Installations

Installation with Scipion

The recommended way for users (not developers) to install and use Xmipp is via the Scipion framework, where you can use Xmipp with other Cryo-EM-related software.

Xmipp will be installed during Scipion installation (pay attention to not include the flag -noXmipp). You can also install Xmipp from 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

Clone the repository and navigate to the folder:

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

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:

Ensure Scipion is installed (refer to the Scipion installation guide).
Use the scipion-em-xmipp repository, located in src/scipion-em-xmipp.
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).

Install Scipion for HPC Follow the instructions provided in the Scipion for HPC installation guide: Scipion HPC Installation Guide.
Install the Scipion Xmipp Plugin Run the following command to install the Xmipp plugin for Scipion:
```
scipion3 installp -p scipion-em-xmipp
```
Locate and navigate the installation directory of softwares of Scipion:
```
cd /path/to/scipion3/software/em/
```
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
```
Create the Configuration File Generate the initial configuration file by running:
```
./xmipp config
```
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.
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
```
Checkout to the specific release
```
git checkout v3.24.12.0-Poseidon
```
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.