Scipion software 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.
sudo apt-get install gcc-10 g++-10 libopenmpi-dev make
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
If you do not have conda already installed (run
which condain 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
Make sure you are running bash shell (run
echo $SHELLin your console), then initialize conda:
Activate base conda environment and install Scipion installer with pip3 provided by conda.
conda activate pip3 install --user scipion-installer
Install Scipion core and generate default config files
python3 -m scipioninstaller -conda -noXmipp -noAsk /path/for/scipion /path/for/scipion/scipion3 config --overwrite
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 plugin. 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
/path/for/scipion/scipion3 installp -p scipion-em-xmipp -j 12 | tee -a install.log
Create an alias for Scipion launcher in your
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.
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.