FAQ

How to make the BSB work with NEST and MUSIC in an MPI context?

Context

When I simulate/reconstruct my BSB network in a context with NEST and MUSIC in parallel (with MPI), I encounter the following bug:

[ERROR] [2024.11.26 16:13:3 /path/to/nest-simulator/nestkernel/mpi_manager.cpp:134 @ MPIManager::init_mpi()] :
When compiled with MUSIC, NEST must be initialized before any other modules that call MPI_Init(). Calling MPI_Abort().
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

Explanation

This issue happens because MUSIC requires you to prepare the NEST context before the MPI context. In other words, you should import nest before importing mpi4py if you have installed NEST with MUSIC. Yet, the BSB leverages MPI for parallelizing the tasks of reconstructing or simulating your network, so it imports mpi4py.

Using the BSB with NEST and MUSIC is therefore only possible through python scripts. At the start of the python scripts that needs to import bsb, add an extra line before to import nest even if you are not using it:

import nest
from bsb import Scaffold

# rest of your code here.

When do I need to recompile my Scaffold?

Context

I have created a configuration and compiled it which produced a scaffold storage file. Now, I have made modification to my configuration file and I want to update the storage file. Is it necessary to recompile entirely my network?

Explanation

The BSB’s reconstruction phase is separated from the simulation. So if you want to make modifications to the simulations section of the BSB then you only need to run the reconfigure command to update the stored configuration file:

bsb reconfigure network.hdf5 network_configuration.json

If otherwise you have changed part of the configuration related to a specific step in the reconstruction pipeline, you can use the --redo with the --only, or --skip flags:

bsb compile --redo --skip-placement # Redo all reconstruction steps except placement
bsb compile --redo --only=stratA,stratB # Redo only stratA and stratB strategies
                                        # and all strategies that depends on it.
bsb compile --redo --skip=stratA # Redo all configuration except stratA

If you have added a new strategy or you want to duplicate its results, you can instead use append:

bsb compile --append --only=stratA # Run only stratA and its dependencies.
                                   # Append the results to the ones already generated

You can see all the compile flags options in Compiling a network. If you modified the topology of the Scaffold, since most of the reconstruction pipeline depends on it, you should recompile your whole network:

bsb compile --redo