Skip to end of metadata
Go to start of metadata

You are viewing an old version of this content. View the current version.

Compare with Current View Version History

Version 1 Next »

Several methods are available to transfer files into and from TRACE-HPC.
 

Paths for TRACE-HPC file spaces

To copy files into any of your TRACE-HPC spaces, you need to know the path to that space on TRACE-HPC. The start of the full paths for your TRACE-HPC directories are:
Home directory     /jet/home/username
Ocean directory   /ocean/projects/groupname/username
To find your groupname, use the command id -Gn. All of your valid groupnames will be listed. You have an Ocean directory for each grant you have.
 

Transfers into your TRACE-HPC home directory

Your home directory quota is 25GB. More space is available in your $PROJECT file space in Ocean. Exceeding your home directory quota will prevent you from writing more data into your home directory and will adversely impact other operations you might want to perform.
 

Commands to transfer files

You can use rsync, scp, sftp or Globus to copy files to and from TRACE-HPC.

 

rsync

You can use the rsync command to copy files to and from TRACE-HPC. A sample rsync command to copy to a TRACE-HPC directory is
rsync -rltpDvp -e 'ssh -l username' source_directory data.trace-hpc.cmu.edu:target_directory
Substitute your username for 'username'. Make sure you use the correct groupname in your target directory. By default, rsync will not copy older files with the same name in place of newer files in the target directory. It will overwrite older files.
We recommend the rsync options -rltDvp. See the rsync man page for information on these options and other options you might want to use. We also recommend the option
-oMACS=umac-64@openssh.com
If you use this option, your transfer will use a faster data validation algorithm.
You may want to put your rsync command in a loop to insure that it completes. A sample loop is
RC=1
n=0
while [[ $RC -ne 0 && $n -lt 20 ]] do
    rsync source-file target-file
    RC = $?
    let n = n + 1
    sleep 10
done
This loop will try your rsync command 20 times. If it succeeds it will exit. If an rsync invocation is unsuccessful the system will try again and pick up where it left off. It will copy only those files that have not already been transferred. You can put this loop, with your rsync command, into a batch script and run it with sbatch.

scp

To use scp for a file transfer you must specify a source and destination for your transfer. The format for either source or destination is
username@machine-name:path/filename
For transfers involving TRACE-HPC,  username is your TRACE username. The machine-name should be given as data.trace-hpc.cmu.edu. This is the name for a high-speed data connector at TRACE. We recommend using it for all file transfers using scp involving TRACE-HPC. Using it prevents file transfers from disrupting interactive use on TRACE-HPC's login nodes.
File transfers using scp must specify full paths for TRACE-HPC file systems. See Paths for TRACE-HPC file spaces for details.

sftp

To use sftp, first connect to the remote machine:
sftp username@machine-name
When  TRACE-HPC is the remote machine, use your TRACE userid as  username. The TRACE-HPC machine-name should be specified as data.trace-hpc.cmu.edu. This is the name for a high-speed data connector at TRACE.  We recommend using it for all file transfers using sftp involving TRACE-HPC. Using it prevents file transfers from disrupting interactive use on TRACE-HPC's login nodes.
You will be prompted for your password on the remote machine. If TRACE-HPC is the remote machine, enter your TRACE password.
You can then enter sftp subcommands, like put to copy a file from the local system to the remote system, or get to copy a file from the remote system to the local system.
To copy files into TRACE-HPC, you must either cd to the proper directory or use full pathnames in your file transfer commands. See Paths for TRACE-HPC file spaces for details.

Transferring files using Two-Factor Authentication

If you are required to use Two-Factor Authentication (TFA) to access TRACE-HPC's filesystems, you must enroll in TRACE DUO. Once that is complete, use scp or sftp to transfer files to and from TRACE-HPC.
TFA users must use port 2222 and TRACE Portal usernames and passwords, not TRACE usernames and passwords. The machine name for these transfers is data.trace-hpc.cmu.edu.
In the examples below, myfile is the local filename, TRACE-username is your TRACE Portal username and /path/to/file is the full path to the file on a TRACE-HPC filesystem. Note that -P (capital P) is necessary.

scp with TFA

Transfer a file from a local machine to TRACE-HPC:
scp -P 2222 myfile TRACE-username@data.trace-hpc.cmu.edu:/path/to/file
Transfer a file from TRACE-HPC to a local machine:
scp -P 2222 TRACE-username@data.trace-hpc.cmu.edu:/path/to/file myfile
sftp

Interactive sftp with TFA

sftp -P 2222 TRACE-username@data.trace-hpc.cmu.edu
Then use the put command to copy a file from the local machine to TRACE-HPC, or the get command to transfer a file from TRACE-HPC to the local machine.

Graphical SSH client

If you are using a graphical SSH client, configure it to connect to data.trace-hpc.cmu.edu on port 2222/TCP. Login using your TRACE Portal username and password.

 

Globus

Globus can be used for any file transfer to TRACE-HPC. It tracks the progress of the transfer and retries when there is a failure; this makes it especially useful for transfers involving large files or many files.
To use Globus to transfer files you must authenticate either via a Globus account or with InCommon credentials.
To use a Globus account for file transfer, set up a Globus account at the Globus site.
To use InCommon credentials to transfer files to/from TRACE-HPC, you must first provide your CILogin Certificate Subject information to TRACE. Follow these steps:

  1. Find your Certificate Subject string
    1. Navigate your web browser to https://cilogon.org/.
    2. Select your institution from the 'Select an Identity Provider' list.
    3. Click the 'Log On' button.  You will be taken to the web login page for your institution.
    4. Login with your username and password for your institution.
      • If your institution has an additional login requirement (e.g., Duo), authenticate to that as well.
    5. After successfully authenticating to your institution's web login interface, you will be returned to the CILogon webpage.
    6. Click on the Certificate Information drop down link to find the 'Certificate Subject'.
  2. Send your Certificate Subject string to TRACE
    1. In the CILogon webpage, select and copy the Certificate Subject text. Take care to get the entire text string if it is broken up onto multiple lines.
    2. Send email to trace-it-help@andrew.cmu.edu.  Paste your Certificate Subject field into the message, asking that it be mapped to your TRACE username.

Your CILogin Certificate Subject information will be added within one business day, and you will be able to begin transferring files to and from TRACE-HPC.
Globus endpoints
Once you have the proper authentication you can initiate file transfers from the Globus site. A Globus transfer requires a Globus endpoint, a file path and a file name for both the source and destination. The endpoints for TRACE-HPC are:

  • trace#trace-hpc-trace if you are using an TRACE User Portal account for authentication
  • trace#trace-hpc-cilogon if you are using InCommon for authentication

These endpoints are owned by trace@globusid.org. If you use DUO MFA for your TRACE authentication, you do not need to because you cannot use it with Globus. You must always specify a full path for the TRACE-HPC file systems. See Paths for TRACE-HPC file spaces for details.

  • No labels