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1 CmdStan Installation

1.1 Installation via conda

CmdStan can be installed via the package management system conda via the conda-forge channel. This will install a pre-built version of CmdStan along with the required dependencies (i.e. a C++ compiler, a version of Make, and required libraries) detailed below under Source installation.

One can create a new conda environment (named stan-env) and install CmdStan with the following command.

conda create -n stan-env -c conda-forge cmdstan

or install it in an existing environment with

conda install -c conda-forge cmdstan

The conda installation is designed so one can use the R or Python bindings to CmdStan seamlessly. Additionally, it provides the command cmdstan_model to activate the CmdStan makefile from anywhere. To enable either of these, ensure your environment is activated¹ with conda activate <env>, where <env> is the name of the environment CmdStan was installed into. In the first command above, the environment was named stan-env, but any name may be used so long as you are consistent.

You can check which version of CmdStan is installed in your current environment by running the following command.

conda list cmdstan

Finally, you can specify a different version for installation by adding =VERSION to the end of the above commands.² For example,

conda install -c conda-forge cmdstan=2.27.0

Please report conda-specific install problems directly to the conda-forge issue tracker, here.

1.2 Source installation

To install CmdStan from source you need:

• A modern C++11 compiler. Supported versions are

  • Linux: g++ 4.9.3 or clang 6.0
  • macOS: the XCode version of clang
  • Windows: g++ 8.1 (available with RTools 4.0) is recommended; alternatively, g++ 4.9.3 (available with RTools 3.5).

• The GNU-Make utility program or the Windows equivalent mingw32-make. On macOS, this is part of the XCode command line tools installed via command xcode-select --install. On Windows, mingw32-make is installed as part of RTools: https://cran.rstudio.com/bin/windows/Rtools/.

• The CmdStan C++ source code and libraries.

  • CmdStan releases are available from GitHub as a compressed tarfile containing all C++ source code and libraries. The most recent CmdStan release is always available as https://github.com/stan-dev/cmdstan/releases/latest.

  • To use the current development version you can clone the GitHub repo.

The CmdStan release unpacks into a directory called cmdstan-<version> where the version string consists of the major.minor.patch version numbers, e.g. cmdstan-2.23.0. Cloning CmdStan from GitHub creates a directory simply called cmdstan. Throughout this manual, we refer to this top-level CmdStan source directory as <cmdstan-home>.

1.2.1 Installing the C++ toolchain

The C++ toolchain consists of a modern C++ compiler and the GNU-Make utility, described in greater detail in the following section.

1.2.1.1 Linux: g++ and make

On Linux, the C++ compiler command g++ and the GNU-Make command is make. These are often installed by default. To check, run commands:

g++ --version
make --version

If these are at least at g++ version 4.9.3 or later and make version 3.81 or later, no additional installations are necessary. It may still be desirable to update the C++ compiler g++, because later versions are faster.

To install the latest version of these tools (or upgrade an older version), use the following commands or their equivalent for your distribution, install via the commands:

sudo apt install g++
sudo apt install make

If you can’t run sudo, you will need to ask your sysadmin or cluster administrator to install these tools for you.

1.2.1.2 MacOS: clang++ and make

To install a C++ development environment on a Mac, use Apple’s Xcode development environment https://developer.apple.com/xcode/.

From the Xcode home page View in Mac App Store.

• From the App Store, click Install, enter an Apple ID, and wait for Xcode to finish installing.
• Open the Xcode application, click top-level menu Preferences, click top-row button Downloads, click button for Components, click on the Install button to the right of the Command Line Tools entry, then wait for it to finish installing.
• Click the top-level menu item Xcode, then click item Quit Xcode to quit.

To test, open the Terminal application and enter:

clang++ --version
make --version

If you have installed XCode, but don’t have make, you can install the XCode command-line tools via command:

xcode-select --install

Note MacOS installations may include old version of the g++ compiler which is a version 4.2.1. CmdStan requires g++ at 4.9.3 or later. Trying to install later versions of g++ using homebrew or macports is no longer recommended; use the XCode toolchain.

1.2.1.3 Windows: g++ and mingw32-make

The Windows toolchain consists of programs g++, the C++ compiler, and mingw32-make, the GNU-Make utility. To check if these are present, open a command shell ³ and type:

g++ --version
mingw32-make --version

Rtools C++ Development Environment

The simplest way to install a full C++ build environment that will work for CmdStan is to use the Rtools package designed for R developers on Windows (even if you don’t plan to use R).

If you don’t have RTools, the latest version is Rtools40 (released April 2020) which can be downloaded from:

• https://cran.r-project.org/bin/windows/Rtools/

After installation is complete, you need to perform one more step: you need to add the location of the Rtools compiler and make utilities to the PATH environment variable. If you have Rtools40, these should be:

C:\RTools\RTools40\usr\bin
C:\RTools\RTools40\mingw64\bin

If you have and earlier version of RTools, use RTools35:

C:\RTools\RTools35\usr\bin
C:\RTools\RTools35\mingw64\bin

See these instructions for details on changing the PATH.

32-bit Builds

CmdStan defaults to a 64-bit build. On a 32-bit operating system, you must specify the make variable BIT=32 as part of the make command, described in the next section.

1.2.2 GNU-Make utility

CmdStan relies on the GNU-make utility to build both the Stan model executables and the CmdStan tools.

GNU-Make builds executable programs and libraries from source code by reading files called Makefiles which specify how to derive the target program. A Makefile consists of a set of recursive rules where each rule specifies a target, its dependencies, and the specific operations required to build the target. Specifying dependencies for a target provides a way to control the build process so that targets which depend on other files will be updated as needed only when there are changes to those other files. Thus Make provides an efficient way to manage complex software.

The CmdStan Makefile is in the <cmdstan-home> directory and is named makefile. This is one of the default GNU Makefile names, which allows you to omit the -f makefile argument to the Make command. Because the CmdStan Makefile includes several other Makefiles, Make only works properly when invoked from the <cmdstan-home> directory; attempts to use this Makefile from another directory by specifying the full path to the file makefile won’t work. For example, trying to call Make from another directory by specifying the full path the the makefile results in the following set of error messages:

make -f ~/github/stan-dev/cmdstan/makefile
/Users/mitzi/github/stan-dev/cmdstan/makefile:58: make/stanc: No such file or directory
/Users/mitzi/github/stan-dev/cmdstan/makefile:59: make/program: No such file or directory
/Users/mitzi/github/stan-dev/cmdstan/makefile:60: make/tests: No such file or directory
/Users/mitzi/github/stan-dev/cmdstan/makefile:61: make/command: No such file or directory
make: *** No rule to make target `make/command'.  Stop.

Makefile syntax allows general pattern rules based on file suffixes. Stan programs must be stored in files with suffix .stan; the CmdStan makefile rules specify how to transform the Stan source code into a binary executable. For example, to compile the Stan program my_program.stan in directory ../my_dir/, the make target is ../my_dir/my_program or ../my_dir/my_program.exe (on Windows).

To call Make, you invoke the utility name, either make or mingw32-make, followed by, in order:

• zero or more Make program options, then specify any Make variables as a series of

• zero of more Make variables, described below

• zero or more target names; the set of names is determined by the Makefile rules.

make <flags> <variables> <targets>

Makefile Variables

Make targets can be preceded by any number of Makefile variable name=value pairs. For example, to compile ../my_dir/my_program.stan for an OpenCL (GPU) machine, set the makefile variable STAN_OPENCL to TRUE:

> make STAN_OPENCL=TRUE ../my_dir/my_program    # on Windows use mingw32-make

Makefile variables can also be set by creating a file named local in the CmdStan make subdirectory which contains a list of <VARIABLE>=<VALUE> pairs, one per line. For example, if you are working on a 32-bit machine, you would put the line BIT=32 into the file <cmdstan-home>/make/local so that all CmdStan programs and Stan models compile properly.

The complete set of Makefile variables can be found in file <cmdstan-home>/cmdstan/stan/lib/stan_math/make/compiler_flags.

Make Targets

When invoked without any arguments at all, Make prints a help message:

> make    # on Windows use mingw32-make
--------------------------------------------------------------------------------
CmdStan v2.23.0 help

  Build CmdStan utilities:
    > make build

    This target will:
    1. Install the Stan compiler bin/stanc from stanc3 binaries.
    2. Build the print utility bin/print (deprecated; will be removed in v3.0)
    3. Build the stansummary utility bin/stansummary
    4. Build the diagnose utility bin/diagnose
    5. Build all libraries and object files compile and link an executable Stan program

    Note: to build using multiple cores, use the -j option to make, e.g.,
    for 4 cores:
    > make build -j4


  Build a Stan program:

    Given a Stan program at foo/bar.stan, build an executable by typing:
    > make foo/bar

    This target will:
    1. Install the Stan compiler (bin/stanc), as needed.
    2. Use the Stan compiler to generate C++ code, foo/bar.hpp.
    3. Compile the C++ code using cc . to generate foo/bar

  Additional make options:
    STANCFLAGS: defaults to "". These are extra options passed to bin/stanc
      when generating C++ code. If you want to allow undefined functions in the
      Stan program, either add this to make/local or the command line:
          STANCFLAGS = --allow_undefined
    USER_HEADER: when STANCFLAGS has --allow_undefined, this is the name of the
      header file that is included. This defaults to "user_header.hpp" in the
      directory of the Stan program.


  Example - bernoulli model: examples/bernoulli/bernoulli.stan

    1. Build the model:
       > make examples/bernoulli/bernoulli
    2. Run the model:
       > examples/bernoulli/bernoulli sample data file=examples/bernoulli/bernoulli.data.R
    3. Look at the samples:
       > bin/stansummary output.csv


  Clean CmdStan:

    Remove the built CmdStan tools:
    > make clean-all

--------------------------------------------------------------------------------

1.2.3 Clone the GitHub CmdStan repository

This section can be skipped if you want to build CmdStan using the release tarfile, which contains all source files an libraries needed to build CmdStan. However, if you wish to use the current (stable) development version of CmdStan, you must clone the CmdStan GitHub repo.

The CmdStan repo contains just the cmdstan module; the Stan inference engine algorithms and Stan math library functions are specified as submodules and stored in the GitHub repositories stan and math, respectively. By cloning the CmdStan repository with argument --recursive, Git automatically initializes and updates each submodule in the repository, including nested submodules if any of the submodules in the repository have submodules themselves.

The following sequence of commands will check out the current CmdStan develop branch on GitHub and assemble and build the command line interface and supporting libraries:

> git clone https://github.com/stan-dev/cmdstan.git --recursive
> cd cmdstan
> make build    # on Windows use mingw32-make

The resulting set of directories should have the same structure as the release:

• directory cmdstan/stan contains the sub-module stan (https://github.com/stan-dev/stan)
• directory cmdstan/stan/lib/stan_math contains the sub-module math (https://github.com/stan-dev/math)

1.2.4 Building CmdStan

Building CmdStan involves preparing a set of executable programs and compiling the command line interface and supporting libraries. The CmdStan tools are:

• stanc: the Stan compiler (translates Stan language to C++).

• stansummary: a basic posterior analysis tool. The stansummary utility processes one or more output files from a run or set of runs of Stan’s HMC sampler. For all parameters and quantities of interest in the Stan program, stansummary reports a set of statistics including mean, standard deviation, percentiles, effective number of samples, and \(\hat{R}\) values.

• diagnose: a basic sampler diagnostic tool which checks for indications that the HMC sampler was unable to sample from the full posterior.

CmdStan releases include pre-built binaries of the Stan language compiler : bin/linux-stanc, bin/mac-stanc and bin/windows-stanc. The CmdStan makefile build task copies the appropriate binary to bin/stanc. For CmdStan installations which have been cloned of downloaded from the CmdStan GitHub repository, the makefile task will download the appropriate OS-specific binary from the stanc3 repository’s nightly release.

Steps to build CmdStan:

• Download the latest release from https://github.com/stan-dev/cmdstan/releases/latest or clone the GitHub repo.

• Open a command-line terminal window and change directories to the CmdStan home directory.

• Run the makefile target build which instantiates the CmdStan utilities and compiles all necessary C++ libraries.

> cd <cmdstan-home>
> make build    # on Windows use mingw32-make

If your computer has multiple cores and sufficient ram, the build process can be parallelized by providing the -j option. For example, to build on 4 cores, type:

> make -j4 build    # on Windows use mingw32-make

When make build is successful, the directory <cmdstan-home>/bin/ will contain the executables stanc, stansummary, and diagnose (on Windows, corresponding .exe files) and the final lines of console output will show the version of CmdStan that has just been built, e.g.:

--- CmdStan v2.23.0 built ---

Warning: The Make program may take 10+ minutes and consume 2+ GB of memory to build CmdStan.

Windows only: CmdStan requires that the Intel TBB library, which is built by the above command, can be found by the Windows system. This requires that the directory <cmdstan-home>/stan/lib/stan_math/lib/tbb is part of the PATH environment variable. To permanently make this setting for the current user, you may execute:

> mingw32-make install-tbb

After changing the PATH environment variable, you must open an new shell in order to these setting to take effect. (This is not necessary on Mac and Linux systems because they can use the absolute path to the Intel TBB library when linking into Stan programs.)

1.3 Checking the Stan compiler

To check that the CmdStan installation is complete and in working order, run the following series of commands from the folder which CmdStan was installed.

On Linux/macOS:

# compile the example
> make examples/bernoulli/bernoulli

# fit to provided data (results of 10 trials, 2 out of 10 successes)
> ./examples/bernoulli/bernoulli sample data file=examples/bernoulli/bernoulli.data.json

# default output written to file `output.csv`,
# default num_samples is 1000, output file should have approx. 1050 lines
> ls -l output.csv

# run the `bin/stansummary utility to summarize parameter estimates
> bin/stansummary output.csv

On Windows:

# compile the example
> mingw32-make examples/bernoulli/bernoulli.exe

# fit to provided data (results of 10 trials, 2 out of 10 successes)
> ./examples/bernoulli/bernoulli.exe sample data file=examples/bernoulli/bernoulli.data.json

# run the `bin/stansummary.exe utility to summarize parameter estimates
> bin/stansummary.exe output.csv

The sample data in file bernoulli.json.data specifies 2 out of 10 successes, therefore the range mean(theta)\(\pm\)sd(theta) should include 0.2.

1.4 Troubleshooting the installation

Updates to CmdStan, changes in compiler options, or updates to the C++ toolchain may result in errors when trying to compile a Stan program. Often, these problems can be resolved by removing the existing CmdStan binaries and recompiling. To do this, you must run the makefile commands from the <cmdstan-home> directory:

> cd <cmdstan-home>
> make clean-all    # on Windows use mingw32-make
> make build

1.4.1 Common problems

This section contains solutions to problems reported on https://discourse.mc-stan.org

Compiler error message about PCH file

To speed up compilation, the Stan makefile pre-compiles parts of the core Stan library. If these pre-compiled files are out of sync with the compiled model, the compiler will complain, e.g.:

error: PCH file uses an older PCH format that is no longer supported

In this case, clean and rebuild CmdStan, as shown in the previous section.

Windows: ‘mingw32-make’ is not recognised

If the C++ toolchain has been installed but not properly registered, then the call to mingw32-make will result in error message:

'mingw32-make' is not recognised as an internal or external command

To fix this, you should make sure that the RTools installation is in your PATH environment variable, as described in the RTools section.

In addition, if you have the RTools 4.0 toolchain, then call the utility pacman to register the right version of make:

pacman -Sy mingw-w64-x86_64-make

See: https://discourse.mc-stan.org/t/cmdstan-installation-on-windows/11287/6

Windows: ‘g++’ or ‘cut’ is not recognized

The CmdStan makefile uses a few shell utilities which might not be present in Windows, resulting in the error message:

'cut' is not recognized as an internal or external command, operable program or batch file.

The solution is to add mingw_64/bin directory to the user PATH environment variable. See: https://discourse.mc-stan.org/t/errors-when-using-cmdstan-model/14984/21

---

1. A special environment, called base, is activated automatically by conda on startup. Installing software directly in base is not recommended by conda, but may be appropriate for some users who do not intend to use multiple environments↩︎

2. You can view available versions with the command conda search -c conda-forge cmdstan↩︎

3. To open a Windows command shell, first open the Start Menu, (usually in the lower left of the screen), select option All Programs, then option Accessories, then program Command Prompt. Alternatively, enter [Windows+r] (both keys together on the keyboard), and enter cmd into the text field that pops up in the Run window, then press [Return] on the keyboard to run.↩︎