[NEST Users] NEST 2.20.0 released / Issue 1394 / NEST 3 to become Master Branch soon

Dear NEST Users! We are very excited about the release of NEST 2.20.0 earlier today, including 454 commits in 82 pull requests by 25 developers since NEST 2.18.0. NEST 2.20.0 brings a wide range of improvements, including * generalized leaky integrate-and-fire neuron models developed by the Allen Institute (Teeter et al, 2018) * STDP synapses with nearest-neighbor spike paring schemes * improved documentation on Read The Docs<https://nest-simulator.readthedocs.io/en/latest/>. Please see below for a complete list of changes. NEST 2.20.0 is available for download from https://github.com/nest/nest-simulator/releases/tag/v2.20.0 To cite NEST 2.20.0, please refer to the Zenodo entry at https://doi.org/10.5281/zenodo.3605514 WARNING: NEST 2.20.0 is affected by issue #1394<https://github.com/nest/nest-simulator/issues/1394>, which may lead to incorrect results under certain circumstances when simulating very large networks across many MPI processes and threads. Simulations using only MPI parallelism, but no threads, work correctly according to our tests. The same holds for simulations using only thread-parallelism. The issue also affects NEST 2.18.0 and 2.16.0, but not 2.14.0. According to our analysis, in affected simulations, a very small number of connections is not created correctly. This happens under random cirucmstances, so that in one series of tests, out of ten identical simulations, five simulations produced correct results, while the remaining five simulations produced different results. For details, please follow the issue on GitHub. We are currently working hard to identify the cause of this issue and hope to be able to provide a fix soon. The next big step forward in NEST development will be the merge of the nest-3 development branch into the master branch on GitHub. NEST 3 will bring major improvements to the user interface and considerable changes under the hood. Please see https://nest-simulator.readthedocs.io/en/nest-3/guides/from_nest2_to_nest3.… https://nest-simulator.readthedocs.io/en/nest-3/ref_material/nest2_vs_3.html for more information on changes to come and modifications required to existing scripts. Best regards, Hans Ekkehard Plesser President, The NEST Initiative ------------------------------------------------ NEST 2.20.0<https://doi.org/10.5281/zenodo.3605514> is the result of 454 commits in 82 pull requests by 25 developers since NEST 2.18.0<https://doi.org/10.5281/zenodo.2605422> which was released on June 7, 2019. This release wraps up the 2.x series of NEST and contains many improvements and bug fixes. Highlights are the addition of the generalized leaky integrate-and-fire neuron models by the Allen Institute<https://portal.brain-map.org/explore/models/glif-single-neuron…on>, STDP synapses with nearest-neighbor spike pairing schemes and improved documentation, available on Read The Docs<https://nest-simulator.readthedocs.io/en/latest/>. Following is a list of all merged pull requests: Enhancements Models * Add STDP synapses with nearest-neighbor spike pairing schemes<https://github.com/nest/nest-simulator/pull/865> * Add generalized leaky integrate-and-fire (GLIF) neuron models by Allen Institute<https://github.com/nest/nest-simulator/pull/1126> * Add iaf_psc_alpha_ps neuron model<https://github.com/nest/nest-simulator/pull/1169> Installation * Add conda-forge installation documentation for Linux and MacOSX<https://github.com/nest/nest-simulator/pull/1204> * Add Fugaku platform CMake file<https://github.com/nest/nest-simulator/pull/1231> * Clean the build process for the NEST Debian packages<https://github.com/nest/nest-simulator/pull/1316> * Hike minimum required CMake to 3.12 and add support for OpenMP with Apple Clang<https://github.com/nest/nest-simulator/pull/1386> * More informative compiler information in CMake summary<https://github.com/nest/nest-simulator/pull/1403> Documentation * Added initial membrane potential options to microcircuit example<https://github.com/nest/nest-simulator/pull/1206> * Add initial membrane potential options to microcircuit example<https://github.com/nest/nest-simulator/pull/1260> * Add new options for installation and improve instructions for NEST<https://github.com/nest/nest-simulator/pull/1262> * Updated/extended macOS install instructions<https://github.com/nest/nest-simulator/pull/1297> * Update DOI and release buttons in README; add Zenodo reference to NEST 2.18.0<https://github.com/nest/nest-simulator/pull/1314> * Add link on website to new PyNEST templates and update citations<https://github.com/nest/nest-simulator/pull/1351> * Provide guidelines to writing to mailing list in documentation<https://github.com/nest/nest-simulator/pull/1368> Kernel * Introduce time-driven spiking connections<https://github.com/nest/nest-simulator/pull/1160> * Add support for sending secondary events to and from devices<https://github.com/nest/nest-simulator/pull/1244> * Add warning about invalid connection descriptors when new connections are created<https://github.com/nest/nest-simulator/pull/1250> * Use an unsigned data type for thread in spike data<https://github.com/nest/nest-simulator/pull/1308> Infrastructure * Fast static check in Travis CI<https://github.com/nest/nest-simulator/pull/1267> PyNEST * New templates for pynest examples and api<https://github.com/nest/nest-simulator/pull/1139> * Add getattr/setattr to GIDCollection<https://github.com/nest/nest-simulator/pull/1249> * Allow specifying arrays of values in the synapse specification when connecting with fixed_total_number<https://github.com/nest/nest-simulator/pull/1266> * Use shape as argument instead of columns/rows/depth and update topology examples to NEST3<https://github.com/nest/nest-simulator/pull/1287> Bug fixes Models * Fix uninitialized variable in iaf_psc_exp<https://github.com/nest/nest-simulator/pull/1225> * Fix handling of rate change in poisson_generator_ps<https://github.com/nest/nest-simulator/pull/1280> Documentation * Remove spurious brackets from code example in tutorial<https://github.com/nest/nest-simulator/pull/1270> * Fix MUSIC example<https://github.com/nest/nest-simulator/pull/1312> Kernel * Fix multiple definition of rho build complain observed on AArch64 with FCC<https://github.com/nest/nest-simulator/pull/1233> * Fix GetConnections to correctly get connections where the target is a global receiving device<https://github.com/nest/nest-simulator/pull/1251> * Fix logical error in elseif-statements in connect functions<https://github.com/nest/nest-simulator/pull/1254> * Check variables of GSL binomial random generator where they are set<https://github.com/nest/nest-simulator/pull/1299> * Ensure number of connections for fixed total number is properly set<https://github.com/nest/nest-simulator/pull/1367> * Fix MyModule by incorporating modelsmodule refactoring from #1069<https://github.com/nest/nest-simulator/pull/1383> * Avoid segfault when using a weight recorder with a probabilistic synapse<https://github.com/nest/nest-simulator/pull/1402> Infrastructure * Fix cppcheck in Travis CI testsuite<https://github.com/nest/nest-simulator/pull/1306> Maintenance Models * Fix namespaces in Hodgkin-Huxley neuron models<https://github.com/nest/nest-simulator/pull/1256> * Make multimeter and voltmeter class names lower case<https://github.com/nest/nest-simulator/pull/1345> Installation * Fix nest_vars in case of undefined PYTHONPATH<https://github.com/nest/nest-simulator/pull/1218> * Cleanup for the K computer specific CMake file for v2.18<https://github.com/nest/nest-simulator/pull/1228> * Fix up dependencies in Ubuntu install instructions<https://github.com/nest/nest-simulator/pull/1230> * Files needed to build Debian packages (.deb)<https://github.com/nest/nest-simulator/pull/1255> * Fix extraction of version number if sources are inside another Git repository<https://github.com/nest/nest-simulator/pull/1362> * Let uninstall of NEST Debian package also delete script in profile.d<https://github.com/nest/nest-simulator/pull/1363> Interpreter * Remove handling of external POSIX signals sent to NEST<https://github.com/nest/nest-simulator/pull/1385> Documentation * Convert topology user manual to ReStructuredText<https://github.com/nest/nest-simulator/pull/1214> * Update links to model directory in docs<https://github.com/nest/nest-simulator/pull/1227> * Documentation update pertaining to maximum line length<https://github.com/nest/nest-simulator/pull/1234> * Fix PyNEST installation instructions<https://github.com/nest/nest-simulator/pull/1240> * Update download page for 2.18 and conda-forge<https://github.com/nest/nest-simulator/pull/1247> * Correct typo in random number documentation<https://github.com/nest/nest-simulator/pull/1268> * Fix PyNEST API generation for documentation using mock<https://github.com/nest/nest-simulator/pull/1274> * Add updated NEST examples to Read The Docs <https://github.com/nest/nest-simulator/pull/1277> * Replace iaf_neuron by iaf_psc_alpha in MUSIC tutorial<https://github.com/nest/nest-simulator/pull/1330> * Autogenerate PyNEST examples from source with sphinx_gallery<https://github.com/nest/nest-simulator/pull/1336> * Update syntax formatting for terms in documentation<https://github.com/nest/nest-simulator/pull/1343> * Fix broken CSS style<https://github.com/nest/nest-simulator/pull/1344> * Update mailing list email address<https://github.com/nest/nest-simulator/pull/1346> * Small typographical updates to user documentation<https://github.com/nest/nest-simulator/pull/1397> Kernel * Refactor registration of models in modelsmodule<https://github.com/nest/nest-simulator/pull/1069> * Increase maximum line length in source code formatting style from 80 to 120<https://github.com/nest/nest-simulator/pull/1177> * Unify coeffarray_as_d and coeffarray_as_uint via union<https://github.com/nest/nest-simulator/pull/1243> * Add missing include of sys/time.h<https://github.com/nest/nest-simulator/pull/1273> * Fix threading issue when connecting<https://github.com/nest/nest-simulator/pull/1276> * Remove spurious thread_local_connectors update<https://github.com/nest/nest-simulator/pull/1333> * Fix rounding issue when setting small resolution<https://github.com/nest/nest-simulator/pull/1356> * Improve information given by error messages typically triggered by Connect<https://github.com/nest/nest-simulator/pull/1399> Infrastructure * Add tests for libnestutil/streamers.h<https://github.com/nest/nest-simulator/pull/1219… * Make version information consistent<https://github.com/nest/nest-simulator/pull/1223> * Update FindLibNeurosim to take Python version into account<https://github.com/nest/nest-simulator/pull/1235> * Remove the remaining markdown config in docs<https://github.com/nest/nest-simulator/pull/1263> * Skip deployment in Travis CI testsuite when not running a build<https://github.com/nest/nest-simulator/pull/1300> * Deploy build artifacts only when the build flag is set in the reply section<https://github.com/nest/nest-simulator/pull/1302> * Change the deployment branch to master<https://github.com/nest/nest-simulator/pull/1304> * Fix cppcheck usage in Travis CI testsuite<https://github.com/nest/nest-simulator/pull/1307> * Switch to GCC8 as default in continuous integration tests on Travis<https://github.com/nest/nest-simulator/pull/1310> * Fix formatting in test_stdp_nn_synapses.py<https://github.com/nest/nest-simulator/pull/131… * Add security guidelines<https://github.com/nest/nest-simulator/pull/1329> * Moving to Python3.x on OsX<https://github.com/nest/nest-simulator/pull/1335> * Replace Python version by newest available on Travis<https://github.com/nest/nest-simulator/pull/1342> PyNEST * Fix warnings when Cythonizing pynestkernel.pyx<https://github.com/nest/nest-simulator/pull/1322> * Allow installation with Python 3.8<https://github.com/nest/nest-simulator/pull/1340> -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no Home http://arken.nmbu.no/~plesser