Instructions for transferring files from pylon2 to pylon5
Pylon2 has been unmounted from the Bridges login nodes. This means that you cannot see or access any pylon2 directory from a login node. You will get a "No such file or directory" error if you try.
You can use the
rsync command or the Globus web application to transfer your files from pylon2 to pylon5. We suggest you use rsync.
Remember to delete your pylon2 files once your transfers have finished.
rsync command can be run on Bridges' compute nodes in an interactive session or a batch job, or by using ssh on one of Bridges' high-speed data transfer nodes. An advantage of
rsync is that if the transfer does not complete, you can rerun the
rsync command, and
rsync will copy only those files which have not already been transferred.
PSC has created a shell script that you can use to move files from pylon2 to pylon5. The shell script can be used in an interactive session or in a batch job.
rsync will overwrite files in the destination directory if a file of the same name with a more recent modified time exists in the source directory. To prevent this, the examples below copy pylon2 files into a new subdirectory on pylon5. Once transferred, please examine the files and move them to the directory where you want them.
In all the examples given here, change groupname, username and new-directory to be your charging group, userid and name of the new subdirectory (if you like) to store the files.
The PSC-provided shell script is /opt/packages/utilities/pylon2to5. It will:
- Copy all files from your pylon2 home directory (/pylon2/groupname/username) to a subdirectory named "from_pylon2" under your pylon5 home directory (/pylon5/groupname/username/from_pylon2)
- Loop until it succeeds for all files or is killed (e.g. due to timeout). This could use a lot of SUs if failures persist.
- Skip copying older files from pylon2 on top of newer files in pylon5 with the same name. This is default rsync behavior.
Start an interactive session, type
To use the PSC-supplied shell script, when your interactive session begins type
If you prefer not to use the PSC-supplied shell script, when your session begins you can use a command like
rsync -av /pylon2/groupname/username/ /pylon5/groupname/username/new-directory
To run the PSC-supplied shell script in a batch job, create a batch script with the following content:
#SBATCH -c 4
#SBATCH -p RM-shared
## newgrp my_other_grant
## The next line runs the shell script
To move files from a grant that is not your default, uncomment the
newgrp command in the script by removing "##" and substitute the correct group name for "my_other_grant".
If you prefer not to use the PSC-supplied shell script, you can create a batch script which runs rsync like the one shown here. Change groupname, username and new-directory to be your charging group, userid and name of the new subdirectory (if you like) to store the files.
#!/bin/bash #SBATCH -p RM-shared rsync -av /pylon2/groupname/username/ /pylon5/groupname/username/new-directory
Submit your batch script by typing (where script-name is the name of your script file)
Data transfer node
Use Bridges' high-speed data transfer nodes to move your files from pylon2 to pylon5. At the Bridges' prompt, type
ssh data.bridges.psc.edu "rsync -av /pylon2/groupname/username/ /pylon5/groupname/username/new-directory"
To use the Globus web application, visit www.globus.org.
- Choose “PSC Bridges with XSEDE Authentication” as each endpoint (you will need to authenticate with your XSEDE login and password).
- For the first path, choose the pylon2 directory that you wish to transfer files from. For example: /pylon2/chargeid/userid
- For the second path, choose the appropriate pylon5 target directory: /pylon5/chargeid/userid
To find your chargeid on Bridges, use the
projects command to see all of the allocations that you have access to.
- At the bottom of the Globus transfer page, choose the Transfer Settings that you wish to use (e.g. “preserve source file modification times”) and transfer your files as you would through any other web application.
There are a variety of file transfer methods available for Bridges:
- scp or sftp
- cp - can be used between Bridges' filesystems, but only if the transfer is under 100MB
If you are required to use Two-factor authentication to access Bridges' filesystems, see Two-factor Authentication for instructions on file transfer.
Paths for Bridges file spaces
For all file transfer methods other than cp, you must always use the full path for your Bridges files. The start of the full paths for your Bridges directories are:
Home directory /home/username
Pylon2 directory /pylon2/groupname/username
Pylon5 directory /pylon5/groupname/username
id -Gn will show all of your valid groupnames. You have a pylon2 and pylon5 directory for each grant you have.
Transfers into your Bridges home directory
Your home directory quota is 10GB, so large files cannot be stored there; they should be copied into one of your pylon file spaces instead. 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.
You can use the rsync command to copy files to and from Bridges. A sample rsync command to copy to a Bridges directory is
rsync -rltpDvp -e 'ssh -l joeuser' source_directory data.bridges.psc.edu:target_directory
Substitute your userid for 'joeuser'. Make sure you use the correct group name 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 you options you might want to use. We also recommend the option
If you use this option your transfer will use a faster data validation algorithm.
You may to 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 ... 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.
Globus can be used for any file transfer to Bridges. 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. This includes transfers between the pylon2 and pylon5 filesystems and file transfers between the Data Supercell and pylon2 or pylon5.
To use Globus to transfer files you must authenticate either via a Globus account or with InCommon credentials.
You can set up a Globus account at the Globus site.
If you wish to use InCommon credentials to transfer files to/from Bridges, you must first provide your CI Login Certificate Subject information to PSC. Follow these steps:
- Find your Certificate Subject string
- Navigate your web browser to https://cilogon.org/.
- Select your institution from the 'Select an Identity Provider' list.
- Click the 'Log On' button. You will be taken to the web login page for your institution.
- 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.
After successfully authenticating to your institution's web login interface, you will be returned to the CILogon webpage. Note the boxed section near the top that lists a field named 'Certificate Subject'.
- Send your Certificate Subject string to PSC
- 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.
- Send email to firstname.lastname@example.org. Paste your Certificate Subject field into the message, asking that it be mapped to your PSC username.
Your CI Login Certificate Subject information will be added within one business day, and you will be able to begin transferring files to and from Bridges.
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 Bridges are:
- psc#bridges-xsede if you are using an XSEDE User Portal account for authentication
- psc#bridges-cilogon if you are using InCommon for authentication
These endpoints are owned by email@example.com. If you use DUO MFA for your XSEDE authentication, you do not need to because you cannot use it with Globus. You must always specify a full path for the Bridges file systems. See Paths for Bridges file spaces for details.
The globus-url-copy command can be used if you have access to Globus client software. Both the
myproxy-logon commands are available on Bridges, and can be used for file transfers internal to the PSC.
globus-url-copy you must have a current user proxy certificate. The command
grid-proxy-info will tell you if you have current user proxy certificate and if so, what the remaining life of your certificate is.
myproxy-logon command to get a valid user proxy certificate if any one of these applies:
- you get an error from the
- you do not have a current user proxy certificate
- the remaining life of your certificate is not sufficient for your planned file transfer
When prompted for your MyProxy passphrase enter your XSEDE Portal password.
globus-url-copy for transfers to a machine you must know the Grid FTP server address. The Grid FTP server address for Bridges is
The use of
globus-url-copy always requires full paths. See Paths for Bridges file spaces for details.
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
For transfers involving Bridges, username is your PSC username. The machine-name should be given as data.bridges.psc.edu. This is the name for a high-speed data connector at PSC. We recommend using it for all file transfers using scp involving Bridges. Using it prevents file transfers from disrupting interactive use on Bridges' login nodes.
File transfers using scp must specify full paths for Bridges file systems. See Paths for Bridges file spaces for details.
To use sftp, first connect to the remote machine:
When Bridges is the remote machine, use your PSC userid as username. The Bridges machine-name should be specified as data.bridges.psc.edu. This is the name for a high-speed data connector at PSC. We recommend using it for all file transfers using sftp involving Bridges. Using it prevents file transfers from disrupting interactive use on Bridges' login nodes.
You will be prompted for your password on the remote machine. If Bridges is the remote machine enter your PSC 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 Bridges you must either
cd to the proper directory or use full pathnames in your file transfer commands. See Paths for Bridges file spaces for details.
If you are required to use two-factor authentication (TFA) to access Bridges' filesystems, you must enroll in XSEDE DUO. Once that is complete, use scp or sftp to transfer files to/from Bridges.
TFA users must use port 2222 and XSEDE Portal usernames and passwords. The machine name for these transfers is data.bridges.psc.edu.
In the examples below, myfile is the local filename, XSEDE-username is your XSEDE Portal username and /path/to/file is the full path to the file on a Bridges filesystem. Note that -P ( capital P) is necessary.
Transfer a file from a local machine to Bridges:
scp -P 2222 myfile XSEDEfirstname.lastname@example.org:/path/to/file
Transfer a file from Bridges to a local machine:
scp -P 2222 XSEDEemail@example.com:/path/to/file myfile
Use sftp interactively:
sftp -P 2222 XSEDEfirstname.lastname@example.org
Then use the
put command to copy a file from the local machine to Bridges, or the
get command to transfer a file from Bridges to the local machine.
Graphical SSH client
If you are using a graphic SSH client, configure it to connect to data.bridges.psc.edu on port 2222/TCP. Login using your XSEDE Portal username and password.
PSC maintains a Web page at http://speedpage.psc.edu that lists average data transfer rates between all XSEDE resources. If your data transfer rates are lower than these average rates or you believe that your file transfer performance is subpar, send email to email@example.com. We will examine approaches for improving your file transfer performance.