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. 2018 Feb 16;12:2. doi: 10.3389/fninf.2018.00002

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Copyright © 2018 Jordan, Ippen, Helias, Kitayama, Sato, Igarashi, Diesmann and Kunkel.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Communication of connectivity data from postsynaptic to presynaptic side for the two-tier connection infrastructure. Example network of 5 neurons (A) with global identifiers (GIDs) 1 to 5 (blue filled circles with white numbers) that are connected via two different types of synapses (pink arrows); for simplicity, the two types have synapse-type index 0 and 1 (solid and dashed arrows, respectively). Neurons are distributed across 2 MPI processes (outer rectangles) and 2 threads per process (inner rectangles); 4 threads in total. Synapses are hosted by the threads of their postsynaptic neurons. (B) From top to bottom: Connection table, source table, and target table of the example network in (A) on rank 0 (left) and rank 1 (right). Color code as in Figure 4A: Synapses, sources, and targets shown as pink, red, and green filled squares, respectively, where white numbers indicate target GIDs, source GIDs, and target GIDs again, respectively. The pink star indicates redundant connection information that is absent in the optimization for small-scale simulations (cf. section 3.3). All tables are three-dimensional resizable arrays: Outermost resizable arrays for threads (vertical axes), middle resizable arrays for synapse types or local neurons (horizontal axes), innermost resizable arrays that hold the individual objects indicated by chevrons. When two neurons are connected, the thread of the postsynaptic neuron adds the new synapse to the connection table and a corresponding Source entry to the source table. Connectivity data needs to be communicated to the presynaptic side at the beginning of the simulation in order to construct the target table. (C,D) MPI send buffer (top) and receive buffer (bottom) that contain the TargetData of the example network, for rank 0 and rank 1, respectively; TargetData bit field shown in dashed line rectangle. Top rows (dark gray): Each field contains zero or two entries, which indicate the (source GID, target GID)-tuple. Bottom rows (light gray): Flags in each TargetData used for communication of status values among all processes (0: default, 1: no more data to send, 2: end of valid data in section, 3: skip this section).