Compilation and Installation

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Create the dependencies for installing the conda environment:

   conda create --name pyem --clone base
   conda activate pyem

3. Install the FFTW dependencies.

   yum install fftw3 --installroot=/root/anaconda3/envs/pyem/lib/python3.8/site-packages
   wget http://fftw.org/fftw-3.3.8.tar.gz
   tar xvf fftw-3.3.8.tar.gz
   cd fftw-3.3.8
   ./configure --prefix=/root/anaconda3/envs/pyem/lib/python3.8/site-packages/FFTW --enable-shared --enable-static --enable-fma --enable-neon
   make -j 32
   make install
   pip3 install pyfftw --trusted-host mirrors.tools.huawei.com -i http://mirrors.tools.huawei.com/pypi/simple

4. Install the dependencies of healpy, pathos, natsort, and numpy.

   conda update --all
   conda install -c conda-forge healpy pathos
   conda install natsort numpy==1.20.1

5. Decompress the pyem installation package.

   tar xvf pyem-0.5.tar.gz

6. Go to the directory generated after the decompression.

   cd pyem-0.5

7. Install pyem.

   pip3 install --no-dependencies -e .

   

   After the installation is successful, the message "Successfully installed pyem" is displayed.

8. Modify the projection_subtraction.py file.
   1. Open the projection_subtraction.py file.

      vi projection_subtraction.py

   2. Press i to enter the edit mode and delete version="projection_subtraction.py 2.1b" from line 291.

      Before the modification:

      291 parser = argparse.ArgumentParser(version="projection_subtraction.py 2.1b")

      After the modification:

      291 parser = argparse.ArgumentParser()

      

      After performing 8.a, press Esc, type :set nu, and press Enter to display the line number.

   3. Press Esc, type :wq!, and press Enter to save the settings and exit.