how to run NEURON in supercomputer

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Posts: 1
Joined: Mon Feb 11, 2008 4:40 pm

how to run NEURON in supercomputer

Post by yuyuguo »

I asked this question, and got very nice answer from Mike and Tom.
This might be helpful for other people, so I post here:

Hello Yugo,
Building instructions for supercomputers tend to be idiosyncratic but
neuron is generally build with graphics, terminal capabilities, and
other interactive modules turned off via the configure options:

--without-x --without-readline --without-memacs

many supercomputers do not allow shared libraries so you would need


you certainly want to use communication between processors so you
definitely need


But the biggest question is whether the supercomputer uses the
same compilers as the login machine from where you launch the
job. If not then you need to cross compile. And that means
building/installing first with the "--with-nmodl-only" with proper
CC and CXX environement variables and then building/installing with
"--without-nmodl" and the CC, CXX, MPICSS and MPICC environment
variables properly set. As an example, for the Pittsburgh Cray XT3
the process is

../nrn/configure --prefix=`pwd` \
'--srcdir=../nrn' --with-nmodl-only --without-x CC=gcc CXX=g++

make install

../nrn/configure --prefix=`pwd` \
'--srcdir=../nrn' '--without-x' '--without-memacs' '--without-readline'
'--disable-shared' '--with-paranrn' '--without-nmodl' \
CC=cc CXX=CC MPICC=cc MPICXX=CC linux_nrnmech=no \
java_dlopen=no \
am_cv_CC_dependencies_compiler_type=dashmstdout \
am_cv_CXX_dependencies_compiler_type=dashmstdout \

make install

Do NOT try to use nrnoc. That contains such a small subset
of NEURON functionality that it is unusable in practice.

We will be happy to help you with your installation.

On Mon, 2008-02-11 at 17:52 -0500, Tom Morse wrote:
> Michael, Ted,
> I just received this request from Yugo.
> Are there generic NEURON building instructions for parallel systems on
> the NEURON web site? Please confirm/edit my response to Yugo and let me
> know if I should send it or if either of you would like to send one.
> -Tom
> yuguo <>
> Yugo,
> You might be able to use the configure commands at the bottom of
> ... de82bdc66e
> to build neuron on the supercomputer.
> When neuron runs on the supercomputer with the mpirun command it will
> not produce graphics.
> yuguo wrote:
> > Hi, Tom
> > I currently want to install NEURON program in linux environment at a
> > supercomputer. We have some issues want to make it clear and want your
> > help. We want to run neuron hoc file in supercomputer but don't need the
> > pop out windows, how could we do that?
> > You know, in windows xp system, in order to run a hoc file, every time
> > we need to open nrngui.hoc window. Is this same at linux environment?
> nrnoc can be used to run without graphics.
> nrngui will run similar to what you are familiar with on windows.
> > Could we compile neuron hoc file to be a executable file, like a C program?
> No, the interpreter is still used however the integration (run(),
> step(), etc. ) calls compiled programs so it runs fast.
> > so any time we just click the executable file, it will run and export
> > the results to an dat file.
> > Thank you.
> >
> > Sincerely
> > Yuguo
> >
> -Tom
> PS Yugo, please ask questions on the NEURON Forum so that other users
> can benefit from the answers.
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