Install parallel NEURON on Bio-Linux

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DriesB
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Install parallel NEURON on Bio-Linux

Post by DriesB » Tue Feb 21, 2017 7:16 am

I've been trying to install parallel NEURON on a machine running Bio-Linux (based on Ubuntu 16.04.2). In this post I want to share some problems that I've run into and how I solved those, to help people trying the same in the future.
I’ve used the following installation guide (including information on how to install MPICH): http://www.neuron.yale.edu/neuron/stati ... n.html#MPI

• I installed MPICH 3.2 from source in /usr/local, following instructions in its README
• When I ran test calculations (/usr/local/mpich-3.2/examples/cpi), I noticed that openmpi, not MPICH, was used to run the calculation. I therefore proceeded to uninstall openmpi. After doing this, MPICH ran successfully.

• I installed NEURON 7.4 (and InterViews) from source based on these instructions: http://www.neuron.yale.edu/neuron/downl ... pile_linux. When reading these instructions, be sure to read the section ´Installation for distributed simulations of cells or networks´.
• Initially, I tried to install NEURON and InterViews in /usr/local. This resulted in problems related to permissions, so I installed in my $HOME directory instead.
• Configuration of InterViews initially failed due to some packages missing. Fortunately, this issue had been solved before in this topic of the NEURON Forum: viewtopic.php?f=31&t=1761.
• After completing the installation from NEURON and InterViews from source, I tested whether I could run $HOME/neuron/nrn/src/parallel/test0.hoc in parallel using MPICH. This test was successful! Note: the parallel test files are only available when NEURON is installed from source; not when NEURON is installed through a DEB package.

I hope this will help users who want to run NEURON in parallel!

ted
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Re: Install parallel NEURON on Bio-Linux

Post by ted » Tue Feb 21, 2017 10:40 am

Thanks, that's useful information.
Note: the parallel test files are only available when NEURON is installed from source; not when NEURON is installed through a DEB package.
While it is true that many test and example files are not included in the compiled installer packages, you can still get them without having to install from source code. Either download and expand the gzipped tar file of source code, or clone the nrn repository, and then search the resulting directory tree for the files of interest. For example, the parallel test files are in
nrn/src/parallel
where nrn is the root directory of the directory tree produced by expanding the gzipped tar file or cloning the nrn repository.

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