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README

Welcome to the repository of the InfOli Project.

This project aims at designing a high-performance
simulator for the Inferior Olivary Nucleus. It was
specifically designed with the Intel Xeon Phi (KNC)
platform in mind, but is expected to work on any
x86-based architecture.

~~~~~~~~~

Structure:
/src holds the source code for the simulator. Notice
that the code is, for the moment, accelerated under 2
distinct programming models (OpenMP and an MPI-OpenMP hybrid).
The makefile distinguishes between building for the
phi accelerator and the Xeon (or any x86-based) processor.
Example of usage: make omp_phi, compiles
and links the simulator for the phi platform, under the
OpenMP coding paradigm.

/tools holds generators for input to the InfOli simulator.
A connectivity matrix (/connectivity) is imperative for
any simulation, while an applied current (/iapp) is optional.
The connectivity matrix is *normally* supplied by the tools
contained in this folder, however current versions of the simulator
operate with a built-in matrix generator - the tools are kept
for experimental usage.
Example of usage: make pct, compiles a connectivity matrix
generator that is based around fixed percentages of network
density.

/scripts holds queuing and bash scripts. The codebase has been
designed to run on computing clusters, such as UK's Hartree
Centre STFC (http://community.hartree.stfc.ac.uk/wiki/site/admin/home.html).
The folder contains scripts for executing the simulator on said
clusters. Furthermore, for home usage and testing, /scripts
holds sample scripts for compiling and using the OpenMP version
of the code on an x86-based architecture (please check sample.sh).

* scripts flagged as work in progress:
	hybrid_phi_queue.sh
	hybrid_xeon_queue.sh
	microlab_omp.sh

** Please note: the simulator executes natively on the KNC
card and requires an ssh connection to it. It assumes
the existence of a common filesystem between host and KNC - as
is common practice for KNC systems - and the sample scripts for
home usage have been set up assuming common filesystems. Should
this not hold true, the script sample_phi.sh will need altering.

~~~~~~~~~

The Project is the fruit of collaboration between
Microprocessors and Digital Systems Laboratory(MicroLAB),
National Technical University of Athens(NTUA)
(http://www.microlab.ntua.gr/),
the Institute of Communication and
Computer Systems
(https://www.iccs.gr/en/)
and
Erasmus Medical Center Rotterdam (EMC)
(http://www.erasmusmc.nl/?lang=en)

For questions regarding this project, contact
George Chatzikonstantis (georgec@microlab.ntua.gr)
and Dr. Harry Sidiropoulos (harry@microlab.ntua.gr)

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