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| -rw-r--r-- | INSTALL.md | 143 |
1 files changed, 113 insertions, 30 deletions
@@ -28,12 +28,17 @@ Dependencies Here are the mandatory dependencies - you cannot install CrystFEL without these: -* Either [CMake](https://cmake.org/) 3.12 or later or [Meson](https://mesonbuild.com/) 0.55.0 or later (Meson is preferred) +* [Meson](https://mesonbuild.com/) 0.55.0 or later * [HDF5](https://www.hdfgroup.org/downloads/hdf5/) 1.8.0 or later (1.10.0 or later is required for many recent data formats which use the 'virtual data set' feature) * [GNU Scientific Library (GSL)](https://www.gnu.org/software/gsl/) * [Bison](https://www.gnu.org/software/bison/) 2.6 or later * [Flex](https://www.gnu.org/software/flex/) +[CMake](https://cmake.org/) 3.12 or later can be used in place of Meson, +but Meson is strongly preferred. The CMake build system is considered +deprecated, already lacks several useful features and will be removed at some +point in the future. + The following dependencies are "optional", in the sense that you can install CrystFEL without them. However, a CrystFEL installation without these will lack important features such as the graphical user interface. The following list is @@ -49,6 +54,9 @@ roughly in order of importance: * [PinkIndexer](https://stash.desy.de/users/gevorkov/repos/pinkindexer) \[\*\] (for indexing electron or wide bandwidth diffraction patterns) * [FFTW](http://fftw.org/) 3.0 or later (required for `asdf` indexing) * [FDIP](https://stash.desy.de/users/gevorkov/repos/fastdiffractionimageprocessing/) \[\*\] (for `peakFinder9` peak search algorithm) +* [libZMQ](https://github.com/zeromq/libzmq/) (for online data streaming) +* [msgpack-c](https://github.com/msgpack/msgpack-c) (for online data streaming) +* [SLURM](https://slurm.schedmd.com/) (development files required for submitting jobs via GUI) Most of the dependencies mentioned above should be available from your Linux distribution's package manager, or from [Homebrew](https://brew.sh/) on Mac OS. @@ -101,58 +109,133 @@ setup file before trying to install CrystFEL, and make sure that the setup file is not automatically referenced in your shell setup files (`.bashrc` and others). -Here are the commands to install all the basic dependencies (including the -optional dependencies, but not the indexing engines) on CentOS and Fedora 22 or -later (for CentOS, replace `dnf` with `yum`): +Fedora 22 or later +------------------ + +All dependencies can be taken from the Fedora repositories: + ``` $ sudo dnf group install 'Development Tools' -$ sudo dnf install hdf5-devel gsl-devel gtk3-devel cairo-devel pango-devel gdk-pixbuf2-devel meson cmake gcc-c++ -$ sudo dnf install fftw-devel zeromq-devel msgpack-devel libccp4-devel +$ sudo dnf install hdf5-devel gsl-devel gtk3-devel cairo-devel pango-devel gdk-pixbuf2-devel meson gcc-c++ fftw-devel zeromq-devel msgpack-devel +$ meson build +$ ninja -C build +$ sudo ninja -C build install ``` -Here are the commands for Ubuntu and Debian: +Up to Fedora 32 (inclusive), you can also install `libccp4-devel` via `dnf`. +This package was removed starting from Fedora 33, but CrystFEL's build system +will take care of it. + + +Ubuntu 18.04 LTS ("Bionic") and 20.04 LTS ("Focal") +--------------------------------------------------- + +The Meson version in these Ubuntu releases is slightly too old for CrystFEL. +Install version 0.55.0 or later from the +[Meson website](https://mesonbuild.com/Getting-meson.html). +You don't need to "install" it, but do remember the location where you unpacked +it. You will need to additionally install `python3`, if it's not already +present. + +All other dependencies are available in the Ubuntu repositories. Make sure +that the "universe" repository is enabled - +[instructions here](https://help.ubuntu.com/community/Repositories/Ubuntu). ``` -$ sudo apt install build-essential -$ sudo apt install libhdf5-dev libgsl-dev gtk3-devel cairo-devel pango-devel gdk-pixbuf2-devel meson cmake gcc-c++ -$ sudo apt install fftw-devel libmsgpack-dev libzmq3-dev libccp4-dev +$ apt install -y build-essential libhdf5-dev libgsl-dev \ + libgtk-3-dev libcairo2-dev libpango1.0-dev \ + libgdk-pixbuf2.0-dev libfftw3-dev \ + git flex bison libzmq3-dev libmsgpack-dev \ + libeigen3-dev libccp4-dev \ + ninja-build python3 +$ /home/user/downloads/meson/meson.py build +$ ninja -C build +$ sudo ninja -C build install +$ sudo ldconfig ``` -For Mac OS X, first install [Homebrew](https://brew.sh/), which will also cause -[Xcode](https://developer.apple.com/xcode/) to be installed. Then: +CrystFEL will install the remaining dependencies (Xgandalf, PinkIndexer, FDIP) +automatically as part of its build process. + + +Ubuntu 16.04 LTS ("Xenial") +-------------------------- + +The Meson version in Ubuntu 16.04 is too old for CrystFEL, and unfortunately +the Python version is also "end of life" and too old for recent versions of +Meson. However, the last release of Meson before it became incompatible with +older Python versions, 0.56.2, is new enough to build CrystFEL. + +Ninja is not available in this Ubuntu release, but fortunately it's an easy +download. + +The Eigen version is too old for XGandalf and PinkIndexer, so you should not +install Eigen from Ubuntu (`libeigen3-dev`), instead let Meson take care of +it during the build process. + +Finally, the dynamic library loader has to be made aware that libraries have +been installed under `/usr/local`. + ``` -$ brew install gsl hdf5 flex bison argp-standalone pkg-config doxygen gtk+3 cairo pango gdk-pixbuf fftw meson cmake -$ export PATH="$(brew --prefix)/opt/bison/bin:$(brew --prefix)/opt/flex/bin:$PATH" -$ export LDFLAGS="-L$(brew --prefix)/opt/bison/lib -L$(brew --prefix)/opt/flex/lib -L$(brew --prefix)/opt/argp-standalone/lib -largp $LDFLAGS" -$ export CFLAGS="-I$(brew --prefix)/opt/flex/include -I$(brew --prefix)/opt/argp-standalone/include/ $CFLAGS" +$ apt install -y build-essential libhdf5-dev libgsl-dev \ + libgtk-3-dev libcairo2-dev libpango1.0-dev \ + libgdk-pixbuf2.0-dev libfftw3-dev \ + git flex bison libzmq3-dev libmsgpack-dev \ + libccp4-dev wget python3 unzip + +$ wget https://github.com/mesonbuild/meson/releases/download/0.56.2/meson-0.56.2.tar.gz +$ tar -xzf meson-0.56.2.tar.gz +$ export MESON=`pwd`/meson-0.56.2/meson.py + +$ wget https://github.com/ninja-build/ninja/releases/download/v1.10.2/ninja-linux.zip +$ unzip ninja-linux.zip +$ export NINJA=`pwd`/ninja + +$ cd crystfel +$ $MESON build +$ $NINJA -C build +$ sudo $NINJA -C build install + +$ sudo echo "/usr/local/lib/x86_64-linux-gnu/" > /etc/ld.so.conf.d/local.conf +$ sudo ldconfig ``` -The `export` commands ensure that the libraries installed via Homebrew can be -found by CrystFEL's build system. +Debian 11 (Bullseye) +-------------------- -Building and installing using Meson (recommended) -------------------------------------------------- +All dependencies can be taken from the Debain repositories: -The actual compilation and installation step is very easy. Here are the -commands: ``` +$ sudo apt install -y build-essential libhdf5-dev libgsl-dev \ + libgtk-3-dev libcairo2-dev libpango1.0-dev \ + libgdk-pixbuf2.0-dev libfftw3-dev \ + git flex bison libzmq3-dev libmsgpack-dev \ + libeigen3-dev libccp4-dev \ + meson ninja-build $ meson build $ ninja -C build $ sudo ninja -C build install +$ sudo ldconfig ``` +Mac OS X +-------- -Building and installing using CMake (deprecated) ------------------------------------------------- +First install [Homebrew](https://brew.sh/), which will also cause +[Xcode](https://developer.apple.com/xcode/) to be installed. Then: -Compiling and installing using CMake is also simple: ``` -$ mkdir build -$ cd build -$ cmake .. -$ make -$ sudo make install +$ brew install gsl hdf5 flex bison argp-standalone pkg-config doxygen gtk+3 cairo pango gdk-pixbuf fftw meson +$ export PATH="$(brew --prefix)/opt/bison/bin:$(brew --prefix)/opt/flex/bin:$PATH" +$ export LDFLAGS="-L$(brew --prefix)/opt/bison/lib -L$(brew --prefix)/opt/flex/lib -L$(brew --prefix)/opt/argp-standalone/lib -largp $LDFLAGS" +$ export CFLAGS="-I$(brew --prefix)/opt/flex/include -I$(brew --prefix)/opt/argp-standalone/include/ $CFLAGS" +$ meson build +$ ninja -C build +$ ninja -C build install ``` +The `export` commands ensure that the libraries installed via Homebrew can be +found by CrystFEL's build system. + Starting up ----------- |