The complete repository of the Inferior Olive Project
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GeorgeChatzikonstantis/infoli
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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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