www.neuron.yale.edu

Hi,

My parallel script fails after upgrading from Neuron version 7.3 and 7.4 to 7.5 with both mpich and openmpi. The error does not happen with the test script or when a single node is used, or when the time step is not fixed. Any ideas what could be causing it? The error output is bellow:

mpiexec -np 16 nrniv -mpi init.hoc

internal error: list index 6 out of range
internal error: list index 6 out of range
internal error: list index 7 out of range
internal error: list index 7 out of range
internal error: list index 6 out of range
internal error: list index 6 out of range
internal error: list index 6 out of range
internal error: list index 6 out of range
internal error: list index 6 out of range
internal error: list index 6 out of range
internal error: list index 6 out of range
internal error: list index 6 out of range
internal error: list index 7 out of range
internal error: list index 7 out of range
internal error: list index 6 out of range
internal error: list index 6 out of range

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 5719 RUNNING AT martynas-S5520SC
= EXIT CODE: 134
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

Thanks,
Martynas

Happens with gap junctions only

To fix this, I would need to reproduce on my machine. Please send a zip file with all the necessary mod, hoc, py, ses, files needed to run a sim.
Email is best for this at michael.hines@yale.edu

There was an internal error fixed by the latest commit
https://github.com/nrnhines/nrn/commit/ ... 055a54edfa
Fixed ParallelContext transfer index error when output buffer size
is greater than number of sgids. Possibly also an error if extracellular
was inserted.

This bug was created during a major change to the partrans.cpp implementation that allowed non-voltage variables to be transferred.
That happened on July 30, 2016.