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Improve NEST performance by revised connection exchange and spike delivery #2926

Merged
merged 146 commits into from
Sep 13, 2023
Merged

Improve NEST performance by revised connection exchange and spike delivery #2926

merged 146 commits into from
Sep 13, 2023

Commits on Mar 7, 2022

  1. Remove while-loop and multi-threading (except for deliver) in gather_… 

    …spike_data; use max spike-data buffer size
    @suku248
    suku248 committed Mar 7, 2022
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Commits on Mar 9, 2022

  1. Ensure spike register is thread-local.

    @heplesser
    heplesser committed Mar 9, 2022
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  2. Fixed formatting.

    @heplesser
    heplesser committed Mar 9, 2022
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Commits on Mar 10, 2022

  1. Merge pull request #2 from heplesser/suku_test_single_threading_in_ga… 

    …ther_spike_data

Ensure thread-local memory allocation
    @suku248
    suku248 authored Mar 10, 2022
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  2. Remove reading thread dimension in spike register for testing

    @suku248
    suku248 committed Mar 10, 2022
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  3. Merge branch 'test_single_threading_in_gather_spike_data' of github.c… 

    …om:suku248/nest-simulator into test_single_threading_in_gather_spike_data
    @suku248
    suku248 committed Mar 10, 2022
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  4. Change spike register to use thread-specific pointers to inner vectors

    @suku248
    suku248 committed Mar 10, 2022
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Commits on Mar 30, 2022

  1. Merge branch 'master' of github.com:nest/nest-simulator into test_sin… 

    …gle_threading_in_gather_spike_data
    @heplesser
    heplesser committed Mar 30, 2022
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  2. Fixed merge error

    @heplesser
    heplesser committed Mar 30, 2022
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Commits on Mar 31, 2022

  1. Process spike receive buffer in a batchwise fashion

    @suku248
    suku248 committed Mar 31, 2022
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  2. Merge branch 'batchwise_processing_spike_receive_buffer' of github.co… 

    …m:suku248/nest-simulator into single_batchwise
    @heplesser
    heplesser committed Mar 31, 2022
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Commits on Apr 1, 2022

  1. Compressed spike mapping with fixed slot per spike.

    @heplesser
    heplesser committed Apr 1, 2022
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  2. Merge remote-tracking branch 'origin/single_batchwise' into hep_test_… 

    …single_threading_in_gather_spike_data

Conflicts:
	nestkernel/event_delivery_manager.cpp
    @heplesser
    heplesser committed Apr 1, 2022
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  3. Fixed thread bugs.

    @heplesser
    heplesser committed Apr 1, 2022
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Commits on Jun 8, 2022

  1. More brute force serialization.

    @heplesser
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Commits on Aug 4, 2022

  1. Added SIONLIB omp barrier skip

    @JoseJVS
    JoseJVS committed Aug 4, 2022
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Commits on Aug 24, 2022

  1. Rearranged deliver events and gather events.

    @JoseJVS
    JoseJVS committed Aug 24, 2022
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  2. Moved deliver events conditional block.

    @JoseJVS
    JoseJVS committed Aug 24, 2022
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Commits on Sep 20, 2022

  1. Shift event_delivery after updating nodes and gather_spikes

    @med-ayssar
    med-ayssar committed Sep 20, 2022
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Commits on Sep 27, 2022

  1. Shift spikes timestemaps

    @med-ayssar
    med-ayssar committed Sep 27, 2022
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  2. Merge branch 'debug_nest' of github.com:med-ayssar/nest-simulator int… 

    …o debug_nest
    @med-ayssar
    med-ayssar committed Sep 27, 2022
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  3. Put the delivery event back at the top of the main while-loop

    @med-ayssar
    med-ayssar committed Sep 27, 2022
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Commits on Sep 28, 2022

  1. Substract lag from mindelay in deliver_event

    @med-ayssar
    med-ayssar committed Sep 28, 2022
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  2. Fix static check error

    @med-ayssar
    med-ayssar committed Sep 28, 2022
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  3. Fix assertion error

    @med-ayssar
    med-ayssar committed Sep 28, 2022
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  4. Fix static check error

    @med-ayssar
    med-ayssar committed Sep 28, 2022
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Commits on Oct 2, 2022

  1. Clean implementation of time stamps on delivery.

    @heplesser
    heplesser committed Oct 2, 2022
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  2. Attempt to fix time stamps for secondary events.

    @heplesser
    heplesser committed Oct 2, 2022
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Commits on Oct 3, 2022

  1. Added minimal unit test for problems when using one-to-one connectivity.

    @heplesser
    heplesser committed Oct 3, 2022
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Commits on Oct 4, 2022

  1. Converted one-to-one-multithreading test to pytest

    @heplesser
    heplesser committed Oct 4, 2022
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Commits on Oct 6, 2022

  1. Update mip_corrdet test for delivery at beginning of slice

    @heplesser
    heplesser committed Oct 6, 2022
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Commits on Oct 19, 2022

  1. Attempt solution for multithreading problem

    @heplesser
    heplesser committed Oct 19, 2022
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  2. Revised compressed_spike_data_map_, removing load balancing over threads

    @heplesser
    heplesser committed Oct 19, 2022
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  3. Fix formatting

    @heplesser
    heplesser committed Oct 19, 2022
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Commits on Oct 20, 2022

  1. Extended onetone_multithreaded test to spike_transmission test

    @heplesser
    heplesser committed Oct 20, 2022
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  2. Fixed formatting

    @heplesser
    heplesser committed Oct 20, 2022
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Commits on Oct 21, 2022

  1. Added comment about fixed MPI buffer size for experimentation

    @heplesser
    heplesser committed Oct 21, 2022
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  2. Disabled all CI steps except MPI_ONLY for time of development

    @heplesser
    heplesser committed Oct 21, 2022
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Commits on Oct 23, 2022

  1. Test direct target buffer construction from compressed_spike_data; no… 

    …t correct yet ci skip
    @heplesser
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  2. Set 'more_targets' flag correctly. Some MPI problems, likely du to si… 

    …ngle comm with no check for buffer size/completeness.
    @heplesser
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Commits on Oct 24, 2022

  1. Added blockwise communication of connectivity to new compressed schem… 

    …e; still buggy
    @heplesser
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Commits on Oct 28, 2022

  1. Single-threaded MPI now working correctly

    @heplesser
    heplesser committed Oct 28, 2022
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Commits on Oct 30, 2022

  1. Temporary fix to AssignedRanks to ensure correct MPI behavior

    @heplesser
    heplesser committed Oct 30, 2022
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Commits on Dec 14, 2022

  1. Merging with main

    @med-ayssar
    med-ayssar committed Dec 14, 2022
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  2. Passing all pytests

    @med-ayssar
    med-ayssar committed Dec 14, 2022
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Commits on Dec 15, 2022

  1. Merge pull request #26 from med-ayssar/deliver_events_first_ 

    Deliver events first
    @heplesser
    heplesser authored Dec 15, 2022
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  2. Re-added support for growing MPI spike buffers. 

    Co-authored-by: Håkon Mørk <hakon.mork@nmbu.no>
Co-authored-by: Susanne Kunkel <susanne.kunkel@nmbu.no>
    @heplesser @hakonsbm @suku248
    3 people committed Dec 15, 2022
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  3. Remove spurious buffer resizing and unnecessary emitted flag

    @heplesser
    heplesser committed Dec 15, 2022
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  4. Fix end vs complete flag use in deliver_events

    @heplesser
    heplesser committed Dec 15, 2022
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Commits on Dec 16, 2022

  1. Add comments on how spike gathering and delivery works.

    @heplesser
    heplesser committed Dec 16, 2022
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  2. Added shrinking of spike buffers

    @heplesser
    heplesser committed Dec 16, 2022
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  3. Revised shrink/grow scheme

    @heplesser
    heplesser committed Dec 16, 2022
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Commits on Dec 19, 2022

  1. Correctly place sw_comm_spikes.stop()

    @heplesser
    heplesser committed Dec 19, 2022
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Commits on Dec 21, 2022

  1. Merge branch 'master' into deliver_events_first

    @heplesser
    heplesser committed Dec 21, 2022
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Commits on Feb 16, 2023

  1. Support SecondaryEvents in deliver_events_first branch

    @heplesser
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Commits on Feb 18, 2023

  1. Fix communication of receive buffer position for 2ndry events with co… 

    …mpressed spikes
    @heplesser
    heplesser committed Feb 18, 2023
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Commits on Feb 19, 2023

  1. Update connection infrastructure correctly from GetConnections

    @heplesser
    heplesser committed Feb 19, 2023
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  2. Remove incorrect compressed_spike_data_map_ resizes

    @heplesser
    heplesser committed Feb 19, 2023
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  3. Adapt rate-neuron input delay handling to deliver events first logic.

    @heplesser
    heplesser committed Feb 19, 2023
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Commits on Feb 20, 2023

  1. Introduce extra growth for spike buffers, improve comments; side effe… 

    …ct are some debug outputs.
    @heplesser
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  2. Revised scheme for exchanging buffer size information for resizing

    @heplesser
    heplesser committed Feb 20, 2023
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  3. Fix formatting

    @heplesser
    heplesser committed Feb 20, 2023
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  4. Merge branch 'master' into deliver_events_first

    @heplesser
    heplesser committed Feb 20, 2023
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  5. Fix merge problem

    @heplesser
    heplesser committed Feb 20, 2023
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  6. Remove unused return value

    @heplesser
    heplesser committed Feb 20, 2023
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  7. Add copy constructor and assignment op for OffGridSpikeData

    @heplesser
    heplesser committed Feb 20, 2023
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  8. Change CSDMapEntry to bitfield

    @heplesser
    heplesser committed Feb 20, 2023
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  9. Activate off grid spikes

    @heplesser
    heplesser committed Feb 20, 2023
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  10. Collocate from offgrid register if needed

    @heplesser
    heplesser committed Feb 20, 2023
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  11. Make test more focused and efficient

    @heplesser
    heplesser committed Feb 20, 2023
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Commits on Feb 21, 2023

  1. Adapt offgrid sending to three-dim register

    @heplesser
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  2. Adjust test to deliver_events_first time logic

    @heplesser
    heplesser committed Feb 21, 2023
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  3. Fix delivery of both on-grid and off-grid spikes

    @heplesser
    heplesser committed Feb 21, 2023
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  4. Made buffer grow/shrink user configurable

    @heplesser
    heplesser committed Feb 21, 2023
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  5. Reactivate full set of github test

    @heplesser
    heplesser committed Feb 21, 2023
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  6. Fixed formatting

    @heplesser
    heplesser committed Feb 21, 2023
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Commits on Feb 22, 2023

  1. Fix warnings arising from signedness

    @heplesser
    heplesser committed Feb 22, 2023
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  2. Fix remaining compiler warnings

    @heplesser
    heplesser committed Feb 22, 2023
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  3. Experimentally re-activate OpenMP for FullMacos CI testing

    @heplesser
    heplesser committed Feb 22, 2023
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  4. Revert "Experimentally re-activate OpenMP for FullMacos CI testing" 

    This reverts commit 03845a5.
    @heplesser
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Commits on Feb 23, 2023

  1. Fixed code formatting

    @heplesser
    heplesser committed Feb 23, 2023
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Commits on Feb 28, 2023

  1. Add debuggigng output

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Commits on Mar 1, 2023

  1. Add more debugging output

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  2. Adding target table dumping

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Commits on Mar 2, 2023

  1. Yet more debugging output

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Commits on Mar 27, 2023

  1. Added debugging output for target exchange

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Commits on Mar 28, 2023

  1. Correct target exchange for compressed case

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  2. Disable debug output and tweak batch size for testing

    @heplesser
    heplesser committed Mar 28, 2023
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  3. Deactivate source dumping

    @heplesser
    heplesser committed Mar 28, 2023
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  4. Make full logging compile-time configurable

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    heplesser committed Mar 28, 2023
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  5. Fixed C++ code formatting

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Commits on Apr 4, 2023

  1. Set BATCH_SIZE back to 8

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Commits on Apr 6, 2023

  1. Fix comment; fix warning due to incorrect logging wrapping.

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  2. More careful macro-protection of full-logging-only code to avoid comp… 

    …iler warnings.
    @heplesser
    heplesser committed Apr 6, 2023
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  3. Remove variable never used and commented-out code.

    @heplesser
    heplesser committed Apr 6, 2023
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  4. Do not deliver events during first slice of simulation.

    @heplesser
    heplesser committed Apr 6, 2023
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  5. Add comment

    @heplesser
    heplesser committed Apr 6, 2023
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Commits on Apr 7, 2023

  1. Fix int/uint problem

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    heplesser committed Apr 7, 2023
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Commits on Apr 10, 2023

  1. Skip tests requiring multiple threads

    @heplesser
    heplesser committed Apr 10, 2023
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Commits on Jul 3, 2023

  1. Skip also connect outdegree test when running without threads

    @heplesser
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  2. Merging main into deliver_events_first.

    @heplesser
    heplesser committed Jul 3, 2023
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  3. Fixed data types

    @heplesser
    heplesser committed Jul 3, 2023
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Commits on Jul 6, 2023

  1. Ensure test_stdp_synapse reference data has not too many spikes; conv… 

    …ert to parametrize
    @heplesser
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  2. Adjusted mip corrdet test to deliver events first scheme

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    heplesser committed Jul 6, 2023
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Commits on Jul 7, 2023

  1. Fix formatting issues

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  2. Restrict test_spike_transmission to single thread if NEST does not su… 

    …pport threads.
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Commits on Aug 8, 2023

  1. Removing AssignedRanks for spike buffers and simplifying SendBufferPo… 

    …sition
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Commits on Aug 10, 2023

  1. Remove lag dimension from emitted_spikes_register

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  2. Merge branch 'master' into def_nolag_mrg

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    heplesser committed Aug 10, 2023
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Commits on Sep 4, 2023

  1. Merge branch 'master' into def_nolag_mrg

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    heplesser committed Sep 4, 2023
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Commits on Sep 7, 2023

  1. Fix lcid and syn_id boundary checks; see also nest#2529 for suggested… 

    … follow-up.
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    heplesser committed Sep 7, 2023
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  2. Remove spurious thread id argument

    @heplesser
    heplesser committed Sep 7, 2023
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  3. Remove debugging output

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    heplesser committed Sep 7, 2023
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  4. Tidy up assertion

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    heplesser committed Sep 7, 2023
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  5. Remove sort_connections flag from tests

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    heplesser committed Sep 7, 2023
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  6. Remove adaptive_spike_buffers flag and max_buffer_size_spike_data ker… 

    …nel parameter
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    heplesser committed Sep 7, 2023
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  7. Improve comment

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    heplesser committed Sep 7, 2023
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  8. Update PyNEST KernelAttributes wrt to removed and added kernel proper… 

    …ties
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    heplesser committed Sep 7, 2023
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  9. Slight refactoring of deliver_events_() for greater clarity

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    heplesser committed Sep 7, 2023
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  10. Reformatted C++ files

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    heplesser committed Sep 7, 2023
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  11. Improve buffer resize logging

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    heplesser committed Sep 7, 2023
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  12. Better variable names

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    heplesser committed Sep 7, 2023
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  13. Avoid technical problems in test

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    heplesser committed Sep 7, 2023
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Commits on Sep 10, 2023

  1. Removed no-longer used methods and fields and improved comments

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    heplesser committed Sep 10, 2023
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  2. Add comments

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    heplesser committed Sep 10, 2023
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Commits on Sep 11, 2023

  1. Remove FULL_LOGGING calls

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    heplesser committed Sep 11, 2023
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  2. Correct placement of timers

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    heplesser committed Sep 11, 2023
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  3. Fix buffer parameter names and stopwatch code location

    @heplesser
    heplesser committed Sep 11, 2023
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  4. Set spike_buffer_shrink_limit to 0 to turn off shrinking by default

    @heplesser
    heplesser committed Sep 11, 2023
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  5. Moved ResizeLog to separate file and rename BufferResizeLog

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    heplesser committed Sep 11, 2023
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  6. Apply suggestions from code review 

    Co-authored-by: Jochen Martin Eppler <jougs@gmx.net>
Co-authored-by: jessica-mitchell <mitchell20j@gmail.com>
    @heplesser @jougs @jessica-mitchell
    3 people authored Sep 11, 2023
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  7. Merge branch 'def_nolag_mrg' of github.com:heplesser/nest-simulator i… 

    …nto def_nolag_mrg
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  8. Update cmake/ProcessOptions.cmake 

    Co-authored-by: Jochen Martin Eppler <jougs@gmx.net>
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    heplesser and jougs authored Sep 11, 2023
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  9. Update libnestutil/config.h.in 

    Co-authored-by: Jochen Martin Eppler <jougs@gmx.net>
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    heplesser and jougs authored Sep 11, 2023
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  10. Update nestkernel/event_delivery_manager.h 

    Co-authored-by: Melissa Lober <47082241+mlober@users.noreply.github.com>
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    heplesser and mlober authored Sep 11, 2023
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  11. Update nestkernel/event_delivery_manager.h 

    Co-authored-by: Melissa Lober <47082241+mlober@users.noreply.github.com>
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    heplesser and mlober authored Sep 11, 2023
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  12. Some improvements around FULL_LOGGING_ONLY

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    heplesser committed Sep 11, 2023
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  13. Merge branch 'def_nolag_mrg' of github.com:heplesser/nest-simulator i… 

    …nto def_nolag_mrg
    @heplesser
    heplesser committed Sep 11, 2023
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  14. Merge branch 'master' of github.com:nest/nest-simulator into def_nola… 

    …g_mrg
    @heplesser
    heplesser committed Sep 11, 2023
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  15. Fix C++ formatting

    @heplesser
    heplesser committed Sep 11, 2023
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  16. Fix tests after merge

    @heplesser
    heplesser committed Sep 11, 2023
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  17. Fix formatting

    @heplesser
    heplesser committed Sep 11, 2023
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  18. Update nestkernel/spike_data.h 

    Co-authored-by: Melissa Lober <47082241+mlober@users.noreply.github.com>
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    heplesser and mlober authored Sep 11, 2023
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Commits on Sep 13, 2023

  1. Fix formatting of kernel SLI documentation

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    heplesser committed Sep 13, 2023
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  2. Merge branch 'def_nolag_mrg' of github.com:heplesser/nest-simulator i… 

    …nto def_nolag_mrg
    @heplesser
    heplesser committed Sep 13, 2023
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  3. Fix typos

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    heplesser committed Sep 13, 2023
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