Transfer data from source to destination on NYU's high performance computing (HPC) cluster.

nyu_hpc_data_transfer.md

Transfer Data to NYU's HPC 🚀

Scope: Transfer data to NYU's high performance computing (HPC) cluster.

Summary of access nodes on "Greene":

Fully-qualified domain name (FQDN)	Purpose
gdtn.hpc.nyu.edu	Data transfer node (DTN)
greene.hpc.nyu.edu	Login node

Summary of data storage on "Greene" (per netID):

Path	Environmental Variable	Purpose	Flushed?	Allocation
/archive/$USER	$ARCHIVE	Long-term storage	No	2TB/20K files
/home/$USER	$HOME	Small files, code	No	50GB/30K files
/scratch/$USER	$SCRATCH	File staging -freq. read/write	Yes. Files unused for sixty (60) days are deleted	5TB/1M files

Preflight check ✔️✈️

You'll need these:

• An active NetID with permission to access HPC resources.
• VPN client if connecting from off-campus.
• An understanding of absolute vs. relative paths.

Transferring Data 🔄

No-frills file transfer with secure copy (scp)

Quickly transfer a small number of file(s) or directory from source to destination:

scp -rv file1 netID@gdtn.hpc.nyu.edu:/home/netID

(when prompted, provide your NetID credentials. A successful transfer will yield: Exit status 0)

Remotely synchronize the contents of two directories (rsync)

Sync the content of a directory(s) from source to destination (recommended for large # of files):

rsync --archive --compress --progress --exclude=".*" directoryname/ netID@gdtn.hpc.nyu.edu:/scratch/netID/directoryname

or more succinctly:

rysnc -azP --exclude=".*" directoryname/ netID@gdtn.hpc.nyu.edu:/scratch/netID/directoryname

(when prompted, provide your NetID credentials.)

rsync notes:

• The trailing / on (directoryname/) in your source matters.
• --exclude=".*" excludes dot . files. This is optional, but recommended.
• Run the rsync command again when your source directory changes to have those changes reflected in your destination directory.
• rsync can pick up where it left off with the: --append option.

Archive data with on-the-fly compression (tar, ssh)

Use tar to compress source directory and push it over SSH to destination (recommended for fast data transfer and/or archiving):

tar --create --gzip --verbose --file - directoryname |ssh netid@gdtn.hpc.nyu.edu "cat > /archive/netid/tarballname.tar.gz"

or more succinctly:

tar czvf - directoryname | ssh netid@gdtn.hpc.nyu.edu "cat > /archive/netid/tarballname.tgz"

To unpack the tar (on the destination side) do:

tar --extract --verbose --gunzip --file tarballname.tgz

or less verbosely:

tar -xvzf tarballname.tgz

Transferring data with no hangups (nohup) 🚫📞

To keep a process running even after exiting your shell or terminal, preface it with: nohup (recommended for time-intensive jobs):

nohup tar -czvf - directoryname | ssh netid@gdtn.hpc.nyu.edu "cat > /scratch/netid/tarballname.tgz"

then stop the command:

Ctrl + z

and send it to background:

bg

To monitor this process, take note of its PID:

ps aux |grep -i ssh

which will yield, e.g.: 67225

then take that PID, and feed it to top:

top -pid 67225 or: top -p 67225

(you can quit top with: q).

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