Installations ---------------------- Installation with Scipion ^^^^^^^^^^^^^^^^^^^^^^^^^^ The recommended way for users (not developers) to install and use Scipion is via the `Scipion framework `_, where you can use Xmipp with other Cryo-EM-related software. Xmipp will not be installed during Scipion installation, to install it use the `plugin manager of Scipion `_ Standlone-installation ^^^^^^^^^^^^^^^^^^^^^^^^^^ This guide explains the standalone installation of Xmipp and the process to link it with Scipion. The standalone version allows you to use Xmipp independently of Scipion. .. note:: This `list of libraries `_ are required in standlone installation and you can install it in the Scipion eviroment if you choose the option 1 to compile Xmipp or in the system for option 2 (see options below) Installation """""""""""""""""" 1. Clone the repository and navigate to the folder: .. code-block:: bash git clone https://github.com/I2PC/xmipp.git xmipp-bundle && cd xmipp-bundle 2. Compile Xmipp. You have two options: **Option 1:** Compile using the Scipion environment. This method installs Xmipp with dependencies managed by Scipion and is the recomended way. .. code-block:: bash scipion3 run ./xmipp **Option 2:** Compile the Xmipp alone. This method installs Xmipp with the required dependencies and versions defined by your environment or defaults. .. code-block:: bash ./xmipp Both methods only compile Xmipp. Linking it to Scipion is explained in the next section. Note. For additional details about the compilation process, run: .. code-block:: bash ./xmipp --help Linking Xmipp to Scipion """""""""""""""""""""""""" To use Xmipp within Scipion, link the standalone installation by following these steps: 1. Ensure Scipion is installed (refer to the *Scipion installation guide*). 2. Use the `scipion-em-xmipp` repository, located in `src/scipion-em-xmipp`. 3. Run the following command to link the binaries: .. code-block:: bash scipion3 installp -p ~/scipion-em-xmipp --devel Replace `~/scipion-em-xmipp` with the path to your `scipion-em-xmipp` folder. Using Xmipp """""""""""""""""" Xmipp is installed in the build directory located in the same directory where the xmipp script is located. To run Xmipp standalone (without Scipion) and to set all necessary environment variables and paths to all Xmipp programs, you can simply run .. code-block:: bash source dist/xmipp.bashrc Installation for HPC Clusters ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ This guide explains how to install Xmipp on High-Performance Computing (HPC). 1. **Install Scipion for HPC** Follow the instructions provided in the Scipion for HPC installation guide: `Scipion HPC Installation Guide `__. 2. **Install the Scipion Xmipp Plugin** Run the following command to install the Xmipp plugin for Scipion: .. code-block:: bash scipion3 installp -p scipion-em-xmipp 3. **Locate and navigate the installation directory** of softwares of Scipion: .. code-block:: bash cd /path/to/scipion3/software/em/ 4. **Clone the Xmipp Repository** Clone there the Xmipp repository and move to the source directory: .. code-block:: bash git clone https://github.com/I2PC/xmipp.git xmippSrc && cd xmippSrc 5. **Create the Configuration File** Generate the initial configuration file by running: .. code-block:: bash ./xmipp config 6. **Edit the Configuration File** Open the `configuration file `__ generated in the previous step and edit the fields as needed. Adjust options such as `CMAKE_C_FLAGS` or `CMAKE_CXX_FLAGS` to match the requirements of your HPC system. 7. **Check the Installed Xmipp Version** Use the following command to verify the version of the binaries the plugin scipion-em-Xmipp requires (something like "v3.24.12.0-Poseidon") .. code-block:: bash scipion3 python -c "from xmipp3.version import _binTagVersion; print(_binTagVersion)" | grep v3 8. **Checkout to the specific release** .. code-block:: bash git checkout v3.24.12.0-Poseidon 9. **Compile and Install Xmipp** Compile Xmipp in production mode with the command: .. code-block:: bash scipion3 run ./xmipp --production True After completing these steps, Xmipp should be successfully installed and configured on your HPC environment. But in any case you can `contact us `__ for advice or support. Xmipp on MareNostrum5 cluster; a successful Installation """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" .. note:: The following is a user-contributed installation report from MareNostrum5 (BSC-CNS, Barcelona), which may serve as a helpful reference when installing Xmipp on similar HPC systems. This is a summary of the steps followed to successfully install Xmipp on the **MareNostrum5** cluster. Due to the restricted environment (no outgoing requests allowed), some manual pre-fetching and modification of build scripts were required. **Fetch Phase (local, in `xmipp` folder)** Dependencies are separated based on how they're used in the build system: 1. **FetchContent_Declare-based dependencies**: must be placed in the `_deps` folder. 2. **ExternalProject_Add-based dependencies**: must be cloned directly in `build`. .. code-block:: bash mkdir build cd build # Case 1: FetchContent_Declare (stored in _deps) mkdir _deps cd _deps git clone https://github.com/MartinSalinas98/libcifpp.git mv libcifpp libcifpp-src git clone https://github.com/google/googletest.git mv googletest googletest-src # Patch libcifpp to fix valarray constexpr conflict nano libcifpp-src/include/cif++/point.hpp # -> Comment out lines 324–331 # -> Replace line 333 with: # value_type length = std::sqrt(q.a*q.a+q.b*q.b+q.c*q.c+q.d*q.d); # Case 2: ExternalProject_Add (cloned in main build directory) cd .. git clone https://github.com/HiPerCoRe/cuFFTAdvisor.git git clone https://github.com/cossorzano/libsvm.git git clone https://github.com/vit-vit/CTPL.git **Disable Auto-Fetching (local)** The `cmake/fetch_*.cmake` scripts must be modified to disable network fetching during CMake configuration. There are **two types** of fetch scripts: 1. **FetchContent_Declare-based**: modify inside the macro to indicate dependency is already "POPULATED". 2. **ExternalProject_Add-based**: remove or comment out the full `ExternalProject_Add()` block. .. code-block:: bash cd ../cmake # Case 1: FetchContent_Declare nano fetch_cifpp.cmake nano fetch_googletest.cmake # -> Inside FetchContent_Declare: # Comment out GIT_REPOSITORY and GIT_TAG lines # Add line: POPULATED TRUE # Case 2: ExternalProject_Add nano fetch_ctpl.cmake nano fetch_libsvm.cmake nano fetch_cuFFTAdvisor.cmake # -> Comment out or remove the entire ExternalProject_Add() block **Prepare Environment (remote, on MareNostrum5)** Load required modules: .. code-block:: bash module load intel module load mkl module load python module load cmake module load openmpi/4.1.5-gcc module load eigen/3.3.4-gcc-ompi module load boost/1.84.0-gcc-ompi module load nvidia-hpc-sdk module load hdf5/1.10.11-nvidia-nvhpcx module load sqlite3/3.45.2-gcc module load fftw/3.3.10-gcc-ompi module load java-openjdk/22.0.1 Set the Eigen path: .. code-block:: bash export Eigen3_DIR=/apps/ACC/EIGEN/3.3.4/GCC/OPENMPI/share/eigen3/cmake **Installation (remote)** Launch the build process: .. code-block:: bash ./xmipp **Remarks** - MareNostrum5 blocks all outgoing HTTP(S) requests, so **all dependencies must be fetched locally and transferred manually** to the build environment. - Distinguish between dependencies using `FetchContent_Declare` and those using `ExternalProject_Add`, as their locations and how they are disabled differ. - Patching `libcifpp` was necessary to resolve `constexpr`/`valarray` issues during compilation.