NEURON on Ranger
Posted: Thu Apr 28, 2011 9:00 pm
Hello, Michael Hines installed NEURON on Ranger for me and so I'm posting the instructions here for other users of Ranger.
Ranger is a Linux cluster at the University of Texas which, according to the website (1), has "62,976 compute cores, 123 TB of total memory and 1.7 PB of raw global disk space." Everything's bigger in Texas, right? Ranger resources can be used by those not associated with UT by acquiring one of NSF's TeraGrid allocations (2).
Users with an account on Ranger have access to three filesystems: HOME, WORK, and SCRATCH. The setup below guides you through installing NEURON on the HOME filesystem, but jobs should be run out of WORK or SCRATCH.
To install NEURON on your Ranger account:
1. On Ranger, cd to your HOME directory:
2. Create a directory named 'neuron':
3. Enter the neuron directory:
4. Put the desired nrn-nn.tar.gz file (either the current standard distribution (3) or a development version (4)) in the neuron directory. Note that you will not be installing Interviews, so iv-nn.tar.gz is not needed.
5. Unpack the file:
6. Rename the unpacked directory:
7. Create the nrninstall.sh script that will install NEURON on Ranger. This file should contain the following text:
There are a few observations to make about this script. First, to paraphrase a previous comment by Ted & Michael (5), it is cross compiling NEURON because the login machine where you submit the job to run your model code is configured differently than the processors on which your model code will actually run. Second, this particular compilation does not include Python, though that is an option. Third, there are several other arguments that you probably didn't include when installing NEURON on your own machine; these arguments are nicely explained elsewhere on the forum (5).
8. In the neuron directory, create a second folder called 'mpi':
This is the directory in which NEURON will be built. The nrn directory will be kept clean, in case you want to build other versions of NEURON on your Ranger account.
9. Enter the mpi directory:
10. From the mpi directory, run the install script and write the output and errors to a log:
Testing the installation and running job scripts are covered in the reply to this post.
Links
1. Ranger User Guide: http://services.tacc.utexas.edu/index.p ... user-guide
2. TeraGrid: http://www.teragrid.org
3. Standard Distribution: http://www.neuron.yale.edu/neuron/download/getstd
4. Development Versions: http://www.neuron.yale.edu/neuron/download/getdevel
5. Cross Compiling NEURON: http://www.neuron.yale.edu/phpBB/viewto ... 71&start=0
~ Marianne Case
Ranger is a Linux cluster at the University of Texas which, according to the website (1), has "62,976 compute cores, 123 TB of total memory and 1.7 PB of raw global disk space." Everything's bigger in Texas, right? Ranger resources can be used by those not associated with UT by acquiring one of NSF's TeraGrid allocations (2).
Users with an account on Ranger have access to three filesystems: HOME, WORK, and SCRATCH. The setup below guides you through installing NEURON on the HOME filesystem, but jobs should be run out of WORK or SCRATCH.
To install NEURON on your Ranger account:
1. On Ranger, cd to your HOME directory:
Code: Select all
cdh
Code: Select all
mkdir neuron
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cd neuron
5. Unpack the file:
Code: Select all
tar xzf nrn-nn.tar.gz
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mv nrn-nn nrn
Code: Select all
#!/bin/sh
../nrn/configure --prefix=`pwd` --with-nmodl-only --without-x
make
make install
../nrn/configure --prefix=`pwd` '--without-nmodl' '--without-x' \
'--without-memacs' '--with-paranrn' 'CC=mpicc' 'CXX=mpicxx' \
'--disable-shared' linux_nrnmech=no
make
make install
8. In the neuron directory, create a second folder called 'mpi':
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mkdir mpi
9. Enter the mpi directory:
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cd mpi
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sh ../nrninstall.sh > & installnotes.log
Links
1. Ranger User Guide: http://services.tacc.utexas.edu/index.p ... user-guide
2. TeraGrid: http://www.teragrid.org
3. Standard Distribution: http://www.neuron.yale.edu/neuron/download/getstd
4. Development Versions: http://www.neuron.yale.edu/neuron/download/getdevel
5. Cross Compiling NEURON: http://www.neuron.yale.edu/phpBB/viewto ... 71&start=0
~ Marianne Case