Using Silo

Silo is the SSCC's secure computing enclave. It consists of secure servers and data storage for working with data covered by HIPAA and other sensitive data. Silo contains Windows-based servers (WinSilo), Linux based servers (LinSilo and LinSiloBig) and a Slurm cluster (SlurmSilo). The website acts as the gateway to Silo: once you log in there you can sign into WinSilo or LinSilo.

Keep reading to learn how to access Silo and use the Windows servers in the Silo environment. Or you can skip ahead for information on:

Getting Access

If you are interested in using Silo, please contact the  SSCC Help Desk. L&S researchers should set up a consultation with the Data and Information Services Center for assistance with getting approval to work with sensitive data. SMPH researchers should set up a consultation with the Clinical and Health Informatics Institute. Depending on the nature of your data you may need to get approval from your IRB, the UW-Madison Office of Cybersecurity, or other relevant authorities. Using Silo will expedite that process because it has already had a formal risk assessment by the Office of Cybersecurity and was found to be low risk, and many of the relevant authorities are already familiar with it.  You can see what software is available in Silo in the SSCC's software database plus the Biomedical Research Software on Silo page.

Connecting to Silo requires multifactor authentication using Duo, the same system used for your UW-Madison NetID. Most people use the Duo app on their smartphone, but you can also use a separate hardware token. When you contact the Help Desk about using Silo please mention which method you prefer. Instructions for obtaining and using a hardware token can be found here. Consider turning on Duo Restore so you can easily continue using Duo after upgrading your phone.

Installing the Citrix Workspace App

To use Silo you'll need to have the Citrix Workspace App installed on your computer. Just click on the appropriate link below and then run the installer after it finishes downloading. If you've already installed the Citrix Workspace App on your computer to use Winstat you do not need to install it again.

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

Logging In

To log in to Silo, you will need to go to the website You will be redirected to the SSCC authentication page,

Getting started page for Duo Single-Sign-On

At the ADFS login screen, first give your SSCC username and password as usual. If it is your first time logging into Silo, you'll be prompted to follow the instructions on the screen to set up Duo on your smartphone. You'll be able to use the same Duo app for both Silo and your NetID. If you're asked to give permission for programs to run, do so. Silo will check to see if you have the Workspace app for your computer already installed.

The Silo File System

Silo has an isolated file system that is separate from the SSCC's primary file system, but they have similar structures. All files are available using either Windows or Linux. The key locations are:

Linux Name Windows Name
Home Directory (Private Space)  ~   Z:  Drive
Project Directories (Shared Space) /project  V:  Drive
SMPH Project Directories (Shared Space) /smph  S:  Drive

Home directories are primarily meant for configuration files, installed packages, and other small files. They have a quota of 40GB and 1 million files. Research data should be stored in project directories which can be shared with the other members of your research group. New project directories will start with a quota of 1TB and a quota of 1 million files per project. If you need more space you can request a quota of 5TB and/or expand your file quota to 5 million using the form on the SSCC website. If you need more space beyond that, you can request a quota of 25TB, again using a web form. Your sponsoring agency will be informed of this request. If you still need more space, up to the technical limit of 60TB, email the Help Desk and we’ll schedule a meeting to discuss your needs. SMPH researchers will be given project space on the S: drive, which is SMPH's space in DoIT's RestrictedDrive service.

You can check your current storage usage and file count on the SSCC self-service portal. You must be on campus or connected to a campus VPN (UW-Madison VPN, SSCC VPN, etc.) to access the portal.

Moving Data To and From Silo

You can move data into or out of Silo using Globus, a tool for securely transferring research data. See Using Globus to Move Data In and Out of Silo for more information.

To easily move results out of Silo, we have created a folder called  silosync in the Z: drive of each Silo user. Every five minutes, an automated script copies anything placed in this folder to a corresponding folder in your Z: drive on the SSCC's primary file system. One easy way to access the SSCC's primary file system is to log into Winstat, which you'll see when you log into Silo. Winstat is very similar to WinSilo but, not being a high-security server, it can communicate with the local hard drive of your computer. After logging into Winstat, you'll see a drive called Local Disk (C: on {your computer}). You can drag files from the Z: drive to this drive to move files from SSCC's file system to your computer. You're also welcome to access the SSCC's primary file system by mapping a drive to it or using FTP.

Using WinSilo

Once you've logged in, WinSilo behaves just like a regular Windows server, with a few important exceptions:

  • Silo cannot access the Internet. This can affect programs in unexpected ways: for example, Stata's findit command takes much longer to run than usual and then only gives partial results, because it tries to reach Stata's web server and does not display any results until that attempt times out. Fortunately the results it does give are the ones you're most likely to need.
  • You can install R packages from CRAN and Bioconductor, Stata packages from SSC, and Python packages from PyPI. If you need to install packages from other locations please follow the instructions in our guide to research computing. If you need further assistance installing packages, contact the Help Desk.
  • You cannot copy and paste between Silo and your own computer.
  • Silo cannot access disk space on your computer.
  • You cannot print from Silo.

Silo Downtime

All of the SSCC’s servers except for Slurm and SlurmSilo are taken offline, patched, and rebooted from 6:00AM-8:00AM on the Wednesday after the third Tuesday of the month (the week after Microsoft’s “Patch Tuesday”).

If you don't anticipate using Silo's Linux servers, you can stop reading at this point. Welcome to Silo!

Silo Linux Servers

Silo has three kinds of Linux servers. To use them, first sign into You can then either log into LinSilo directly or log into WinSilo and connect to the Linux servers from there.

LinSilo is a cluster of two servers ( linsilo001, linsilo002) with 44 cores and you can use up to 250GB of memory. When you log into LinSilo, you'll be automatically directed to the least busy server.

LinSiloBig is a single server (linsilobig001) with 80 cores and you can use up to 500GB of memory. 

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 SlurmSilo.

SlurmSilo is a cluster of five servers identical to LinSilo and one identical to LinSiloBig. They run jobs submitted to Slurm from LinSilo or LinSiloBig. Slurm allows you to submit jobs that will run on any of the servers in the cluster, reserving the cores and memory they need (up to 80 cores and 750GB of memory).

The Linux servers in the Silo environment were funded by SMPH. Other researchers are welcome to use them, but SMPH researchers have priority.

To learn how to use the Linux servers in Silo, please see the Guide to Research Computing at the SSCC.

Logging in to Silo Using a Hardware Token

If you would like to use a token to log into Silo and have one already, please contact the Help Desk and include the serial number printed on the back of your token in your email. The token must be black and white colored, with the words "OTP c100" printed on the front - we cannot use the blue and green tokens that say "Duo" on the front. If you do not have a token, please let us know and we will issue you one.

Silo token types

Log in by going to and giving your SSCC username and password as usual. By default, Silo will try to authenticate you via Duo Push to your smartphone, or whatever the last method you used to log on was. If it's your first time using a Hardware token, select "Other options" on the first logon page, then choose "Hardware token", then input the 6-digit number from your token and click Verify.

3-step screenshot process for using a hardware token to logon

If later you wish to add a smartphone app to your Silo account so you can authenticate with either the app or a token, note the "Manage devices" option in the above screenshot - clicking that (and entering your token code to verify your identity first) is how you will go to the Duo Device Management page and add additional MFA options.

If you have any questions about using Silo, feel free to contact the Help Desk.

Keywordssilo winsilo linsilo winrd hipaa secure server   Doc ID102689
OwnerZach H.GroupSocial Science Computing Cooperative
Created2020-05-31 10:23:37Updated2024-07-16 14:33:57
SitesSocial Science Computing Cooperative
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