Accessing Files

From Molecular Modeling Wiki

Problem

Frequently, some visualization of data (inputs, results) in user's $HOME directory is required and programs like molden, VMD, and others are often run on cluster servers to display images on the user's workstation through the X-Window system. However, this method has major disadvantages - it is slow, as a huge amount of graphical data is transferred through the network (especially when the object consisting of many atoms moves and rotates), and it often does not work at all (mostly because of incompatible versions of OpenGL libraries on the cluster server and user's workstation). The solution is to run visualization programs locally (on user's workstation) and bring data to the program, instead of bringing the program to data. For this, you do not need to copy data from server to your workstation - there is a way to embed (mount) your remote $HOME directory to your local file system.

Sshfs

One of the systems which allow to mount the remote directory to local filesystem is called sshfs. To use it, follow these instructions (specific for Ubuntu, see also this howto):

Install the sshfs package and add yourself to the fuse group (this has to be done only once)

sudo apt-get install sshfs
sudo gpasswd -a $USER fuse

Once you have added yourself to the fuse group, you should log out and log back in again for the change to take effect.

For every filesystem you want to mount do

mkdir -p ~/mnt/SERVERNAME
sshfs -o idmap=user USERNAME@SERVERNAME:/home/USERNAME ~/mnt/SERVERNAME

replacing SERVERNAME with the name of remote server (cluster) and USERNAME with your login name on this server (cluster). For example

mkdir -p ~/mnt/zinc
sshfs -o idmap=user novak@zinc:/home/novak ~/mnt/zinc

Note:

This process can be repeated for as many cluster servers as needed.

Note:

The directories (mountpoints) need to be created only once for every remote directory.

Once the remote directory is mounted, you can use it as if it was local, so, for example, you can call your local installation of VMD or molden and open a (remote) file in it browsing to ~/mnt/SERVERNAME/...

To unmount (disconnect) the remote directory from your local filesystem call

fusermount -u ~/mnt/SERVERNAME

Notes

This method can also be used to mount cluster $HOME directory to your home computer. For this, however, opening the firewall with knock is needed before calling sshfs.

The same sshfs functionality in Windows XP/7/8 can be achieved by open source software called Dokan SSHFS (credits to Lukasz Cwiklik).