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Getting Started: General Information

VPN and Cardinal Key

Connections to many Stanford computing resources, particularly from off-campus, will require authentication on Stanford’s Virtual Priavate Network (VPN). Instructions to download, install, and configure a VPN client are provided by UIT here:

UIT also provides the Cardinal Key service, which will streamline your login to many Stanford resources:

Installing an SSH client

Connections to CEES HPC and Tool Servers are made via Secure Shell (SHH).

Windows users may need to install a *nix VM client or similar applicattion. Examples include:

On Unix, Linux, MacOS, and other .nix systems, the ssh client is typically either installed as a standard component or or easily acquired. In most cases, it can be installed using a package manager. For example, in Debian, Ubuntu, and Mint (note: the exact syntax and package names may vary):

    $ apt-get update
    $ apt-get install ssh-client

will install an ssh client (note it may be necessary to run these commands using sudo elevated privileges).

    $ apt-get update
    $ apt-get install ssh-server

will install both ssh-client and ssh-server components.

On CentOS and other RedHad derivative distributions,

    yum -y install openssh-server openssh-clients

Software

Software is available from three basic sources:

  1. Pre-installed, “always on,” libraries
  2. Modules libraries
  3. User installed software

Pre-installed software

These are libraries and programs that system administrators make available to all uers, all the time. They automatically load on login. These libraries may include default versions of software that can be superceeded by loading modules or custom SW installations.

Modules LIbraries:

Because some computational tasks can have very specific requirements, it can be challenging and resource intensive to (attempt to) construct a single, one-size-fits-all computing configuration. In order to cater to a large user-base, custom configurations are facilitated by loading user defined lists of code “modules”. This enables, for example, a user to load the newest, or perhaps an older verision of a software package A known to perform best with some other package B.

Typical module commands for most users will include,

  • module load <list of module names>: Load one or more module
  • module list : List loaded modules
  • module avail: Show a list of modules available to the system
  • module unload: Unload a module

An interactive workflow, for example, to load a specific version of Python might look like:

    $ module avail | grep python
    python/2.7
    python/3.5
    python/3.6
    python/3.7

To load Python 3.6,

    $ module load python/3.6

In a typical workflow, a user migh determine a list of necessary modules to execute a particular task, and then script those module load statements into the batch script, between the resource allocation and task execution (just as they would be run interactively).

User Installed Software:

If a piece of software is not available by default or as a module, it can be installed by the user into their $HOME, $GROUP_HOME, or even $SCRATCH space. For example, pip install --user <package name> provides an easy syntax to install Python packages into $HOME, or any other location, with a bit of configuration.

Note that in some cases, custom installations can become quite large, especially if preformed carelessly. For example, it is not uncommon for Anaconda, or documentation related to packages available from conda, to include a complete Python installation, so it is imporant to pay attention to the installation instructions. For packages that are legitimately just big, or for packages that may be useful to other users, talk to the CEES support team about installing a module.

Mounting a Remote (HPC) Filesystem

It can be convenient to mount the Mazama filesystem to your local workstation. Most file explorers provide GUI options to do this. In some cases, the system will attemt to auto-reconnect to remote resources, which can lead to repeated failures if secondary connection requirements are not met (password is not cached, 2-factor authentication is requiered, VPN, etc.), which can trigger automated security features, whicn can result in your account being suspended.

In light of this risk, it can be preferable to simply connect manually (or semi-manually, using a script). On Linux, MacOS, and other *nix systems, use sshfs. Note, the OS requires a “mount point”, which is a directory that in most cases must exist in advance. For example to mount your Mazama $HOME to a folder called $HOME/HPC_home on your local system,

    $ mkdir ~/HPC_home
    $ sshfs <SUNetID>@hpc_server:. ~/HPC_home

Mazama

If necessary, create the mount point – this must be done once, and you can name the mount point whatever you want:

    $ mkdir ~/mazama_home

Then, mount your Mazama $HOME via a tool server,

    $ sshfs <SUNetID>@cees-tool-<n>:. ~/mazama_home 

Note that the dot . following the server_name: implies the default directory when you log in (to that server), which is your $HOME drive. Similarly, the /data drive can be mounted to a mount point called ~/mazama_data using,

    $ sshfs <SUNetID>@cees-tool-<n>:/data ~/mazama_data 

Sherlock

To mount the Sherlock $HOME filesystem (to a mount point called sherlock_home ; note the option -o volname is optional):

    $ sshfs <SUNetID>@dtn.sherlock.stanford.edu:/home/users/<SUNetID> $HOME/sherlock_home -o volname=sherlolck_home

Similarly, your scratch directory can be loaded as the default for a dtn server:

    $ sshfs <SUNetID>@dtn.sherlock.stanford.edu:. $HOME/sherlock_home -o volname=sherlolck_home

Un-mounting (disconnecting) a Filesystem

A filesystem is then unmounted, or disconnected, using the umount command. For Mazama (detailed above):

    $ umount ~/mazama_data
    $ umount ~/mazama_home

If there was an error or some other form of ungraceful dismount of one of the drives, it may not be possible to read the filesystem, un mount the drive, or remount the drive. Mac OSX will likely prompt you to run diskutil – something like,

    $ diskutil unmount ~/mazama_home

Similar tools presumably can be found for other *nix systems and for Windows.