Configuration — ViennaRNA Package

# Configuration

The ViennaRNA Package includes additional executable programs such as

- `RNAforester`,

- `Kinfold`,

- `Kinwalker`,

- `RNAlocmin`, and

- `RNAxplorer`.

Furthermore, we include several features in our C-library that may be activated by default, or have to be explicitly turned on at configure-time. Below we list a selection of the available configure options that affect the features included in all executable programs, the RNAlib C-library, and the corresponding scripting language interface(s).

## Streaming SIMD Extension

Since version 2.3.5 our sources contain code that implements a faster multibranch loop decomposition in global MFE predictions, as used e.g. in `RNAfold`. This implementation makes use of modern processors streaming SIMD extension (SSE) that provide the capability to execute particular instructions on multiple data simultaneously (SIMD - single instruction multiple data, thanks to W. B. Langdon for providing the modified code). Consequently, the time required to assess the minimum of all multibranch loop decompositions is reduced up to about one half compared to the runtime of the original implementation. This feature is enabled by default since version 2.4.11 and a dispatcher ensures that the correct implementation will be selected at runtime. If for any reason you want to disable this feature at compile-time use the following:

    ./configure --disable-simd

## Scripting Language Interfaces

The ViennaRNA Package comes with scripting language interfaces for `Perl 5`, `Python` (provided by SWIG), that allow one to use the implemented algorithms directly without the need of calling an executable program. The necessary requirements are determined at configure-time and particular languages may be deactivated automatically if the requirements are not met.

Note

Building the Python 2 interface is deactivated by default since it reached its end-of-life on January 1st, 2020. If for any reason you still want to build that interface, you may use the `--with-python2` configure option to turn it back on.

You may also switch-off particular languages by passing the `--without-perl` and/or `--without-python` configure options, e.g.:

    ./configure --without-perl --without-python

will turn-off the `Perl 5` and `Python 3` interfaces.

Tip

Disabling the scripting language support all-together can be accomplished using the following switch:

    ./configure --without-swig

## Cluster Analysis

The programs `AnalyseSeqs` and `AnalyseDists` offer some cluster analysis tools (split decomposition, statistical geometry, neighbor joining, Ward’s method) for sequences and distance data. To also build these programs add `--with-cluster` to your configure options.

## Kinfold

The `kinfold` program can be used to simulate the folding dynamics of an RNA molecule, and is compiled by default. Use the `--without-kinfold` option to skip compilation and installation of Kinfold.

## RNAforester

The `RNAforester` program is used for comparing secondary structures using tree alignment. Similar to `kinfold`, use the ``--without-forester` option to skip compilation and installation of `RNAforester`.

## Kinwalker

The `kinwalker` algorithm performs co-transcriptional folding of RNAs, starting at a user specified structure (default: open chain) and ending at the minimum free energy structure. Compilation and installation of this program is deactivated by default. Use the `--with-kinwalker` option to enable building and installation of `kinwalker`.

## RNAlocmin

The `RNAlocmin` program is part of the Basin Hopping Graph Framework and reads secondary structures and searches for local minima by performing a gradient walk from each of those structures. It then outputs an energetically sorted list of local minima with their energies and number of hits to particular minimum, which corresponds to a size of a gradient basin. Additional output consists of barrier trees and Arhenius rates to compute various kinetic aspects. Compilation and installation of this program is activated by default. Use the `--without-rnalocmin` option to disable building and installation of `RNAlocmin`.

## RNAxplorer

The `RNAxplorer` is a multitool, that offers different methods to explore RNA energy landscapes. In default mode it takes an RNA sequence as input and produces a sample of RNA secondary structures. The repellant sampling heuristic used in default mode iteratively penalizes base pairs of local minima of structures that have been seen too often. This results in a diverse sample set with the most important low free energy structures. Compilation and installation of this program is activated by default. Note, that this tool depends on the `LAPACK` library. Use the `--without-rnaxplorer` option to disable building and installation of `RNAxplorer`.

## Link Time Optimization

To increase the performance of our implementations, the ViennaRNA Package tries to make use of the Link Time Optimization (LTO) feature of modern C-compilers. If you are experiencing any troubles at make-time or run-time, or the configure script for some reason detects that your compiler supports this feature although it doesn’t, you can deactivate it using the flag:

    ./configure --disable-lto

Note, that `gcc` before version 5 is known to produce unreliable LTO code, especially in combination with SIMD. We therefore recommend using a more recent compiler (GCC 5 or above) or to turn off one of the two features, LTO or SIMD optimized code.

## OpenMP

To enable concurrent computation of our implementations and in some cases parallelization of the algorithms we make use of the OpenMP API. This interface is well understood by most modern compilers. However, in some cases it might be necessary to deactivate OpenMP support and therefore transform RNAlib into a C-library that is not entirely thread-safe. To do so, add the following configure option:

    ./configure --disable-openmp

## POSIX threads

To enable concurrent computation of multiple input data in `RNAfold`, and for our implementation of the concurrent unordered insert, ordered output flush data structure `vrna_ostream_t` we make use of POSIX threads (pthread). This should be supported on all modern platforms and usually does not pose any problems. Unfortunately, we use a threadpool implementation that is not compatible with Microsoft Windows yet. Thus, POSIX thread support can not be activated for Windows builds until we have fixed this problem. If you want to compile `RNAfold` and RNAlib without POSIX threads support for any other reasons, add the following configure option:

    ./configure --disable-pthreads

## SVM Z-score filter

By default, `RNALfold` that comes with the ViennaRNA Package allows for Z-score filtering of its predicted results using a Support Vector Machine (SVM) provided by the LIBSVM library. However, this library is statically linked to our own RNAlib. If this introduces any problems for your own third-party programs that link against RNAlib, you can safely switch off the Z-scoring implementation using:

    ./configure --without-svm

## GNU Scientific Library

The program `RNApvmin` computes a pseudo-energy perturbation vector that aims to minimize the discrepancy of predicted, and observed pairing probabilities. For that purpose it implements several methods to solve the optimization problem. Many of them are provided by the GNU Scientific Library (GSL), which is why the `RNApvmin` program, and the RNAlib C-library are required to be linked against `libgsl`. If this introduces any problems in your own third-party programs that link against RNAlib, you can turn off a larger portion of available minimizers in `RNApvmin` and linking against `libgsl` all-together, using:

    ./configure --without-gsl

## Multiple-precision Floating-Point Computations

Our Non-redundant Boltzmann Sampling implementation uses multi-precision floating-point computations provided by the GNU MPFR library by default. This requires linking against `libmpfr` and `libgmp`. You can switch off this feature using:

    ./configure --disable-mpfr

## Universal binaries

If you intend to build the ViennaRNA for Mac OS X such that it runs on both, `x86_64` and the `arm64` (Apple Silicon Processors) architectures, you need to build a so-called universal binary. Note, however, that to accomplish this task, you might need to deactivate any third-party library dependency as in most cases, only one architecture will be available at link time. This includes the `Perl 5` and `Python` interfaces but might also concern also MPFR and GSL support, possibly even more. In order to compile and link the programs, library, and scripting language interfaces of the ViennaRNA Package for multiple architectures, we’ve added a new configure switch that sets up the required changes automatically:

    ./configure --enable-universal-binary

Note

With link time optimization turned on, MacOS X’s default compiler (`llvm`/`clang`) generates an intermediary binary format that can not easily be combined into a multi-architecture library. Therefore, the `--enable-universal-binary` switch turns off Link Time Optimization!

## Disable C11/C++11 features

By default, we use C11/C++11 features in our implementations. This mainly accounts for unnamed unions/structs within RNAlib. The configure script automatically detects whether or not your compiler understands these features. In case you are using an older compiler, these features will be deactivated by setting a specific pre-processor directive. If for some reason you want to deactivate C11/C++11 features despite the capabilities of your compiler, use the following configure option:

    ./configure --disable-c11

## Deprecated symbols

Since version 2.2 we are in the process of transforming the API of our RNAlib. Hence, several symbols are marked as deprecated whenever they have been replaced by the new API. By default, deprecation warnings at compile time are deactivated. If you want to get your terminal spammed by tons of deprecation warnings, enable them using:

    ./configure --enable-warn-deprecated

## Single precision

Calculation of partition functions (via `RNAfold -p`) uses double precision floats by default, to avoid overflow errors on longer sequences. If your machine has little memory and you don’t plan to fold sequences over 1,000 bases in length you can compile the package to do the computations in single precision by running:

    ./configure --enable-floatpf

Warning

Using this option is discouraged and not necessary on most modern computers.

## Help

For a complete list of all `./configure` options and important environment variables, type:

    ./configure --help

For more general information on the build process see the INSTALL file.