Compilation on Linux/Unix

Gwyddion Unix build system is based on GNU autotools (autoconf, automake, libtool), like most of current Unix Free and Open Source Software. If you have ever compiled software from source code, you very likely met autotools and already know how to proceed. This section shall describe the compilation procedure in enough detail even for the uninitiated though. File INSTALL in the top-level directory of the source tarball contains generic GNU autotools installation instructions.

Quick Instructions

If you know the drill:

tar -jxvf gwyddion-2.49.tar.xz
cd gwyddion-2.49
make install

Source Unpacking

Unpack the source code tarball with

tar -Jxvf gwyddion-2.49.tar.xz

replacing 2.49 with the actual version number. It will create directory gwyddion-2.49 (again, with the actual version number in place of 2.49), cd to this directory. All other compilation actions will take place there.

If your operating system does not come with xz you might want to download gwyddion-2.49.tar.gz (compressed with gzip) instead and unpack it with

tar -zxvf gwyddion-2.49.tar.gz

However, modern Unix and Unix-like systems come with both xz and gzip, so the considerably smaller gwyddion-2.49.tar.xz should be normally the better choice.




to configure Gwyddion.

The configure shell script attempts to guess correct values for various system-dependent variables used during compilation. It uses those values to create a Makefile in each directory of the package, a couple of header .h files containing system-dependent definitions and a few other system-dependent auxiliary files. Finally, it creates a shell script config.status that you can run in the future to recreate the current configuration, and a file config.log. This file contains the details of the detection process and it is helpful to include it in compilation related bug reports. At the end, configure also prints a summary of enabled/disabled optional features, including the reasons why features were disabled.

If configure reports missing required packages, install these packages and re-run it. The same applies to the case when configure passes but you find you have not installed an optional package you want to compile Gwyddion with. It is possible a package is not found or it is misdetected even if you have installed it, namely when it is installed into a non-standard directory. In this case it is necessary to adjust certain environment variables to make configure able to find the packages:


Most packages come with so called pkg-config files (.pc) that describe how programs should compile and link with them. configure uses information from these files, therefore PKG_CONFIG_PATH must be set to list all non-standard directories with relevant pkg-config files. To add for instance a GTK+ installation in /opt/gnome and a FFTW3 installation in $HOME/opt/fftw3 one can do



It may be necessary to adjust these variables to include non-standard directories with executables and libraries of relevant packages, respectively. Variables LD_LIBRARY_PATH and DYLD_LIBRARY_PATH both set the search path for shared libraries, but the former is used in Linux and BSD systems, while the latter on OS X.


It may be necessary to adjust these variables to include non-standard directories with header files and libraries of packages that do not come with pkg-config files, for example for libTIFF in /usr/local one can set:

export LDFLAGS

Option --prefix of configure sets the base installation directory. Program components will be installed into its bin, lib, share, etc. subdirectories (that will be created if they do not exist). More detailed control is possible with options specifying particular subdirectories as --bindir, --libdir. The default prefix is /usr/local/bin, to install Gwyddion into your home directory you may want to use for instance

./configure --prefix=$HOME/opt/gwyddion

If you install Gwyddion for personal use it is recommended to use a similar installation directory as no steps need to be performed as root in this case.

Configuration tweaks

Optional features can be enabled/disabled with options such as --with-foo/--without-foo or --enable-foo/--disable-foo. For instance compilation with zlib can be disabled with:

./configure --without-zlib

By default all optional features are enabled if their prerequisites are found. A brief summary of enabled and disabled optional features is printed near the end of configure output.

The complete list of configure options and important variables can be obtained with:

./configure --help

The list is long and most of the options and variables control inclusion/exclusion of individual optional features or provide compiler and linker flags for the various libraries. For instance, by setting FFTW3_CFLAGS and FFTW3_LIBS you can specify (or override) how compilation and linking with FFTW3 should be done. However, this manual specification is only a fallback if the much more convenient pkg-config method does not work.

Some interesting general options are explained in the following paragraphs.

User's tweaks

Gwyddion comes with various desktop integration files defining MIME types, menu entries, file associations, thumbnailers, etc. If you install Gwyddion to a system prefix they usually end up in the correct location. However, if you install it somewhere to your home directory then these files need to be placed elsewhere, namely into certain dot-directories in your home.

This can be requested using --enable-home-installation option of configure. Note that using this option causes installation of files outside the specified prefix.

Packager's tweaks

If Gwyddion is installed into a staging area for a subsequent packaging it is necessary to disable certain post-installation actions that need to be done on the target system, not while packaging.

Updating of Freedesktop files can be disabled with --disable-desktop-file-update. Installation of GConf2 schemas can be disabled with --disable-schemas-install. Usually, this does not have to be done explicitly as installations into a staging area use non-empty DESTDIR (see installation). If DESTDIR is found to be non-empty the build system skips post-installation actions automatically.

Pasing --enable-library-bloat to configure enforces linking modules with all libraries. This is automatically enabled on MS Windows where it is required. On Unix systems, linking modules with libraries that are loaded into the main program anyway only needlessly slows things down (both during build and program execution). So modules are not explicitly linked with base libraries such as GLib. If your environment or policy demands linking modules with all libraries using this option will ensure it.

Pasing --disable-module-bundling to configure prevents the bundling of all modules of the same class (file, process, …) to a single shared library, which is normally done to save space and speed up program startup. Although bundling changes nothing functionally, it changes the set of installed files considerably. If you, for whatever reason, depend on the file existing on disk then please stop. But meanwhile you can use this option to force the traditional installation where each module was in a separate file.

Developer's tweaks

If you intend to patch or otherwise modify Gwyddion source code pass option --enable-maintainer-mode to configure to enable various update and rebuild rules that are not used in plain compilation. Depending on the nature of the modifications, some of the additional tools described in section Subversion Checkout, Development may be necessary.

By default, the C API reference documentation is not rebuilt. Pre-built HTML is distributed in the tarball, the documentation seldom changes and generating it takes a rather long time. To enable the generation of API documentation pass option --enable-gtk-doc to configure. Of course, you also need gtk-doc. Note that configure warns if you enable the maintainer mode but disable gtk-doc (which can be useful to avoid pointless repeated documentation rebuilds). Unless you are going to do make dist, this is harmless.




and wait until Gwyddion is compiled. If configure finished without errors the compilation should pass too. To shorten the wait, enable parallel compilation by running make as

make -j6

replacing 6 with the number of processor cores.

If you find you need to do unusual things to compile the package, please try to figure out how configure could detect whether and what to do, and e-mail patches or instructions to the bug-report address so they can be considered for the next release.


Gwyddion has to be installed to be run, it is not possible to run it uninstalled.


make install

to install Gwyddion to the target directory. If you install Gwyddion to a system directory you have to become root for running this command. This is the only command that you might have to run as root during the installation. For example using sudo:

sudo make install

To install Gwyddion to a staging area, for example for packaging, set make DESTDIR variable to a prefix that will be prepended to all target directories:

make install DESTDIR=/var/tmp/gwyddion-buildroot

Do not override individual directory variables as bindir, libdir.

If you do not install to a system directory, e.g. to a subdirectory of your home directory, you may need to adjust the following variables during installation:

  • GCONF_SCHEMA_CONFIG_SOURCE – location of GConf2 schemas
  • KDE4_MODULE_DIR – location of KDE4 modules

Also, variable XDG_DATA_DIRS might need to be adjusted after installation to get full desktop integration.

If you install Gwyddion into /usr/local and get error message that cannot be found your system probably lacks standard library directories in the dynamic linker configuration. Notably, this happens on Ubuntu. Edit file /etc/ and add the line




Running Gwyddion does not normally require any additional setup.

The misfeatures of some desktop environments, however, may render Gwyddion unusable and need to be disabled. The hijacking of program main menu in Unity makes most of Gwyddion menus inaccessible. It can be disabled by by unsetting UBUNTU_MENUPROXY while running Gwyddion:




make uninstall

in the directory you previously compiled Gwyddion to remove it. If you have lost the source directory meanwhile you can try to unpack, configure and build it exactly as before and then issue make uninstall, although this relies on your ability to reproduce the build process.

RPM Packages

It is possible to build RPM packages on RPM-based GNU/Linux distributions directly from source code tarballs with

rpmbuild -tb gwyddion-2.49.tar.xz

where 2.49 is to be replaced with the actual version as above. This method was tested mainly on Fedora, openSuSE and Mandriva and the RPM spec file contains some specific provisions for these systems. Specific support for other RPM-based systems can be added on request.