SPHIRE beta 2017/06/02


For this release, we officially support only the installer for CentOS6, which we tested carefully. Nevertheless, the EMAN2 download page provides the installers for CentOS7 and Mac also. SPHIRE does not support Windows.

Tutorial issues

Note 2017/06/02:
Because so many commands are changed, we were not able to provide an up-to-date tutorial and precalculated results for this version yet. However, we provide a short tutorial that was used in our workshop. As soon as it is available, we will let you know via our mailing list!

Until then, please use our old SPHIRE demo dataset which you can download from here. There are small changes in the GUI settings and outputs. Nevertheless, to get an overall idea about the parameters and the overall workflow in SPHIRE, you can have a look in our old tutorial.

Installation preparation

In order to avoid conflicts with existing installations, we recommend to use a system environment that does not contain any environment variables related to OpenMPI, EMAN2, EMAN, and SPHIRE installations.

Especially, the output of

echo $PATH

should not contain paths to any existing OpenMPI, EMAN2, EMAN, and SPARX installations and

which ompi_info

should output

ompi_info not found.

In case that one is still present, contact your system administrator and ask him/her to remove those PATH variables from the system wide environment settings.

Installation instructions

The following installation describes the installation of binary packages. (You can find additional information about the installation at the Installing EMAN2 page.)

Download the installer, run it by typing

cd <Download directory>
bash sphire_beta_20170602.sh

and follow the instruction of the installer.

This creates the directory you specified during installation (default ${HOME}/EMAN2).

Now restart your terminal (Logout & Login) and make sure that the path to the <path to EMAN2 directory>/bin folder is present in your PATH variable afterwards.

echo $PATH
<path to EMAN2 directory>/bin:<more PATH content>

The shipped version of OpenMPI and system wide OpenMPI installations will not work most of the time. That is why we recommend to follow the reinstallation process below. (If you wish to install your own OpenMPI, you can find information at the Installing EMAN2 page.)

1. Change to the installation directory you specified during installation

 cd <path to EMAN2 directory> 

2. Remove the OpenMPI provided:

 bash utils/uninstall_openmpi.sh 

3. Rebuild OpenMPI:

 bash utils/build_and_install_openmpi.sh 

4. Rebuild Pydusa:

 bash utils/build_pydusa_numpy.sh 1.8 --no-test 

Note 2017/06/02: With the current version of installer, “no-test” option is necessary to avoid installation error. It is a known issue to be fixed in future.
5. Install Pydusa:

 bash utils/install_pydusa_numpy.sh 1.8 

Now restart your terminal (Logout & Login).

Test the installation

If the following commands do not throw any errors, the installation is successful.

  In [1]: import mpi
  In [2]: Util.version()
    Compile time of util_sparx.cpp  May 31 2017  --  22:17:16
    Modification time: 05/24/2017  11:43 AM
  In [3]: quit

Congratulations you installed SPHIRE!

Installations issues

During rebuild step 4, an error might occur.

Can't build /home/stevel/EMAN2/recipes/fftw-mpi due to environment creation error:
Downloaded bytes did not match Content-Length
  url: http://www.fftw.org/fftw-3.3.6-pl1.tar.gz
  target_path: /home/stevel/EMAN2/conda-bld/src_cache/fftw-3.3.6.tar.gz
  Content-Length: 4179807
  downloaded bytes: 208916

If you encounter this error, please do the following:
rm conda-bld/src_cache/fftw-3.3.6.tar.gz
bash utils/build_pydusa_numpy.sh 1.8 --no-test

Release notes

- ISAC2 – Rapid and stable 2D Clustering We optimized the popular ISAC algorithm for 2D Clustering (Yang et al., Structure, 2012). ISAC yields now validated 2D class averages > 10-15x faster than before. In addition, the new Beautifier tool allows further refinement and sharpening of the ISAC 2D class averages in order to reveal high-resolution features in 2D.

- MERIDIEN – Rapid ML 3D Refinement We introduced the polar coordinates methodology (Penczek et al., 1992) and optimized the parallelization of the program to speed up the structure refinement, reduce the memory requirements and enable calculation on single nodes. MERIDIEN is now > 10-15x faster than the previous version. Cryo-EM structure determination with SPHIRE is now possible within a few days on small clusters and desktop machines.

- RSORT3D – Reproducible 3D sorting We re-implemented and improved the 3D sorting procedure and methodology. The updated RSORT3D is 3-4x faster and capable to run on desktop machines. More importantly, it produced better results for several high resolution projects in our lab.

- Icosahedral, Tetrahedral and Octahedral Symmetry Refinement of particles with icosahedral, tetrahedral, and octahedral symmetries is now supported.

- Easy installation The release of SPHIRE Beta Patch 1 is synchronized with the release of EMAN 2.2. The new Anaconda Installer allows a fast and smooth co-installation of both programs. At the moment we only support CentOS6, but we work hard on developing a MacOS Installer for the upcoming stable release.

(Follow us on Twitter: https://twitter.com/SPHIRE_Package)

Installing Unblur & Summovie

Please follow the installation instructions on the developers homepage.

Known Issues

A list of the known issues can be found here: SPHIRE 2017/06/02 Known Issues