1 Local workspace
Start by creating a folder on your local machine for the files that you download. You must have permission to write to this folder. It will be referred to as your local workspace throughout these instructions.
Open a terminal window on your laptop and change to your local workspace.
2 SCP
SCP (Secure Copy) is a command-line utility that allows you to securely transfer files between your local machine and a remote server, such as an HPC cluster.
2.1 Download from HPC
Let’s assume that you have a file named results.txt in the following folder on the HPC cluster:
/nobackup/proj/disk/naiss2026-4-1504/shared/username/somefolder/Replace username and somefolder with your real username and folder name. Run this command in a local terminal.
To download the file to your local workspace, type:
scp username@login.hpc.arrhenius.naiss.se:/nobackup/proj/disk/naiss2026-4-1504/shared/username/somefolder/results.txt .The final . specifies the current directory on your local machine as the destination.
If you want to download an entire folder from HPC to your local workspace, you can use the -r option with scp:
scp -r username@login.hpc.arrhenius.naiss.se:/nobackup/proj/disk/naiss2026-4-1504/shared/username/somefolder .If you want to use wildcards to download multiple files at once, you can use patterns like *.txt to match all text files:
scp 'username@login.hpc.arrhenius.naiss.se:/nobackup/proj/disk/naiss2026-4-1504/shared/username/somefolder/*.txt' .Note the use of single quotes around the remote path when using wildcards. This prevents the local shell from expanding the wildcard before it is sent to the remote server.
2.2 Upload to HPC
Now let’s imagine that you have developed a script named script.sh on your laptop and want to upload it to the HPC cluster. From your local workspace, run:
Replace username and somefolder with your real username and folder name. Run this command in a local terminal. The destination folder must already exist on the HPC cluster.
scp script.sh username@login.hpc.arrhenius.naiss.se:/nobackup/proj/disk/naiss2026-4-1504/shared/username/somefolder/3 Rsync
Rsync is a command-line utility that allows you to efficiently transfer and synchronize files between your local machine and a remote server, such as an HPC cluster.
The rsync command is useful for large or repeated transfers because it transfers only changed data. The -a option copies directories recursively and preserves file attributes, -v shows what is being transferred, and -P displays progress and keeps partially transferred files so that interrupted transfers can resume.
rsync is normally available on Linux and macOS. On Windows, run it through WSL or another environment that provides rsync. Run all commands below in a local terminal, and replace username and folder names as described above.
3.1 Download from HPC
To download a single file to your local workspace, run:
rsync -avP username@login.hpc.arrhenius.naiss.se:/nobackup/proj/disk/naiss2026-4-1504/shared/username/somefolder/results.txt .To download the contents of an entire folder, run:
rsync -avP username@login.hpc.arrhenius.naiss.se:/nobackup/proj/disk/naiss2026-4-1504/shared/username/somefolder/ ./somefolder/The trailing / on the source path means that rsync copies the contents of somefolder. Without the trailing slash, it copies the folder itself.
3.2 Upload to HPC
To upload a single file, run:
rsync -avP script.sh username@login.hpc.arrhenius.naiss.se:/nobackup/proj/disk/naiss2026-4-1504/shared/username/somefolder/To upload the contents of a local folder, run:
rsync -avP localfolder/ username@login.hpc.arrhenius.naiss.se:/nobackup/proj/disk/naiss2026-4-1504/shared/username/somefolder/