I am now trying to run the Soltesz Lab dentate gyrus network model available from OpenSourceBrain.org: http://www.opensourcebrain.org/projects/dentate
and I am trying to run it through the Neuroscience Gateway (NSG) Portal using NEURON7.3.
First I cloned the source code from the link provided on the model's opensourcebrain page: https://bitbucket.org/mbezaire/dentate
Then I compressed this directory into a zip file and uploaded it to the NSG portal and for the parameters specified the main input filename as model-2.3.hoc and specified the subdirectory that main input filename is in as NEURON.
However I get the following error message:
Code: Select all
NEURON -- VERSION 7.3 ansi (1119:b3f8ab0f8203) 2014-07-18
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2014
See http://www.neuron.yale.edu/neuron/credits
5 /projects/ps-nsg/home/nsguser/applications/neuron7.3/nrn-7.3/x86_64/bin/nrniv: can't open model-2.3.hoc
7 /projects/ps-nsg/home/nsguser/applications/neuron7.3/nrn-7.3/x86_64/bin/nrniv: can't open model-2.3.hoc
1 /projects/ps-nsg/home/nsguser/applications/neuron7.3/nrn-7.3/x86_64/bin/nrniv: can't open model-2.3.hoc
2 /projects/ps-nsg/home/nsguser/applications/neuron7.3/nrn-7.3/x86_64/bin/nrniv: can't open model-2.3.hoc
3 /projects/ps-nsg/home/nsguser/applications/neuron7.3/nrn-7.3/x86_64/bin/nrniv: can't open model-2.3.hoc
4 /projects/ps-nsg/home/nsguser/applications/neuron7.3/nrn-7.3/x86_64/bin/nrniv: can't open model-2.3.hoc
0 /projects/ps-nsg/home/nsguser/applications/neuron7.3/nrn-7.3/x86_64/bin/nrniv: can't open model-2.3.hoc
6 /projects/ps-nsg/home/nsguser/applications/neuron7.3/nrn-7.3/x86_64/bin/nrniv: can't open model-2.3.hoc
--------------------------------------------------------------------------
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.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
orterun has exited due to process rank 2 with PID 41423 on
node trestles-11-12.sdsc.edu exiting improperly. There are two reasons this could occur:
1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.
2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"
This may have caused other processes in the application to be
terminated by signals sent by orterun (as reported here).
--------------------------------------------------------------------------
[trestles-11-12.sdsc.edu:41420] 7 more processes have sent help message help-mpi-api.txt / mpi-abort
[trestles-11-12.sdsc.edu:41420] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
Thanks for the help in advance!