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File storage and transfer

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Now that we can get onto the cluster, we want to get our data and files onto it as well.

There are four main areas that you may want to store data/files on:

  • Home
  • Scratch
  • Depot
  • Fortress

We will discuss in more detail what each of these areas are in the week 4 section.

For now, we will put everything into our home directories, as that is where we land whenever we log into the clusters.

There are several ways to get data and files onto and off of the clusters:

1) Open OnDemand

2) Globus

3) scp

4) rsync

5) sftp

GUI Methods

In the files tab of the Open on Demand page, there are upload and download buttons, but they are limited in what they can do. e.g. there is a file size limit of 100 GB to upload and if your connection is flaky at all, you're going to have a bad time.

ood_transfer

For transferring large data to the cluster, you will want to use the Globus transfer service. If you want to transfer files from your local machine to the cluster, you will need to install the Globus Connect Personal software on your local computer.

From the Globus transfer service, you can select a source and a destination. It will handle the actual transferring of the file(s) for you, resuming if there's network connectivity problems.

globus_transfer

Command Based Methods

scp stands for secure copy protocol and is the server version of the cp we saw last week. It needs a source and a destination, but one of them may be a server.

Copying to a cluster: 

$ scp ./source_file USERNAME@CLUSTER.rcac.purdue.edu:~/some_dir/cluster_file_name
Copying from a cluster: 
$ scp USERNAME@CLUSTER.rcac.purdue.edu:~/some_dir/cluster_file_name ./destination_file
When copying from a cluster, the destination file will go into the directory you are currently in. You can also specify a path you want the destination file to go to. This path can be either relative, or absolute.

rsync is similar to scp, but much more fully-featured. It is especially useful for transferring directories, syncing changed files, and resuming interrupted transfers.

Copying a file to a cluster: 

$ rsync ./source_file USERNAME@CLUSTER.rcac.purdue.edu:~/some_dir/cluster_file_name

Copying a file from a cluster: 

$ rsync USERNAME@CLUSTER.rcac.purdue.edu:~/some_dir/cluster_file_name ./destination_file

Copying a directory to a cluster: 

$ rsync -av ./my_directory/ USERNAME@CLUSTER.rcac.purdue.edu:~/some_dir/

Copying a directory from a cluster: 

$ rsync -av USERNAME@CLUSTER.rcac.purdue.edu:~/some_dir/my_directory/ ./my_directory/

A few common options are:

  • -a for archive mode, which preserves file structure, permissions, and timestamps
  • -v for verbose, which shows what is being transferred
  • -h for human-readable file sizes
  • --progress to show transfer progress
  • --partial to keep partially transferred files if a transfer is interrupted

sftp stands for secure file transfer protocol is a reliable way to transfer files between the cluster and another computer.

Essentially, sftp starts a file transfer shell on a remote computer. Simple use the command sftp USERNAME@CLUSTER.rcac.purdue.edu to start the file transfer session. After logging in, use the get and put programs to transfer to and from the cluster you are connected to:

$ sftp USERNAME@CLUSTER.rcac.purdue.edu

    (transfer TO CLUSTER)
sftp> put sourcefile somedir/destinationfile
sftp> put -P sourcefile somedir/

    (transfer FROM CLUSTER)
sftp> get sourcefile somedir/destinationfile
sftp> get -P sourcefile somedir/

sftp> exit
When transferring to and from the cluster via sftp, the transferring on the side of your local computer will be relative to the directory you were in when you initiated the sftp session.

Helpful RCAC programs for file management

The following two programs can be helpful for you as you navigate using the clusters. As a note, these are RCAC specific programs, meaning that we implemented these and other supercomputers may not have them.

myquota

myquota is run without any arguments and tells you where you have access to read and write files. It also tells you what the space quotas are for each of those spaces and how much you have used already. We'll talk more about filesystems in Week 4

$ myquota
Type     Location   Size    Limit    Use   Files   Limit    Use
===============================================================
home     username  809KB   25.0GB  0.00%       -       -      -
scratch  cluster    36KB  200.0TB  0.00%      0k  2,000k  0.00%
depot    group    92.0MB    1.0TB     1%       -       -      -

flost

RCAC regularly backs up data in home and depot spaces, so that if something is accidentally deleted or overwritten, it can be recovered (if it's been there sufficiently long). We have daily, weekly, and monthly snapshots for varying amounts of time. If you lost something in your scratch space, we don't have backups of those, so you're out of luck.

$ flost
This script will help you try to recover lost home or group directory contents.
NB: Scratch directories are not backed up and cannot be recovered.

Currently anchoring the search under: $HOME
If your lost files were on a different filesystem, exit now with Ctrl-C and
rerun flost with a suitable '-w WHERE' argument (or see 'flost -h' for help).

Please enter the date that you lost your files: 2024-10-01

Continue to Week 3