Welcome to the Expanded Silo!

A guide for early adopters from SMPH.

The Social Science Computing Cooperative is pleased to welcome the School of Medicine and Public Health as our newest member, and we're pleased to welcome you to the newly expanded Silo secure computing environment as an early adopter. Please keep in mind that the new servers are still being worked on: they may occasionally be taken offline, and you may find things that don't work yet. Known issues are listed on the Silo Expansion home page; please report any other problems you run into to the SSCC Help Desk. We're counting on our early adopters to help us make the official launch as smooth as possible: SSCC staff do not have the expertise to properly test specialized software for biomedical research.

One major component that is not yet in place is automated processes for bringing data into Silo. We invite you to explore Silo, try out the tools, and see what happens. But if manually transferring your data would make your testing more productive—or maybe even let you do some real work—contact the Help Desk and we'll find a way.

Interested in being an early adopter? First speak with your local IT staff, and then contact the SSCC Help Desk. For more information about the Silo Expansion visit the project home page.

Setting Up

To use Silo you'll need to have the Citrix Workspace App installed on your computer. If you're using your own computer just click on the appropriate link below and then run the installer after it finishes downloading.

If you're using a managed computer, speak to your local IT staff about how to install the Citrix Workspace App.

See Using Winstat for more information about using the Citrix Workspace App.

You'll also need to use multi-factor authentication via Duo, the same system you use for your NetID. If you normally use the Duo app on your smartphone it can support Silo too. If you normally use a token, the Help Desk will help you set it up.

Logging In

To log in, open a browser and go to silo.ssc.wisc.edu. You'll need to give your SSCC username (almost certainly the same as your NetID) and password, then authenticate using Duo. If you haven't set up Duo for Silo, it will walk you through the process.

Once you've authenticated, click on Silo LDS to connect to Silo.

The Windows Desktop

After logging in, you'll start with a Windows desktop running on Silo LDS. This is your gateway to the rest of the Silo environment, but it's also a powerful server with a variety of research software and you are welcome to use it.

The Silo File System

The Windows and Linux servers in the Silo environment share the same file system; they just access it in different ways. That means you can manage files, write code, etc. using Windows if you prefer and then use the Linux servers just to run jobs.

The DoIT-provided Isilon storage is available in Linux as /smph, or in Windows as the S: drive. Contact the Help Desk to have a subdirectory created for your project.

Your home directory is available in Linux as ~ or /home/{first letter of your username}/{your username} (e.g. /home/r/rdimond), or in Windows as the Z: drive. This is primarily intended for configuration files and packages and is relatively small (20GB). Research data should go under /smph.

You'll also see /project, or the V: drive. This is the equivalent of /smph for non-SMPH SSCC researchers. It, along with home directories, are in SSCC's storage.

Getting Data In and Out of Silo

We are reaching out to data providers like the Biotechnology Center to create automated ways of getting data from them into Silo. But if you're eager to get started using Silo with your real data, tell the Help Desk and we'll find a way.

For publicly-available data (data that do not require any special security), you can copy the files to a folder in your Linux home directory (Z: drive) on SSCC's regular file system, then email the Help Desk and ask them to copy it to Silo. You can then access SSCC's regular file system using FTP or by mapping a drive to it (Windows/Mac).

To get results or non-sensitive data out of Silo, in your home directory is a folder called silosync. Once every five minutes, anything in this folder will be copied to your Linux home directory (Z: drive) on SSCC's regular file sysem. You can then get access to it using FTP or by mapping a drive to it (Windows/Mac). You are responsible for making sure anything you put in silosync can appropriately be stored on SSCC's regular file system.

Linux Servers

Silo has three kinds of Linux servers:

LinSilo is a cluster of three servers (linsilo001, linsilo002, linsilo003) with 40 cores and 384GB of memory each. When you log into LinSilo, you'll be automatically directed to the least busy server. If you start a long job on a server, you'll need to go back to the same server to manage it. You can switch to a different server with the ssh command; e.g. to get to linsilo1 type:

ssh linsilo001

LinSiloBig is a cluster of two servers (linsilobig001, linsilobig002) with 80 cores and 768GB of memory each. Again, when you log into LinSiloBig you'll be the directed to the least busy server, but you can switch with ssh. In fact, using LinSiloBig is so similar to using LinSilo that you can assume instructions for using LinSilo apply to LinSiloBig unless we say otherwise.

Jobs that cannot run without the additional memory LinSiloBig provides should have first priority on LinSiloBig. Jobs that can take full advantage of the additional cores it provides are second priority. Please do not use LinSiloBig for jobs that could run just as well on LinSilo or CondorSilo.

CondorSilo is a cluster of nine servers with 40 cores and 384GB of RAM each. It runs jobs submitted via HTCondor. CondorSilo is not available yet.

Logging into LinSilo

To log into LinSilo, click on the Windows logo button and find the LinSilo folder in the programs list. Then click on the LinSilo or LinSiloBig icon. This will start a program called X-Win32. The first thing you'll see is a utility window that you can ignore (but don't close it or it will close the entire program—minimize it instead). The login prompt will come up shortly thereafter, and then a terminal window once you log in.

If you'll use these frequently, you can pin them so that they'll come up as soon as you click the Windows logo button by right-clicking on them.

If you don't need graphics, you can also log into LinSilo using SecureCRT.

Running Programs on LinSilo

Most of the (long) list of software that's been requested is installed, and we're working on the rest. See the project home page for the list of what's been requested and what's not yet installed. Here are the commands to run a few selected programs on LinSilo:

Program Command to run it interactively Command to run a long job that will continue after you log out
R R nohup R CMD BATCH myprogram.R &
Python 3.7 (command line) python nohup python myprogram.py &
Python 2.7 (command line) python2 nohup python2 myprogram.py &
Spyder (Python IDE) spyder  
Jupyter Notebook jupyter notebook  
Stata xstata nohup stata -b do mydofile &
SAS sas nohup sas myprogram.sas &

Of course there are many ways to run these programs, and many more programs!

Running RStudio on LinSilo

To run RStudio on LinSilo, go to the LinSilo folder in the programs list and double-click on the LinSilo RStudio Server or LinSiloBig RStudio Server icon. (Again, if you'll use these frequently you can pin them.) This will open a web browser on the Windows server containing an RStudio interface that connects to R running on LinSilo or LinSiloBig. Jobs run in RStudio will continue to run even if you log out.

Again, welcome to the expanded Silo, and we greatly appreciate your taking the time to test it as an early adopter. Please report any problems you run into to the Help Desk.

Last Revised: 3/26/2020