Research Infrastructure

Accessing your CSF (or iCSF or zCSF) Home and Scratch Directory

Introduction

Please note that the virtual desktop system has very little home directory space and is not backed up so we ask that you don’t store files on it. No recovery of lost files will be possible!

You mainly use nyx5,6,7 to log in to other remote systems such as the CSF or iCSF. So most of the time you’ll want to leave the files on those systems and work with the files directly on those systems. Your home directory on the CSF or iCSF is on the RDS (aka isilon) storage system – the centrally-provided Research Data Storage system.

However, occasionally you may want to transfer files to the nyx desktop or to transfer files between your local desktop/laptop and the CSF, iCSF … via the nyx servers (for example, if you are off campus, you’ll need to transfer the files via a nyx server. If you’re on campus you can transfer files directly to the CSF, or other, login node.) In this case you’ll need to make your CSF (or other) home directory or scratch directory visible on the nyx server. We refer to this as mounting your CSF (or other) directory.

Please note: this is only recommended for transferring small files via the nyx servers. It is not an efficient method for transferring large data files and there is not enough space on the nyx servers to keep large data files there. For large file transfers please use the RDS-SSH service which provides a much better method of transferring large files to your CSF / iCSF (i.e., isilon storage) directory – from on or off campus.

Mounting your Remote Directory (home or scratch)

Access to your isilon home directory (i.e., CSF / iCSF home directory) or the scratch directory local to those systems is possible by running one of the following simple commands on nyx5, nyx6 or nyx7 which will mount your remote directory on nyx5, nyx6 or nyx7 (ensure you run this command in a window that is not logged in to the CSF, for example):

Remote system on which you have an account Command run on nyx5/6/7 Directory created on nyx5,6,7
CSF mntcsf ~/csf3
mntcsfscratch ~/csfs3cratch
iCSF mnticsf ~/icsf
mnticsfscratch ~/icsfscratch
Zrek (zCSF) mntzrek ~/zrek
mntzrekscratch ~/zrekscratch
  • To mount your CSF home directory as a directory named ~/csf3 and your CSF scratch directory as a directory named ~/csf3scratch on nyx5,6,7 run the following commands on nyx5,6,7:
    mntcsf
    mntcsfscratch

    Enter your CSF password when asked.

  • To mount your iCSF home director as a directory named ~/icsf and ~/icsfscratch on nyx5,6,7:
    mnticsf
    mnticsfscratch
    

    Enter your iCSF password when asked.

  • To mount your Zrek directories as directories named ~/zrek and ~/zrekscratch on nyx5,6,7:
    mntzrek
    mntzrekscratch
    

    Enter your Zrek password when asked.

Note: if you have access to more than one of the above systems you only need to mount one of the home directories because they all share the same home directories. The scratch directories are not shared between systems so you should mount the particular scratch directories you require.

If you don’t have an account on any of the above systems but you have been given access to the RDS-SSH service (rds-ssh.itservices.manchester.ac.uk) then you can mount your rds-ssh directory (which is your main isilon / RDS directory) as a directory named ~/rds-ssh on nyx5,6,7 using:

mntrds
# Note: there is no scratch directory on the rds-ssh machine

Notes on Mounting your Remote Directory (home or scratch)

  • Users that have access to more than one of the above systems, your home directory on those systems will be shared between them. Hence you only need to run one of the above commands.
  • If you mounted the directory on nyx5 it is not automatically mounted on nyx6 or nyx7. Simply run the scripts on both machines if you login to them both.
  • The scripts above will automatically create the directory (~/csf or ~/csfscratch and so on) on nyx5,6,7 if it doesn’t already exist. This is the mount point.
  • You can access the files in the mount point by treating it like any other directory. For example:
    ls ~/csf
    

    will show the files from your CSF home directory.

    cd ~/csf
    mkdir test5
    

    will go in to the CSF home directory then create a new subdirectory there.

  • The mount-point will generally still be active between login sessions. However, it can be disconnected by the system in which case your ~/csf directory will appear empty. Simply run mntcsf again. It won’t do any harm if you run this while the mount point is still connected – it will simply report that your CSF home directory is already mounted.
  • You can upload files from your desktop to the nyx5,6,7 mount point (i.e., the ~/csf directory) and the files will be transferred to your CSF directory. However, if you are transferring large files this is can be very slow so we have an alternative method available – please contact its-ri-team@manchester.ac.uk to request access to the RDS-SSH service for large file transfers (from on or off campus).

Unmounting your Remote Directory (home or scratch)

You can leave your remote directory mounted on nyx5,6,7 but if you wish to unmount your remote directory from nyx5,6,7 simply run the above script with -u as a flag. For example:

mntcsf -u
mntcsfscratch -u

The mount point (the ~/csf3 or ~/csfs3cratch directories on nyx5,6,7) will then appear empty. However, your CSF files are safe – you just can’t see them on nyx5,6,7 now.

Mounting the Remote directory manually

If you wish to mount the directory manually follow the instructions below (the scripts above do these commands for you):

  • Make a directory to use as an access point for your CSF home-directory (you only ever need to do this once):
    # Run this command on nyx5,6,7 (not the CSF)
    mkdir ~/csf3
  • Mount your CSF home-dir by using sshfs — enter your IT password when prompted:
    # Run this command on nyx5,6,7 (not the CSF)
    sshfs csf3.itservices.manchester.ac.uk:  ~/csf3
            #                             #   #
            #                             #   # Local directory on nyx5,6,7
            #                             #   # (this directory must already exist)
            #                             #
            #                             # Notice the : at the
            #                             # end of the hostname
            #
            # Remote system whose home dir you wish to mount on nyx5,6,7
    
  • View your CSF files as usual:
    ls csf3

Last modified on June 11, 2020 at 5:00 pm by George Leaver