Requirements
Supported OS
We have tested Xmipp compilation on the following operating systems: Ubuntu 20.04, 22.04 and 24.04 and Centos 7. While compilation and execution might be possible on other systems, it might not be straightforward.
Hardware requirements
At least 2 processors are required to run Xmipp. In some virtual machine tools only one is assigned, please check that at least two processors are assigned to the virtual machine.
Software dependencies
Compiler
Xmipp requires C++17 compatible compiler (see table below for minimum versions). We have had good experience with using GCC. Clang is mostly untested. Mind that when compiling with CUDA, a compatible compiler must be installed and findable (although it may not be used for non-CUDA sources) for Xmipp.
Compiler |
Minimum Version |
|---|---|
GCC |
8.4 |
Clang |
5.0 |
Cmake
Xmipp requires CMake 3.17 or above.
Warning
Ubuntu 20.04 only supports CMake 3.16.3. If you experience any issues, please install CMake using Conda in the Scipion3 environment:
scipion3 run conda install cmake
Cuda
CUDA is optional but highly recommended. By default Xmippp will search your CUDA installation. Xmipp supports Cuda 10.2 through 12.6. We recommend you to use the newest version available for your operating system. Pay attention to the compiler - CUDA compatibility.
To install CUDA for your operating system, follow the official install guide.
Warning
CUDA 11.5 is not compatible with GCC - 9, please change one of these.
Full list of dependencies
Before installing Xmipp, you need to ensure that your system meets certain requirements. Here are the necessary packages and dependencies:
GCC: compiler for C
GXX: Compiler for C++
libfftw3-dev: FFTW3 library development files.
libopenmpi-dev: OpenMPI development files.
libhdf5-dev: HDF5 library development files.
python3-numpy: NumPy library for Python 3.
python3-dev: Python 3 development headers.
libtiff5-dev: LibTIFF development files.
libsqlite3-dev: SQLite3 development files.
default-jdk: Default Java Development Kit.
git: Version control system for source code management.
cmake: Cross-platform build system.
libjpeg-dev: Compress, decompress, transform JPEG images.
You can install these packages on Ubuntu-based systems using the following command:
Note
The the installation of the compiler is not included in the next command
sudo apt install -y libfftw3-dev libopenmpi-dev libhdf5-dev python3-numpy python3-dev libtiff5-dev libsqlite3-dev default-jdk git cmake libjpeg-dev
Installing dependencies via yum
Note
Note: For HDF5 to be available Extra Packages for Enterprise Linux (EPEL) repository needs to be activated in certain distros with yum install epel-release
Note
Note: On CentOS-7 the gcc available by default is not compatible with Xmipp. You can enable newer gcc releases using:
yum install centos-release-scl
yum install devtoolset-10
scl enable devtoolset-10 bash
yum install python3-devel python3-numpy fftw-devel openmpi-devel hdf5-devel sqlite-devel libtiff-devel libjpeg-turbo-devel java-17-openjdk-devel git cmake gcc g++
These requirements will ensure that your system is ready for installing and using Xmipp. If you encounter a problem, please refer to known and fixed issues. Let us know if something is not working.