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mountcluster.md

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Access your cluster files from your local machine

This documentation is based on GenomeDK cluster documentaion and another website.

A folder that is accessible on a remote computer can be mounted in your local machine, if you have ssh access to the remote computer. This means that you can create a directory on your local computer that will reflect the contents of a folder in the cluster. I use this method, for example, to edit scripts using my preferred text editor from my local machine (sublime) or to transfer small files back and forth from my local computer to the cluster. This documentation is for macOS and Linux users, although there are also similar methods to do the same on Windows (read this link).

NOTE: This works great when the internet connection to the remote computer is good. But if the connection is slow or unreliable, this approach can lead to a frozen terminal or editor when the remote system cannot be accessed. sshfs has many options and your mileage may vary.

1. Install sshfs

A. For Ubuntu, Mint, etc. users :

In your local machine run:

$ apt-get install sshfs

B. For Fedora, CentOS etc. users :

In your local machine run:

$ yum install sshfs

C. For macOS users:

Download and install the SSHFS and FUSE from the OSX FUSE website.

2. Create your mirror directory

In your local machine, create a directory where the filesystem will be mounted:

$ mkdir ~/Cluster

Of course, you can place it wherever you prefer and name it with another name; you only need to be consistent.

3. Mount the cluster

Now, you can easily mount the filesystem by running this command in your terminal:

$ sshfs -o idmap=user KUID@racimocomp01fl:/home/KUID ~/Cluster

Note that KUID needs to be changed to your id and that you can change the directory mounted to your machine (/home/KUID in this case) or the server you are connecting to (instead of racimocomp01fl, you can connect to racimocomp02fl). The -o idmap=user option maps the user/group id on the cluster to the user id on your local machine.

Congratulations! You can now easily and conveniently access your files from your local machine!

If you want to unmount the cluster form your computer, you can just simply run:

$ umount ~/Cluster

4. Convenient trick

If you add the following lines:

alias mountcluster="mkdir -p ~/Cluster; sshfs -o idmap=user KUID@racimocomp01fl:/home/KUID ~/Cluster"
alias umountcluster="umount ~/Cluster"

to your .bash_profile file with a text editor in your local machine, you will be able to mount the cluster with the mountcluster command and unmount it with the umountcluster command.