Parallel jobs fail after upgrading to Neuron version 7.5

General issues of interest both for network and
individual cell parallelization.

Moderator: hines

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BlueBirdFlies
Posts: 3
Joined: Thu Jun 13, 2013 11:00 am

Parallel jobs fail after upgrading to Neuron version 7.5

Post by BlueBirdFlies »

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
BlueBirdFlies
Posts: 3
Joined: Thu Jun 13, 2013 11:00 am

Re: Parallel jobs fail after upgrading to Neuron version 7.5

Post by BlueBirdFlies »

Happens with gap junctions only
hines
Site Admin
Posts: 1601
Joined: Wed May 18, 2005 3:32 pm

Re: Parallel jobs fail after upgrading to Neuron version 7.5

Post by hines »

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
hines
Site Admin
Posts: 1601
Joined: Wed May 18, 2005 3:32 pm

Re: Parallel jobs fail after upgrading to Neuron version 7.5

Post by hines »

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.
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