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3 Compiling a Stan Program

A Stan program must be in a file with extension .stan. The CmdStan makefile rules specify all necessary steps to translate files with suffix .stan to a CmdStan executable program. This is a two-stage process:

  • first the Stan program is translated to C++ by the stanc compiler
  • then the C++ compiler compiles all C++ sources and links them together with the CmdStan interface program and the Stan and math libraries.

3.1 Invoking the Make utility

To compile Stan programs, you must invoke the Make program from the <cmdstan-home> directory. The Stan program can be in a different directory, but the directory path names cannot contain spaces - this limitation is imposed by Make.

> cd <cmdstan_home>

In the call to the Make program, the target is name of the CmdStan executable corresponding to the Stan program file. On Mac and Linux, this is the name of the Stan program with the .stan omitted. On Windows, replace .stan with .exe, and make sure that the path is given with slashes and not backslashes. To build the Bernoulli example, on Mac and Linux:

> make examples/bernoulli/bernoulli

On Windows, the command is the same with the addition of .exe at the end of the target (note the use of forward slashes):

> make examples/bernoulli/bernoulli.exe

The generated C++ code (bernoulli.hpp), object file (bernoulli.o) and the compiled executable will be placed in the same directory as the Stan program.

The compiled executable consists of the Stan model and the CmdStan command line interface which provides inference algorithms to do MCMC sampling, optimization, and variational inference. The following sections provide examples of doing inference using each method on the example model and data file.

3.2 Dependencies

When executing a Make target, all its dependencies are checked to see if they are up to date, and if they are not, they are rebuilt. If the you call Make with target bernoulli twice in a row, without any editing bernoulli.stan or otherwise changing the system, on the second invocation, Make will determine that the executable is already newer than the Stan source file and will not recompile the program:

> make examples/bernoulli/bernoulli
make: `examples/bernoulli/bernoulli' is up to date.

If the file containing the Stan program is updated, the next call to make will rebuild the CmdStan executable.

3.3 Compiler errors

The Stan probabilistic programming language is a programming language with a rich syntax, as such, it is often the case that a carefully written program contains errors.

The simplest class of errors are simple syntax errors such as forgetting the semi-colon statement termination marker at the end of a line, or typos such as a misspelled variable name. For example, if in the bernoulli.stan program, we introduce a typo on line \(9\) by writing thata instead of theta, the Make command fails with the following

--- Translating Stan model to C++ code ---
bin/stanc  --o=bernoulli.hpp bernoulli.stan

Semantic error in 'bernoulli.stan', line 9, column 2 to column 7:
     7:  }
     8:  model {
     9:    thata ~ beta(1, 1);  // uniform prior on interval 0, 1
    10:    y ~ bernoulli(theta);
    11:  }

Identifier 'thata' not in scope.

make: *** [bernoulli.hpp] Error 1

Stan is a strongly-typed language; and the compiler will throw an error if statements or expressions violate the type rules. The following trivial program foo.stan contains an illegal assignment statement:

data {
  real x;
transformed data {
  int y = x;

The Make command fails with the following:

Semantic error in 'foo.stan', line 5, column 2 to column 12:
     3:  }
     4:  transformed data {
     5:    int y = x;
     6:  }

Ill-typed arguments supplied to assignment operator =: lhs has type int and rhs has type real

The Stan Reference Manual provides a complete specification of the Stan programming language. The Stan User’s Guide also contains a full description of the errors and warnings stanc can emit.

3.4 Troubleshooting C++ compiler or linker errors

If the stanc compiler successfully translates a Stan program to C++, the resulting C++ code should be valid C++ which can be compiled into an executable. The stanc compiler is also a program, and while it has been extensively tested, it may still contain errors such that the generated C++ code fails to compile.

The Make command prints the following message to the terminal at the point when it compiles and links the C++ file:

--- Compiling, linking C++ code ---

If the program fails to compile for any reason, the C++ compiler and linker will most likely print a long series of error messages to the console.

If this happens, please report the error, together with the Stan program on either the Stan Forums or on the Stan compiler GitHub issues tracker.

3.5 C++ compilation and linking flags

Users can set flags for the C++ compiler and linker and compiler to optimize their executables. We advise users to only do this once they are sure their basic setup of Cmdstan without flags works.

The CXXFLAGS and LDFLAGS makefile variables can be used to set compiler and linker flags respecitvely. We recommend setting these in the make/local file.

For example:


A recommend a set of CXXFLAGS and LDFLAGS flags can be turned on by setting STAN_CPP_OPTIMS=true in the make/local file. These are tested compiler and link-time optimizations that can speed up execution of certain models. We have observed speedups up to 15 percent, but this depends on the model, operating system and hardware used. The use of these flags does considerably slow down compilation, so they are not used by default.

3.5.1 Optimizing by ignoring range checks

When assigning or reading from with vectors, row_vectors, matrices or arrays using indexing, Stan performs cheks that a supplied index is valid (not out of range). These check avoids segmentation faults and other runtime errors that can be difficult to debug.

For some models these checks can represent a significant part of the models execution time. By setting the STAN_NO_RANGE_CHECKS=true makefile flag in the make/local file the range checks can be removed. Use this flag with caution (only once the indexing has been validated). In case of any unexpected behavior remove the flag for easier debugging.