Parallel Neuron Help! - BAD TERMINATION

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

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Grado

Parallel Neuron Help! - BAD TERMINATION

Post by Grado » Fri Sep 11, 2015 1:52 pm

I recently upgraded to Neuron 7.4. I was able to configure Neuron with both python and mpi support. It may be of note that I had to use the flags --with-paranrn=dynamic and --with-nrnpython=dynamic to get make to run properly (viewtopic.php?f=4&t=3362). Neuron 7.4 now launches without issue.

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~ » nrniv                                                                                                ~ [12:51:44] 
NEURON -- Release 7.4 (1351:8f462ea7e030) 2015-07-21
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits

oc>
However, when I try to run a program with the -mpi flag, I get an error. The error is shown below:

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parallel » cd /Applications/nrn74/nrn-7.4/src/parallel        /Applications/nrn74/nrn-7.4/src/parallel [12:45:02] 11 ↵
parallel » mpiexec -n 1 nrniv test0.hoc -mpi                      /Applications/nrn74/nrn-7.4/src/parallel [12:45:12] 
[x-10-104-234-156:57704] *** Process received signal ***
[x-10-104-234-156:57704] Signal: Segmentation fault: 11 (11)
[x-10-104-234-156:57704] Signal code: Address not mapped (1)
[x-10-104-234-156:57704] Failing at address: 0x440000b0
[x-10-104-234-156:57704] [ 0] 0   libsystem_platform.dylib            0x00007fff96049f1a _sigtramp + 26
[x-10-104-234-156:57704] [ 1] 0   ???                                 0x0000000000000080 0x0 + 128
[x-10-104-234-156:57704] [ 2] 0   libnrnmpi.dylib                     0x000000010492187e f_nrnmpi_init + 254
[x-10-104-234-156:57704] [ 3] 0   nrniv                               0x0000000103e31958 main + 136
[x-10-104-234-156:57704] [ 4] 0   libdyld.dylib                       0x00007fff8a6f95c9 start + 1
[x-10-104-234-156:57704] *** End of error message ***

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 57704 RUNNING AT x-10-104-234-156.uofm-secure.wireless.umn.edu
=   EXIT CODE: 11
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault: 11 (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
I haven't been able to find this error anywhere on the forums, or the internet for that matter. Can anyone help me?

ted
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Re: Parallel Neuron Help! - BAD TERMINATION

Post by ted » Fri Sep 11, 2015 2:39 pm

What happens if you just
nrniv test0,hoc
?
And
mpiexec -n 1 nrniv -mpi test0,hoc
?

Grado

Re: Parallel Neuron Help! - BAD TERMINATION

Post by Grado » Fri Sep 11, 2015 2:48 pm

Running nrniv test0.hoc...

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parallel » nrniv test0.hoc                                        /Applications/nrn74/nrn-7.4/src/parallel [13:47:01] 
NEURON -- Release 7.4 (1351:8f462ea7e030) 2015-07-21
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits

I am 0 of 1
Running mpiexe -n 1 nrniv -mpi test0.hoc...

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parallel » mpiexec -n 1 nrniv -mpi test0.hoc                      /Applications/nrn74/nrn-7.4/src/parallel [13:47:10] 
[x-10-104-234-156:34555] *** Process received signal ***
[x-10-104-234-156:34555] Signal: Segmentation fault: 11 (11)
[x-10-104-234-156:34555] Signal code: Address not mapped (1)
[x-10-104-234-156:34555] Failing at address: 0x440000b0
[x-10-104-234-156:34555] [ 0] 0   libsystem_platform.dylib            0x00007fff96049f1a _sigtramp + 26
[x-10-104-234-156:34555] [ 1] 0   ???                                 0x0000000000000080 0x0 + 128
[x-10-104-234-156:34555] [ 2] 0   libnrnmpi.dylib                     0x000000010e04287e f_nrnmpi_init + 254
[x-10-104-234-156:34555] [ 3] 0   nrniv                               0x000000010d540958 main + 136
[x-10-104-234-156:34555] [ 4] 0   libdyld.dylib                       0x00007fff8a6f95c9 start + 1
[x-10-104-234-156:34555] *** End of error message ***

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 34555 RUNNING AT x-10-104-234-156.uofm-secure.wireless.umn.edu
=   EXIT CODE: 11
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault: 11 (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

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