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 Docshttps://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 #1394https://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.h... 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
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NEST 2.20.0https://doi.org/10.5281/zenodo.3605514 is the result of 454 commits in 82 pull requests by 25 developers since NEST 2.18.0https://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 Institutehttps://portal.brain-map.org/explore/models/glif-single-neuron, STDP synapses with nearest-neighbor spike pairing schemes and improved documentation, available on Read The Docshttps://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 schemeshttps://github.com/nest/nest-simulator/pull/865 * Add generalized leaky integrate-and-fire (GLIF) neuron models by Allen Institutehttps://github.com/nest/nest-simulator/pull/1126 * Add iaf_psc_alpha_ps neuron modelhttps://github.com/nest/nest-simulator/pull/1169
Installation
* Add conda-forge installation documentation for Linux and MacOSXhttps://github.com/nest/nest-simulator/pull/1204 * Add Fugaku platform CMake filehttps://github.com/nest/nest-simulator/pull/1231 * Clean the build process for the NEST Debian packageshttps://github.com/nest/nest-simulator/pull/1316 * Hike minimum required CMake to 3.12 and add support for OpenMP with Apple Clanghttps://github.com/nest/nest-simulator/pull/1386 * More informative compiler information in CMake summaryhttps://github.com/nest/nest-simulator/pull/1403
Documentation
* Added initial membrane potential options to microcircuit examplehttps://github.com/nest/nest-simulator/pull/1206 * Add initial membrane potential options to microcircuit examplehttps://github.com/nest/nest-simulator/pull/1260 * Add new options for installation and improve instructions for NESThttps://github.com/nest/nest-simulator/pull/1262 * Updated/extended macOS install instructionshttps://github.com/nest/nest-simulator/pull/1297 * Update DOI and release buttons in README; add Zenodo reference to NEST 2.18.0https://github.com/nest/nest-simulator/pull/1314 * Add link on website to new PyNEST templates and update citationshttps://github.com/nest/nest-simulator/pull/1351 * Provide guidelines to writing to mailing list in documentationhttps://github.com/nest/nest-simulator/pull/1368
Kernel
* Introduce time-driven spiking connectionshttps://github.com/nest/nest-simulator/pull/1160 * Add support for sending secondary events to and from deviceshttps://github.com/nest/nest-simulator/pull/1244 * Add warning about invalid connection descriptors when new connections are createdhttps://github.com/nest/nest-simulator/pull/1250 * Use an unsigned data type for thread in spike datahttps://github.com/nest/nest-simulator/pull/1308
Infrastructure
* Fast static check in Travis CIhttps://github.com/nest/nest-simulator/pull/1267
PyNEST
* New templates for pynest examples and apihttps://github.com/nest/nest-simulator/pull/1139 * Add getattr/setattr to GIDCollectionhttps://github.com/nest/nest-simulator/pull/1249 * Allow specifying arrays of values in the synapse specification when connecting with fixed_total_numberhttps://github.com/nest/nest-simulator/pull/1266 * Use shape as argument instead of columns/rows/depth and update topology examples to NEST3https://github.com/nest/nest-simulator/pull/1287
Bug fixes Models
* Fix uninitialized variable in iaf_psc_exphttps://github.com/nest/nest-simulator/pull/1225 * Fix handling of rate change in poisson_generator_pshttps://github.com/nest/nest-simulator/pull/1280
Documentation
* Remove spurious brackets from code example in tutorialhttps://github.com/nest/nest-simulator/pull/1270 * Fix MUSIC examplehttps://github.com/nest/nest-simulator/pull/1312
Kernel
* Fix multiple definition of rho build complain observed on AArch64 with FCChttps://github.com/nest/nest-simulator/pull/1233 * Fix GetConnections to correctly get connections where the target is a global receiving devicehttps://github.com/nest/nest-simulator/pull/1251 * Fix logical error in elseif-statements in connect functionshttps://github.com/nest/nest-simulator/pull/1254 * Check variables of GSL binomial random generator where they are sethttps://github.com/nest/nest-simulator/pull/1299 * Ensure number of connections for fixed total number is properly sethttps://github.com/nest/nest-simulator/pull/1367 * Fix MyModule by incorporating modelsmodule refactoring from #1069https://github.com/nest/nest-simulator/pull/1383 * Avoid segfault when using a weight recorder with a probabilistic synapsehttps://github.com/nest/nest-simulator/pull/1402
Infrastructure
* Fix cppcheck in Travis CI testsuitehttps://github.com/nest/nest-simulator/pull/1306
Maintenance Models
* Fix namespaces in Hodgkin-Huxley neuron modelshttps://github.com/nest/nest-simulator/pull/1256 * Make multimeter and voltmeter class names lower casehttps://github.com/nest/nest-simulator/pull/1345
Installation
* Fix nest_vars in case of undefined PYTHONPATHhttps://github.com/nest/nest-simulator/pull/1218 * Cleanup for the K computer specific CMake file for v2.18https://github.com/nest/nest-simulator/pull/1228 * Fix up dependencies in Ubuntu install instructionshttps://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 repositoryhttps://github.com/nest/nest-simulator/pull/1362 * Let uninstall of NEST Debian package also delete script in profile.dhttps://github.com/nest/nest-simulator/pull/1363
Interpreter
* Remove handling of external POSIX signals sent to NESThttps://github.com/nest/nest-simulator/pull/1385
Documentation
* Convert topology user manual to ReStructuredTexthttps://github.com/nest/nest-simulator/pull/1214 * Update links to model directory in docshttps://github.com/nest/nest-simulator/pull/1227 * Documentation update pertaining to maximum line lengthhttps://github.com/nest/nest-simulator/pull/1234 * Fix PyNEST installation instructionshttps://github.com/nest/nest-simulator/pull/1240 * Update download page for 2.18 and conda-forgehttps://github.com/nest/nest-simulator/pull/1247 * Correct typo in random number documentationhttps://github.com/nest/nest-simulator/pull/1268 * Fix PyNEST API generation for documentation using mockhttps://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 tutorialhttps://github.com/nest/nest-simulator/pull/1330 * Autogenerate PyNEST examples from source with sphinx_galleryhttps://github.com/nest/nest-simulator/pull/1336 * Update syntax formatting for terms in documentationhttps://github.com/nest/nest-simulator/pull/1343 * Fix broken CSS stylehttps://github.com/nest/nest-simulator/pull/1344 * Update mailing list email addresshttps://github.com/nest/nest-simulator/pull/1346 * Small typographical updates to user documentationhttps://github.com/nest/nest-simulator/pull/1397
Kernel
* Refactor registration of models in modelsmodulehttps://github.com/nest/nest-simulator/pull/1069 * Increase maximum line length in source code formatting style from 80 to 120https://github.com/nest/nest-simulator/pull/1177 * Unify coeffarray_as_d and coeffarray_as_uint via unionhttps://github.com/nest/nest-simulator/pull/1243 * Add missing include of sys/time.hhttps://github.com/nest/nest-simulator/pull/1273 * Fix threading issue when connectinghttps://github.com/nest/nest-simulator/pull/1276 * Remove spurious thread_local_connectors updatehttps://github.com/nest/nest-simulator/pull/1333 * Fix rounding issue when setting small resolutionhttps://github.com/nest/nest-simulator/pull/1356 * Improve information given by error messages typically triggered by Connecthttps://github.com/nest/nest-simulator/pull/1399
Infrastructure
* Add tests for libnestutil/streamers.hhttps://github.com/nest/nest-simulator/pull/1219 * Make version information consistenthttps://github.com/nest/nest-simulator/pull/1223 * Update FindLibNeurosim to take Python version into accounthttps://github.com/nest/nest-simulator/pull/1235 * Remove the remaining markdown config in docshttps://github.com/nest/nest-simulator/pull/1263 * Skip deployment in Travis CI testsuite when not running a buildhttps://github.com/nest/nest-simulator/pull/1300 * Deploy build artifacts only when the build flag is set in the reply sectionhttps://github.com/nest/nest-simulator/pull/1302 * Change the deployment branch to masterhttps://github.com/nest/nest-simulator/pull/1304 * Fix cppcheck usage in Travis CI testsuitehttps://github.com/nest/nest-simulator/pull/1307 * Switch to GCC8 as default in continuous integration tests on Travishttps://github.com/nest/nest-simulator/pull/1310 * Fix formatting in test_stdp_nn_synapses.pyhttps://github.com/nest/nest-simulator/pull/1311 * Add security guidelineshttps://github.com/nest/nest-simulator/pull/1329 * Moving to Python3.x on OsXhttps://github.com/nest/nest-simulator/pull/1335 * Replace Python version by newest available on Travishttps://github.com/nest/nest-simulator/pull/1342
PyNEST
* Fix warnings when Cythonizing pynestkernel.pyxhttps://github.com/nest/nest-simulator/pull/1322 * Allow installation with Python 3.8https://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@nmbu.no Home http://arken.nmbu.no/~plesser