Install parallel NEURON on Bio-Linux
Posted: 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!
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!