From outside the cluster

Last updated on 2026-10-27 | Edit this page

Estimated time: 15 minutes

Overview

Questions

  • What does scp do when the transfer stops, and what does rsync do?
  • Where is /archive/$USER mounted, and what has to happen before a compute node can read that tree?

Objectives

  • Continue a partial copy with rsync, and recognise that scp starts over.
  • Name Globus, iRODS iCommands, daget, and an rclone WebDAV remote for Research Drive.
  • Keep the Data Archive on login and staging nodes, which are the nodes that mount /archive.

From your own computer

scp starts again from the first file if the transfer stops. rsync continues a partial file. Globus moves between endpoints you registered. On Snellius, the iRODS iCommands below are the documented 2023 modules. The Data Archive is /archive/$USER on login and staging nodes only. daget stages tape, and compute nodes do not mount /archive. Research Drive works as an rclone WebDAV remote. SURF documents the setup.

SRC and DEST are Globus endpoints you registered. RD is the rclone remote in the SURF Research Drive example.

BASH 

scp -r run/ USER@snellius.surf.nl:/scratch-shared/$USER/run
rsync -a --partial --info=progress2 run/ \
  USER@snellius.surf.nl:/scratch-shared/$USER/run/
globus transfer SRC:run/ DEST:run/
module load 2023
module load iRODS-iCommands/4.3.0
iput -r run
daget /archive/$USER/run
srun -t 1:00:00 -p staging cp -r /archive/$USER/run /scratch-shared/$USER/
rclone copy run/ RD:run/

snellius.surf.nl is the SSH host. archive.surf.nl is the Data Archive login host.

The srun line is one hour on the staging partition. It copies from /archive/$USER/run onto /scratch-shared/$USER/. Run daget on a login or staging node first. A compute node has no /archive mount, so a job there cannot open that path.

The SURF pages, by topic:

  • Connecting to the system, host snellius.surf.nl.
  • Data Archive from Snellius: daget, /archive, partition staging, login host archive.surf.nl.
  • How to use Rclone with Research Drive, remote RD.
  • Snellius filesystems: $TMPDIR and scratch-node, used in the next episode.
Challenge

The transfer stops halfway

You started scp -r run/ USER@snellius.surf.nl:/scratch-shared/$USER/run and the connection dropped. You still have a partial tree on scratch. Which command continues that partial copy, and which command starts again from the first file?

rsync -a --partial --info=progress2 continues a partial file. Run the same command again. scp starts again from the first file if the transfer stops.

Key Points
  • scp starts again from the first file. rsync -a --partial continues.
  • Globus uses endpoints you registered (SRC, DEST). iRODS iCommands on Snellius are the 2023 modules iRODS-iCommands/4.3.0.
  • /archive/$USER is on login and staging nodes. daget stages tape. Compute nodes do not mount /archive.
  • archive.surf.nl is the Data Archive login host. snellius.surf.nl is the SSH host.
  • Research Drive is an rclone WebDAV remote named RD in the SURF example.