NEST 2.18.0

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WARNING: This version of NEST is affected by issue #1394, which can lead to incorrect simulation results under certain circumstances. Please double-check all simulation results obtained with this version and if in doubt, re-run using a different split between MPI processes and threads. The description of the issue contains more details and will be updated when new information becomes available.

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NEST 2.18.0 is the result of 116 pull-requests (1128 commits) by 31 developers since NEST 2.16.0 which was released on 2018-08-21.

This release provides a number of new neuron and plasticity models and additional functionality. It improves memory allocation and performance during network construction. It includes a number of bug fixes and is the first release that can be installed via aptitude and in an Conda environment directly from conda-forge.

Enhancements

Model

• Add iaf_cond_alpha_multisynapse model
• Add conductance based I&F model with beta shaped PSCs
• Implemented step_rate_generator for piecewise constant rate input
• Add Clopath STDP synapse and two supported neuron models
• Add new neuron model hh_cond_beta_gap_traub
• Added test_multiarea_model_siegert_rates
• Add optional escape noise in iaf_psc_exp
• Add iaf_psc_alpha_ps neuron model

Installation

• Add conda-forge installation documentation for Linux and MacOSX

Documentation

• Add documentation in Topology User Manual
• hpc_benchmark.sli is now invariant under different MPI-process/thread splits with fixed VP number
• Implement breathe extension and improve generation/format of model documentation for website
• Add documentation on how to create C++-level unit tests

Kernel

• Code compatibility with C++17
• New container for connections
• Allow compile-time configuration of bit-field sizes in Target class
• Add ostream operator template for std::vectors
• Connection sorting using Boost's sorting function

Infrastructure

• Docker image for the NEST simulator
• Build on Travis using clang and gcc compilers
• Conditional travis builds using build stages
• Travis build on OSX

Pynest

• Make detailed exceptions from lower levels available in PyNEST
• Show periodic boundary conditions for masks and kernel
• Serialize output of GetStatus and GetDefaults for JSON
• Add PyNEST function to synchronize MPI processes
• Change to dynamic import in PyNEST API
• Simplify dynamic import of PyNEST submodules

Bug-Fixes

Model

• Fix header installation and multiplicity handling in MyModule
• Fix stability of iaf_psc_exp_ps for equal membrane and synaptic time constants
• Fix creation of inhomogeneous poisson generator with parameters
• Fix normalization factor for iaf_cond_beta
• Fix uninitialized variable in iaf_psc_exp

Installation

• Fix bug in JURON CMake file
• MyModule example missing Event methods
• Fix static linking of modules
• Fix header installation and multiplicity handling in MyModule
• Change target directory for doxygen from source to build

Interpreter

• Fix interpretation of verbosity and debug command line arguments as input script filename
• Prevent execution of --debug and --verbosity options as files

Documentation

• Correct documentation on libneurosim requirements
• Fix broken internal links in doc/guides

Kernel

• Handle number_of_connections<1 in topology
• Make GetConnection filter by synapse label when only target attribute is given
• Take multiplicity into account in local_spike_counter
• Throw error if creating too many connections on one thread
• Enable the use of connections without delay in Topology
• Bugfix: Reliably create masked layer when using topology's convergent connect
• Fix MPI synchronization problem in presence of very small layers
• Fix multiple definition of rho build complain observed on AArch64 with FCC

Infrastructure

• Make test_refractory.py run with make installcheck
• Make testsuite run when nosetests is unavailable
• Fix bug in test_stdp_multiplicity.py
• Use configured instead of standard Python executable
• Make python mpitest run during installcheck
• Fix postsynaptic trace edge case
• Use relative path to logo in documentation
• Fix incorrect flag in ProcessOptions.cmake

Pynest

• Fix issue when running hh_phaseplane.py with Python 2
• nest.Disconnect parameters are consistent with documentation
• Fix broken PyNEST, remove traces of ResumeSimulation
• Check recorder type_id instead of model name in plotting modules

Maintenance

Model

• Make stdp_facetshw synapse consistent with the temporal fix for STDP numerical imprecision
• Update description of rate model neurons and change parameter names
• Fix issues in siegert_neuron
• Add deprecation warnings and changed format of the warnings
• Remove unused functions in hh_psc_alpha models

Installation

• JURON support: Add platform specific CMake files
• Follow-up patch on the CMake with-warning variable and add -Xg flag to CMAKE_CXX_FLAGS
• Add CMake flag to enable/disable hpc synapses
• 32-bit compatibility (64-bit gid on 32-bit architecture)
• CMake option and documentation for using the Intel compiler
• Fix nest_vars in case of undefined PYTHONPATH
• Cleanup for the K computer specific CMake file for v2.18
• Fix up dependencies in Ubuntu install instructions

Interpreter

• Add skip_if_without_music to nest dictionary

Documentation

• New User Documentation for NEST
• Fix the documentation (semantics) for get_synaptic_elements_vacant()
• Refactor source code comment blocks
• Change HTML to CGI module import to eliminate extra Python2 dependency
• Source code comment blocks refactored
• Remove outdated README and empty directory from PyNEST examples
• Upgrade pyyaml in doc requirements due to vulnerability
• Minor updates to pynest tutorial part 2
• Fix documentation in sinusoidal_gamma_generator example
• Correcting documentation on current input in precise neurons (fixes #226).
• Remove outdated plot scripts from examples
• Add advice against using NEST in threaded processes; addresses #361.
• Fix links to NEST resources throughout the source code
• Improve documentation of get_verbosity and set_verbosity in PyNEST
• Convert topology user manual to ReStructuredText
• Update parallel computing docs regarding configuration
• Update links to model directory in docs
• Documentation update for #1177 ("Increase maximum line length in source code formatting style from 80 to 120")

Kernel

• Make lid to gid conversion (and vice versa) in the VPManager more consistent
• Move ConnectionManager methods from impl to h
• Use reverse iterator in get_history
• Rename {get,set}_delay to {get,set}_delay_steps
• Remove unused variables
• Remove old references to resume()
• Refactor GetConnections to improve performance
• Improve connection performance over threads
• Fix code formatting issue introduced by merging #1060
• Add documentation on splitting and repeating simulations, and deprecation warning for ResetNetwork
• Increase maximum line length in source code formatting style from 80 to 120

Infrastructure

• Move Travis-CI build script to extras directory
• Remove outdated release-making script
• Remove emacs support for SLI
• Make the check for copyright headers and unused Names part of the CI run
• Explicit indices
• Add MPI test for correct number of spikes when multiplicity > 1
• Automatic discovery of sli examples in example runner
• Replace bash by sh to eliminate extra dependency
• Add tests for libnestutil/streamers.h
• Make version information consistent

Pynest

• Restore PyNEST functions to top level modules