Last updated: 2024-09-16

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Knit directory: rss/

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This page shows how to install the Variational Bayes (VB) scripts in rss/src_vb/. In a standard computing environment with internet connection, the installation time is typically less than 10 minutes.

Step-by-step guide

0. Install git (optional)

To simplify Step 1 below, you may consider installing git in your computing environment (if it is not available there). Please see this excellent tutorial on installing git.

Please note that RSS software does not depend on git. You can complete Step 1 without installing git.

1. Clone rss repository

With git installed, you can easily clone rss by running the following command in Terminal.

git clone git@github.com:stephenslab/rss.git

Without git, you can manually download rss as follows.

wget https://github.com/stephenslab/rss/archive/master.zip
unzip master.zip
rm master.zip
mv rss-master rss

2. Compile mex file

Go to rss/src_vb and open MATLAB.

cd rss/src_vb
matlab -nodesktop

Run rss/src_vb/install.m in MATLAB. You may get the following output.

>> run install.m
Building with 'gcc'.
MEX completed successfully.
Compilation of MEX files is complete.

After successfully running rss/src_vb/install.m, you will find a file rss_varbvsr_update_matlab.mexa64 (in Linux) in the directory rss/src_vb, which is the workhorse for variational Bayes computations.

Computing environment

Please note that RSS VB codes have only been extensively tested in the following environments.

  • version 9.3.0.713579 (R2017b) of MATLAB for 64-bit Linux

  • version 8.4.0.150421 (R2014b) of MATLAB for 64-bit Linux

  • version 8.2.0.701 (R2013b) of MATLAB for 64-bit Linux

  • version 8.1.0.604 (R2013a) of MATLAB for 64-bit Linux

If you have any trouble installing RSS VB codes, please open an issue or email me (xiangzhu[at]uchicago[and/or]stanford.edu). To help me better understand your problems, please provide details of your computing environment.

MEX files

The most tricky part of this installation is probably compiling MEX files in MATLAB (Step 2).

Before running rss/src_vb/install.m, please make sure that you have the compiler compatible with your version of MATLAB, and that you can compile the MEX files in the tutorials given on the MathWorks website.

In addition, please ensure that you compile and run the scripts in the same version of MATLAB. For example, if you have compiled MEX files using MATLAB Release R2017b, please use the compiled output rss_varbvsr_update_matlab.mexa64 only in MATLAB R2017b.

For more information on MEX, please see: