Configuration of MPI

The code is able to use multiple CPU to speed up the operations. It can even use GPU during the fitting phase. However, you need to have a valid hostfile to inform MPI of what are the available nodes on your computer. By default, the code searches for the file circus.hosts in the spyking-circus folder, create during the installation $HOME/spyking-circus/. Otherwise, you can provide it to the main script with the -H argument (see documentation on the parameters):

>> spyking-circus path/mydata.extesion -H mpi.hosts

Structure of the hostfile

Such a hostfile may depend on the fork of MPI you are using. For MPICH, this will typically look like (if you want to use only 4 cores per machine):

For OpenMPI, this will typically look like (if you want to use only 4 cores per machine): max-slots=4 max-slots=4 max-slots=4 max-slots=4 max-slots=4

If this is your parameter file, and if you launch the code with 20 CPUs:

>> spyking-circus path/mydata.extension -c 20

Then the code will launch 4 instances of the program on the 5 nodes listed in the hostname.hosts file


If you are using multiple machines, all should read/write in a shared folder. This can be done with NFS or SAMBA on Windows. Usually, most clusters will provide you such a shared /home/user folder, be sure this is the case


For now, the code is working with MPICH versions higher than 3.0, and OpenMPI versions below 3.0. We plan to make this more uniform in a near future, but the two softwares made different implementation choices for the MPI library

Shared Memory

With recent versions of MPI, you can share memory on a single machine, and this is used by the code to reduce the memory footprint. If you have large number of channels and/or templates, be sure to use a recent version of MPICH (>= 3.0) or OpenMPI (> 1.8.5)