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Installing Scipion

Scipion is written in python and it is comprised by 3 core pip packages and a launcher (scipion3): scipion-pyworkflow, scipion-em and scipion-app. All is needed is either conda available or virtualenv to install Scipion.

Installation

  1. If you do not have conda already installed (run which conda in your console), install Miniconda as in example below. Alternatively, proceed to step 3.

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p /path/for/miniconda

  1. Make sure you are running bash shell (run echo $SHELL in your console), then initialize conda:

source /path/for/miniconda/etc/profile.d/conda.sh

  1. Activate base conda environment and install Scipion installer with pip3 provided by conda.

conda activate
pip3 install --user scipion-installer

  1. Install Scipion core and generate default config files

python3 -m scipioninstaller -conda -noAsk /path/for/scipion
/path/for/scipion/scipion3 config --overwrite

Note

For HPC admins or curious minds, pass –dry and the installer will just print what it would have done instead of doing it. See https://pypi.org/project/scipion-installer/

Congratulations! You have installed Scipion. But a plain vainilla Scipion is useless. You will need some plugins and binaries associated.

For HPC Clusters

Do not let Scipion’s plugins install any software. Although many plugins by default will install 3rd party software, HPC clusters probably already have them installed and optimized, so it is recommended in this scenario to CANCEL any installation done by Scipion.

You are going to need on scipion installation per CPU compatible architecture. You may also want to protect scipion installation by preventing pip USER installations.

Open /path/to/scipion/config/scipion.conf file and append the variable:

SCIPION_DONT_INSTALL_BINARIES = True

PYTHONUSERBASE = $CONDA_PREFIX/lib/python3.8/site-packages

Note

Any value will cancel the installation of binaries

Now you can install the plugins your users have asked for.

3rd party prerequisites (non HPC installations)

Most of the software Scipion installs requires GCC (GCC10 recommended) and OpenMPI already installed. CUDA (11.4 recommended) is optional but highly recommended. Scipion uses conda package manager for installation. Before starting, make sure you do not have other cryo-EM software in your PATH / LD_LIBRARY_PATH as it might conflict with Scipion installation.

For Ubuntu:

sudo apt-get install gcc-10 g++-10 libopenmpi-dev make

For CentOS:

sudo yum -y install epel-release
sudo yum-config-manager --enable epel
sudo yum -y install libzstd-devel hdf5-devel gcc gcc-c++ openmpi-devel

Open /path/for/scipion/config/scipion.conf file and append the variables below to the end of the file. Make sure they point to correct locations for CUDA, OpenMPI and other software necessary for Xmipp:

CUDA = True
CUDA_BIN = /usr/local/cuda-11.4/bin
CUDA_LIB = /usr/local/cuda-11.4/lib64
MPI_BINDIR = /usr/lib64/mpi/gcc/openmpi/bin
MPI_LIBDIR = /usr/lib64/mpi/gcc/openmpi/lib
MPI_INCLUDE = /usr/lib64/mpi/gcc/openmpi/include
OPENCV = False

See Configuration guide for more details about these and other possible variables.

Install xmipp

Xmipp is a good partner for Scipion in cryoem. It binds to Scipion environment offering file format (stk, vol, mrc, tiff, dm4,…) conversions for many cryo em methods

To install Xmipp plugin run:

/path/for/scipion/scipion3 install -p scipion-em-xmipp -j 12 | tee -a install.log

Note

For HPC clusters the above command should not have installed (compiled) xmipp. You need to compile it manually. Go here: https://i2pc.github.io/docs/Installation/Standlone-installation/index.html

We have tested Xmipp compilation on the following operating systems: Ubuntu 16.04, Ubuntu 18.04, Ubuntu 20.04, Ubuntu 22.04 and Centos 7. A list of dependencies can be found here. Command example below is using 12 threads

  1. Create an alias for Scipion launcher in your .bashrc file:

alias scipion3="/path/for/scipion/scipion3"

If any of the steps above fails, check install.log file for errors and refer to the Troubleshooting guide.

Installing other plugins

To list available plugins you can use the plugin manager (recommended) or, alternatively, use the command line tool.

To open the plugin manager, start Scipion (run scipion3) and choose Others > Plugin manager on the top bar. There, any plugin can be easily installed.

Please, refer to the Plugin manager guide to get more details about plugin installation options.

If you have binaries installed for some of the plugins you can have a look at Linking existing software page.

Integration with queue engines (slurm, others)

To configure Scipion to send jobs to a queue engine like Slurm you will need to edit the host file

Test the installation

  • Complete some of the Scipion tests:

    • Verify Scipion core plugins by running: scipion3 test --grep pyworkflowtests --run (<1 min)

    • Verify Xmipp compilation by running scipion3 tests pwem.tests.protocols.test_protocols_import_volumes (<1 min). Double check by opening the test project and displaying output volumes with Scipion viewer.

    • Check whether CUDA and MPI work properly: scipion3 tests xmipp3.tests.test_protocols_xmipp_3d.TestXmippProjMatching (2 min)

  • Complete some of the Scipion Tutorials.