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):
192.168.0.1:4
192.168.0.2:4
192.168.0.3:4
192.168.0.4:4
192.168.0.5:4
For OpenMPI, this will typically look like (if you want to use only 4 cores per machine):
192.168.0.1 max-slots=4
192.168.0.2 max-slots=4
192.168.0.3 max-slots=4
192.168.0.4 max-slots=4
192.168.0.5 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