Soltesz Lab dentate gyrus network model (2014)

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kfolw
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Joined: Tue Dec 30, 2014 1:22 pm

Soltesz Lab dentate gyrus network model (2014)

Post by kfolw » Mon Mar 09, 2015 12:33 pm

Hi, I don't know how much you deal with running NEURON through the Neuroscience Gateway Portal but any help would be appreciated!

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
I'm unsure why nrniv can't find the model-2.3.hoc file or if I should enter a different main input filename but I'm pretty sure this is the correct one.

Thanks for the help in advance!

ted
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Re: Soltesz Lab dentate gyrus network model (2014)

Post by ted » Mon Mar 09, 2015 5:13 pm

Case matters in UNIX/Linux-related operating systems. The instructions at https://bitbucket.org/mbezaire/dentate say that
Model-2.0.hoc
is the main file.

kfolw
Posts: 6
Joined: Tue Dec 30, 2014 1:22 pm

Re: Soltesz Lab dentate gyrus network model (2014)

Post by kfolw » Wed Mar 11, 2015 10:25 am

The hoc file from bitbucket is model-2.3.hoc and I get the same error when I specify my input filename as Model-2.3.hoc

ted
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Re: Soltesz Lab dentate gyrus network model (2014)

Post by ted » Wed Mar 11, 2015 5:51 pm

kfolw wrote:The hoc file from bitbucket is model-2.3.hoc and I get the same error when I specify my input filename as Model-2.3.hoc
Indeed, it is called model-2.3.hoc, so the instructions are incorrect. But that doesn't account for the problem you ran into.
I don't know how much you deal with running NEURON through the Neuroscience Gateway Portal
Quite a bit, actually. Problems, when they occur, are usually caused by bugs in the code I'm trying to run.

That aside, have you been successful in running the particular code of interest to you on your own local hardware? Almost certainly you have at least a dual core machine, so if you have MPI installed you ought to be able to
mpiexec -n 2 nrniv -mpi model-2.0.hoc
That said, properly parallelized NEURON code should even run serially
nrniv model-2.0.hoc

So try running it on your own local hardware, either with mpi and -n 2 or serially, and see what happens. If it won't run there, it won't run on NSG.

When I try on my own machine, I get a bunch of msgs, most of which are error msgs, but none of which are like what you saw--

Code: Select all

ls: cannot access ../results/none: No such file or directory
 so I will create it now
mkdir: cannot create directory `../results/none': No such file or directory
cp: cannot stat `../setupfiles/lowindex.hoc': No such file or directory
cp: cannot stat `../stimulation/sintrainparams.hoc': No such file or directory
cp: cannot stat `../cells/allsyns.dat': No such file or directory
sh: ../results/none/hg_status.out: No such file or directory
sh: ../results/none/hg_diff.out: No such file or directory
0 nrniv: ../results/none/runreceipt.txt :file is not open
All of this is with NEURON 7.4 (1208:51e217f4738e) 2015-01-22, which has given me no problems with other models.

From which I infer that this particular code may be a work in progress and not ready for general use, or perhaps the code has advanced out of sync with the instructions (i.e. the code is OK, but something else needs to be done, like creating certain directories, before launching a simulation); you might want to contact the author about this.

ted
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Re: Soltesz Lab dentate gyrus network model (2014)

Post by ted » Wed Mar 11, 2015 10:20 pm

These three are easy to understand:

Code: Select all

cp: cannot stat `../setupfiles/lowindex.hoc': No such file or directory
cp: cannot stat `../stimulation/sintrainparams.hoc': No such file or directory
cp: cannot stat `../cells/allsyns.dat': No such file or directory
They happen because the source files named in the arguments to these cp commands do not exist.

ted
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Re: Soltesz Lab dentate gyrus network model (2014)

Post by ted » Wed Mar 11, 2015 10:48 pm

Just tried the code on NSG with 2 cores on one node, and got pretty much the same error messages as when I tried running it on my own quad core desktop PC under MPI. I suspect that the missing files may contain simulation parameters, but the quickest way to resolve this is to contact the author of the source code and ask how to run it.

Still don't understand why you got such very different error messages.

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