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.

Installation

  1. Clone the repository and navigate to the folder:

    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.

    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.

    ./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:

./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:

    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

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:

    scipion3 installp -p scipion-em-xmipp

  3. Locate and navigate the installation directory of softwares of Scipion:

    cd /path/to/scipion3/software/em/

  4. Clone the Xmipp Repository Clone there the Xmipp repository and move to the source directory:

    git clone https://github.com/I2PC/xmipp.git xmippSrc && cd xmippSrc

  5. Create the Configuration File Generate the initial configuration file by running:

    ./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”)

    scipion3 python -c "from xmipp3.version import _binTagVersion; print(_binTagVersion)"  | grep v3

  8. Checkout to the specific release

    git checkout v3.24.12.0-Poseidon

  9. Compile and Install Xmipp Compile Xmipp in production mode with the command:

    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.

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.

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:

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:

export Eigen3_DIR=/apps/ACC/EIGEN/3.3.4/GCC/OPENMPI/share/eigen3/cmake

Installation (remote)

Launch the build process:

./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.