwood/common/cottonwood-vg2-1-lv1/XX/<uNID> , then:
    • On Windows, you need to map a network drive using the path:  \\cottonwood-vg2-1-lv1.chpc.utah.edu\XX-home\<uNID> .  NOTE - when doing the mapping, your username is ad\<uNID>.
    • On a MAC:  smb://ad;<uNID>@cottonwood-vg2-1-lv1.chpc.utah.edu/XX-home/<uNID> 
    • On Linux: If you have root, you cancifs mountCHPC file spaces by (you will be prompted for your password): 

      mount.cifs //cottonwood-vg2-1-lv1.chpc.utah.edu/XX-home/<uNID>  /mnt -o user=<uNID>

  • For group directories:  When the PI obtains group space, CHPC provides the information on mounting and using the group spaces.  A user in a particular group can also get this information by connecting to an interactive node via ssh, and then issuing acd to the group space followed by  df -h | grep -B 1 groupspacename .  As an example, for a space called name-group1, if the df command gives cottonwood-vg1-3-lv1.chpc.utah.edu:/uufs/cottonwood/common/cottonwood-vg1-3-lv1/name then:
    • On Windows, you need to map a network drive using the path:  \\cottonwood-vg1-3-lv1.chpc.utah.edu\name-group1. 
    • On a MAC:  smb://ad;<uNID>@cottonwood-vg1-3-lv1.chpc.utah.edu/name-group1 
    • On Linux: If you have root, you can cifs mount  CHPC  file spaces by (you will be promted for your password): 

      mount.cifs //cottonwood-vg1-3-lv1.chpc.utah.edu/name-group1  /mnt -o user=<uNID>

Mounting with SSHFS

NOTE 18 April 2019- we are seeing issues with SSHFS connections to the  CHPC PE and general file system mounts leading to AD lockouts. We continue to explore to see if there is a workaround or a fix.  If you are seeing AD lock outs, that is you are unable to connect to the PE or general resources, please determine if any of your devices are using SSHFS. If you do, remove the SSHFS connection and try logging in again. ****

SSHFS allows to mount a remote file system using sftp - a secure file transfer protocol. This is equivalent to terminal access with ssh.

sshfs on Linux

To use sshfs on Linux, one needs to install the sshfs package and create a mount point. The installation of the sshfs package requires root priviledges, but the rest can be done as an user, e.g. on CentOS:
sudo yum install fuse-sshfs
mkdir $HOME/HIPAA

 This then follows by mounting the remote file server, e.g. for CHPC's PE home directory:
sshfs uNID@redwood1.chpc.utah.edu:/uufs/chpc.utah.edu/common/HIPAA/uNID $HOME/HIPAA

Unmounting is achieved by:
fusermount -u $HOME/HIPAA

sshfs on Windows

On Windows the situation is not that simple, as there are several different sshfs clients which vary in their stability. Only the SFTP Net Drive seems to support 2 factor authentication needed for the Protected Environment

In the general environment, we have had success with two sshfs clients which seem to be actively developed:

  • SFTP Net Drive - this is a simple install and running the program provides a dialog where one enters the machine to sshfs to (e.g. kingspeak1.chpc.utah.edu). Disconnect by clicking the Disconnect button in the program's dialog window.
    • For PE, in the connection dialog, choose AuthenticationKeyboard-interactive, and Serverredwood1.chpc.utah.edu. Then push connect. At the first password prompt enter your password, at the second prompt enter 1, which will push a 2-factor authentication request to your phone, OK that and the PE home directory should get mounted.
  • SSHFS-Win - to install and use this program do the following:
    • Install the latest stable version of WinFSP
    • Install the latest stable version of SSHFS-Win
    • Open File Explorer, right click on This PC, choose Map Network Drive, enter drive letter and uNID@kingspeak1.chpc.utah.edu. Windows will ask for your CHPC password and your CHPC home directory will appear as aa drive letter of your choice.
    • To disconnect, right click on that drive letter and choose Disconnect.

Local authenticated transfers of small data sets

In some scenarios, a research workflow requires the movement of a few small input files to a computational cluster and/or a few small output files back to a local desktop for storage, final reporting and/or analysis.   For this case, CHPC suggests two options:

  • the use of simple graphical tools to move data to/from a local machine.  Examples are WinSCP on Windows machines, CyberDuck on Macs. In these cases you can "drag and drop" files from one system to the other.
  • the use of Linux commands and tools (scp, rsnyc over ssh, sftp, wget, curl are examples) on CHPC interactive nodes or on the specialized Data Transfer Nodes (DTNs).  Note the DTN usage is described in the next section. Detailed information of the use of these commands can readily be obtained either from the man pages (links above) or via a web search.

Optimized Wide Area Network (WAN) authenticated transfers for large datasets

For science workflows that transfer very large files and/or very large data sets between national labs, industry partners, or peer institutions, users require more advanced parallel transfer tools running on tuned endpoint devices such as Data Transfer Nodes (DTNs).  CHPC supports various parallel transfer tools that support the known science workflows at the University of Utah.  If a research group requires the support of an additional transfer tool, the group may request it through helpdesk@chpc.utah.edu.  CHPC supports these tools on several tuned and dedicated Data Transfer Nodes.

Data Transfer Nodes

Network traffic from most systems located at CHPC and at other locations on campus has traditionally passed through the campus firewall when communicating  with resources off campus. For many small data transfer usage cases, this traffic flow is acceptable.  However, large research computing workflows require more bandwidth requirements and more connections/sessions than the campus firewall can reasonably handle well.  These characteristics of research computing workflows can easily overwhelm the capacity of the campus firewall, impacting much of the day to day usage for the rest of campus.  To help address these research computing workflow needs, the campus has created a Science DMZ which is a  different network segment with different security approaches.  This network segment allows for transfers with specific high performance, low latency, and other special network and security characteristics.   CHPC offers a number of dedicated Data Transfer Nodes (DTNs) that utilize the Science DMZ for data transfers.  For more information regarding the specifics of a Data Transfer Node, see "What makes a Data Transfer Node?".

The general environment  DTNs are:

  • dtn01-dmz.chpc.utah.edu (connected at 40gbs)
  • dtn03.chpc.utah.edu (connected at 10gbs)
  • dtn04-dmz.chpc.utah.edu (connected at 10gbs)
  • airplane01-dmz.chpc.utah.edu (connected at 40gbs)
  • airplane02-dmz.chpc.utah.edu (connected at 40gbs)
  • airplane03-dmz.chpc.utah.edu (connected at 40gbs)
  • airplane04-dmz.chpc.utah.edu (connected at 40gbs)

All CHPC users are able to utilize these DTNs and leverage all the parallel transfer tools that CHPC supports.  The airplane DTNs operate individually, and together as a Globus Endpoint with Concurrent machines for moving large data sets with lots of files. 

CHPC also supports additional specialized  tools for moving data to/from cloud storage.   Some of these tools are specific to a single cloud storage provider (such as s3cmd for Amazon cloud services), whereas others such as rclone work with different cloud storage providers.

CHPC also supports a number of group owned DTNs.  If you need any information about an existing group owned DTN or are interested in having a group dedicated DTN, please contact us. 

NEW -- 10 May 2018:  We now have a set of DTNs in the protected environment:

  • pe-dtn01.chpc.utah.edu
  • pe-dtn02.chpc.utah.edu

You can use one of the above or use pe-dtn.chpc.utah.edu and it it will round-robin between the two servers.  These are currently connected at 40gbs. Globus is now an option for data transfers in the PE.  See the Globus page referenced below for details.

 

Parallel Transfer Tools

There are a number of options available to use for large scale data transfer.  In the following we list ones that we have installed on CHPC resources. See the application database for more information on CHPC installations of these tools.  These can be used on the Data Transfer Nodes mentioned in the above section (recommended for any large file transfers), or from the other CHPC maintained resources that have access to the CHPC application.  

RClone    (Recommended)

 Rclone is a command-line program that supports  file transfers and syncing of files between local storage and Google Drive as well as a number of other storage services, including Dropbox and Swift/S3-based services. Rclone offers options to optimize a transfer and reach higher transfer speeds than other common transfer tools such as scp and rsync. For more information on using rclone as well as configuring it for both transferring data to google drive storage and to the CHPC archive storage, see the CHPC Rclone Software Documentation page.

Globus    (Recommended)

The Globus service is comprised of a set of tools developed to facilitate parallel, load-balanced, fault tolerant data transfers. There are a few steps involved in getting set up to use this service at CHPC, which are detailed on the Globus Software Documentation page.   For further information please visit: https://www.globus.org/quickstart 

FDT - Fast Data Transfer

FDT, Fast Data Transport, is a Java based file transfer application.  CHPC has  an installation that is located at /uufs/chpc.utah.edu/sys/pkg/fdt/0.9.20.  FDT can be used in three modes: server, client and SCP.

  •  In Server mode the FDT will start listening for incoming client connections. The server may or may not stop after the last client finishes the transfer.
  • In Client mode the client will connect to the specified host, where an FDT Server is expected to be running. The client can either read or write file from/to the server.
  • In the SCP (Secure Copy) mode the local FDT instance will use SSH to start/stop the FDT server and/or client.  The security is based on ssh credentials. The server started in this mode will accept connections ONLY from the "SCP" client.

To use: java -jar /uufs/chpc.utah.edu/sys/pkg/fdt/0.9.20/fdt.jar --help or visit the FDT site.

BBCP 

BBCP is a point-to-point network file copy application developed at SLAC National Accelerator Laboratory that allows for sending data in multiple simultaneous streams, developed for the BABAR is a particle physics experiment  Complete documentation on bbcp usage can be found at BBCP website.

To use: /uufs/chpc.utah.edu/sys/pkg/bbcp/std/bin/bbcp --help  or visit the BBCP site.

Aspera

Aspera is IBM's high-performance file transfer software which allows for the transfer large files and data sets with predictable, reliable and secure delivery regardless of file size or transfer distance from a location that has the aspera transfer server running.  The NCBI recommend the use of aspera for transfer of data sets from their site.  The command line client is installed on CHPC at /uufs/chpc.utah.edu/sys/installdir/aspera/3.6.1/connect/bin.

To use the command line client:

   module load aspera/3.6.1

   ascp --help

See the CHPC Aspera software page for additional information. 

The aspera transfer guid via NCBI can be found at https://www.ncbi.nlm.nih.gov/books/NBK242625/

The currently up-to-date documentation for ascp can be found at http://downloads.asperasoft.com/en/documentation/8

fpsync

Fpsync, part of the fpart package, is a shell script that wraps fpart and rsync to launch multiple rsyncs in parallel

To use:

   module load fpsync 

   fpsync -h 

 

NOTE: Large transfers are very dependent on the characteristics of the resources on both ends of the transfer.  If you need assistance in initiating, monitoring, or troubleshooting large transfers, you can reach out to CHPC via helpdesk@chpc.utah.edu.

Temporary Guest Transfer Service

CHPC provides a mechanism for our users to transfer files to and/or from individuals without CHPC accounts. This service is called guest-transfer.

What is it for?

  • At times, CHPC users need to transfer files to or from individuals that don't have CHPC accounts. These files are often quite large (many gigabytes), and thus unsuitable for other transport mechanisms (email, DVD).
  • These file transfers often need to happen with little or no warning. They may also need to occur outside CHPC's support hours. Thus, the guest-transfer service must function without intervention or assistance from CHPC staff.

What is it not for?

  • The guest transfer service is not for repeated events.
  • The guest transfer service is not for long-term data storage.
  • The guest transfer service is not for restricted (PHI/HIPAA/HITECH/FERPA) or sensitive data.
  • The guest transfer service is not for huge data transfers (it's currently restricted to approximately 5 terabytes).

How do I get a guest account?

  • When you need to use the guest transfer service, visit  https://guest-transfer.chpc.utah.edu/ and fill out the form. This form creates a guest transfer account. You then gives the guest account username and password to your colleague. You and your colleague can now share files.

How do I use the service?

  • Once you have created a guest-transfer account and given it to your colleague, you and he copy your files to guest-transfer.chpc.utah.edu with your scp/sftp client (scp, sftp, WinSCP, etc).

Things to remember:

  • The process is completely automatic. You fill out the form, it immediately gives you a guest account.
  • Only CHPC users can create accounts.
  • The person who creates the guest account is responsible for all activity of the guest account.
  • This guest account is only usable for the guest transfer service. It provides no access to any other CHPC or University resources.
  • Files are transferred via scp/sftp. Interactive logins are disabled.
  • Files are automatically removed after 90 days (based on last-access time).
  • Files in the guest-transfer service can be read or changed by any other user.
  • Consider using encryption to protect and verify your files.
  • DO NOT USE THIS SERVICE FOR SENSITIVE OR RESTRICTED DATA!

 

Last Updated: 9/25/19