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Uploading/downloading/editing files#

Uploading/downloading files#

To transfer files from and to the HPC, see the section about transferring files of the HPC manual

dos2unix#

After uploading files from Windows, you may experience some problems due to the difference in line endings between Windows (carriage return + line feed) and Linux (line feed only), see also https://kuantingchen04.github.io/line-endings/.

For example, you may see an error when submitting a job script that was edited on Windows:

sbatch: error: Batch script contains DOS line breaks (\r\n)
sbatch: error: instead of expected UNIX line breaks (\n).

To fix this problem, you should run the dos2unix command on the file:

$ dos2unix filename

As we end up in the home directory when connecting, it would be convenient if we could access our data and VO storage. To facilitate this we will create symlinks to them in our home directory. This will create 4 symbolic links (they're like "shortcuts" on your desktop) pointing to the respective storages:

$ cd $HOME
$ ln -s $VSC_SCRATCH scratch
$ ln -s $VSC_DATA data
$ ls -l scratch data
lrwxrwxrwx 1 vsc40000 vsc40000 31 Mar 27 2009 data ->
    /user/data/gent/vsc400/vsc40000
lrwxrwxrwx 1 vsc40000 vsc40000 34 Jun 5 2012 scratch ->
    /user/scratch/gent/vsc400/vsc40000

Editing with nano#

Nano is the simplest editor available on Linux. To open Nano, just type nano. To edit a file, you use nano the_file_to_edit.txt. You will be presented with the contents of the file and a menu at the bottom with commands like ^O Write Out The ^ is the Control key. So ^O means Ctrl-O. The main commands are:

  1. Open ("Read"): ^R

  2. Save ("Write Out"): ^O

  3. Exit: ^X

More advanced editors (beyond the scope of this page) are vim and emacs. A simple tutorial on how to get started with vim can be found at http://www.openvim.com/.

Copying faster with rsync#

rsync is a fast and versatile copying tool. It can be much faster than scp when copying large datasets. It's famous for its "delta-transfer algorithm", which reduces the amount of data sent over the network by only sending the differences between files.

You will need to run rsync from a computer where it is installed. Installing rsync is the easiest on Linux: it comes pre-installed with a lot of distributions.

For example, to copy a folder with lots of CSV files: 

$ rsync -rzv testfolder vsc40000@login.hpc.ugent.be:data/

will copy the folder testfolder and its contents to $VSC_DATA on the , assuming the data symlink is present in your home directory, see symlinks section.

The -r flag means "recursively", the -z flag means that compression is enabled (this is especially handy when dealing with CSV files because they compress well) and the -v enables more verbosity (more details about what's going on).

To copy large files using rsync, you can use the -P flag: it enables both showing of progress and resuming partially downloaded files.

To copy files to your local computer, you can also use rsync: 

$ rsync -rzv vsc40000@login.hpc.ugent.be:data/bioset local_folder
This will copy the folder bioset and its contents on $VSC_DATA to a local folder named local_folder.

See man rsync or https://linux.die.net/man/1/rsync for more information about rsync.

Exercises#

  1. Download the file /etc/hostname to your local computer.

  2. Upload a file to a subdirectory of your personal $VSC_DATA space.

  3. Create a file named hello.txt and edit it using nano.

Now you have a basic understanding, see next chapter for some more in depth concepts.