MPI - cannot specify as many cores as the machine has

[lrebscher]

mpi - not enough slots available to satisfy 9 slots, although my machine has 16 cores

[lrebscher]

mpi doesn't consider hyperthreads by default: open-mpi/ompi#6020

Two options:

1. Use --use-hwthread-cpus option in mpiexec command so that it will use physical cores + hyperthreads
2. Allow user only to select physical cores, can be done by using psutil.cpu_count(logical=False)

We will go with option 1.

@salvadord implication for Netpyne: add --use-hwthread-cpus to the mpiexec command in grid.py

command = '%s -n %d nrniv -python --use-hwthread-cpus -mpi %s simConfig=%s netParams=%s' % (mpiCommand, numproc, script, cfgSavePath, netParamsSavePath)

[salvadord]

@lrebscher shouldn't the "--use-hwthread-cpus" go before the "nrniv" commands, since it's an optional argument of "mpiexec"?

[lrebscher]

yes you're right & I just noticed that you don't have to edit anything in netpyne for now.

That part in grid.py is connected to hpc_slurm method, for mpi_bulletin we handle this in netpyne-ui

So you could apply this change if this makes sense in the slurm context, but for now we're good to go with the changes made in Netpyne-UI :)