SPHIRE beta 2016/12/16

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Installation instructions

After downloading the binaries, the package must be uncompressed in its final directory. For example, to install SPHIRE in $HOME/Software you should

cd $HOME/Software
tar xvf sphire_beta_20161216.tar.gz

This will create a folder called EMAN2. You need to go inside the folder and run the eman2-installer

cd EMAN2
./eman2-installer


Important: The installer will create a file named eman2.bashrc, which defines all the necessary environment variables to run SPHIRE properly. This is also key when you want to do the MPI installation (see below). You need to either add the content of this file to your bash profile or source it to you bash terminal. For example:

cat eman2.bashrc >> ~/.bashrc

will do the trick. Congratulations, now you have a serial installation of SPHIRE!


Most programs within SPHIRE require MPI to run properly. SPHIRE uses the MyMPI package to parallelize many routines. To install this you need a working MPI enviroment and pydusa. A specifically modified version of pydusa needs to be downloaded for SPHIRE (You can find it at the top of the page). Most clusters will already have a working MPI environment. If you want to install this on a workstation you can download openmpi and compile like:

tar xvf openmpi.2.0.1.tar.gz
cd openmpi-2.0.1
./configure --prefix=/path/to/install/location --disable-dlopen
make -j 4
make install

The –disable-dlopen flag is necessary, otherwise SPHIRE will have issues with mpirun.


After the MPI and EMAN2 environments are properly set up, you need to uncompress pydusa and install MyMPI. For instance if you downloaded pydusa into the EMAN2 folder you should

cd $EMAN2DIR
tar xvf pydusa-1.15es-fftmpi-6__2016_09_07.tgz
cd pydusa-1.15es-fftmpi-6
./install_mpi.py

This will create all the necessary files, and append the new environmental setting to the eman2.bashrc file. To test the installation start a fresh terminal and source the eman2.bashrc file.

In case you do not have a working mpi environment and also you do not want to compile one from scratch, pydusa can perform a local installation for you with the command

./install_mpi.py --force

Finally source again the eman2.bashrc file and run

sx.py
import mpi
quit

If no error occur while importing mpi then, congratulations your MPI version of SPHIRE is working. Happy processing!


Known Issues

A list of the known issues can be found here: SPHIRE 2016/12/16 Known Issues