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NEURON 8.2

8.2.2

Release Date : 15-12-2022

What's New

  • Python 3.11 support
  • Re-enabled MUSIC support in NEURON (#1896)
  • CVode.poolshrink(1) deletes unused mechanism pools. (#2033)

Bug Fixes

  • Bugfix for rxd reactions involving rxd parameters. #1933

Improvements / Other Changes

  • Documentation
    • windows build updates (#1991)
      • how to build NEURON
      • adapt scripts for local usage
    • added NMODL documentation in various constructs in hoc and python (#2011)
  • SETUPTOOLS_USE_DISTUTILS=stdlib (#1924)
  • Update CoreNEURON submodule to latest version

For the complete list of commits, see the list in GitHub Issue #2109

8.2.1

Release Date : 12-08-2022

What's New

  • Change mcomplex.dat normalization to hh/5. (#1895)
  • Jupyter support for ModelView #1907

Bug Fixes

  • nrnivmodl_core_makefile: fix SDKROOT (#1942)
  • First time declaration of section in template must be at command level. (#1914)
  • setup.exe installer must distribute env.exe (neuronsimulator#1941)

Improvements / Other Changes

  • Documentation
    • added new INCF/CNS 2022 online material (#1932)
    • updates (dealing with sims, generating movie, modelview, more #1925 )
    • transfer from Yale website (#1867)
  • nrnmpi_load: drop printf for already loaded lib (#1938)

For the complete list of commits, see the list in GitHub Issue #1944

8.2.0

Release Date : 01-07-2022

What's New

  • Allow multiple BEFORE/AFTER blocks of same type in a MOD file. #1722
  • Several documentation updates, including randomness in NEURON models #1727, NEURON course exercise sets from 2018 #1735 and publications using NEURON #1819.
  • CMake: improved documentation targets. (#1725)

Breaking Changes

  • Support for Python 3.6 was dropped, as it has reached end-of-life (#1733).
  • In this release, more declarations of NEURON methods (typically nrn_ and hoc_ functions) are implicitly included in translated MOD files. This can cause compilation errors with MOD files that include incorrect declarations of these methods in VERBATIM blocks. (#1755, #1811, #1825).
  • Declaring STATE variables as GLOBAL is now disallowed. (#1723)

Deprecations & future changes

  • NEURON is in the process of being fully migrated to a C++ codebase.
    Starting with next major release 9.0.0, MOD files will be converted to C++ instead of C. This will break compatibility with some legacy MOD files containing VERBATIM blocks and code may have to be updated given that some valid C code is not valid C++. A migration guide is being compiled in the latest online documentation (note that it may change post release).
  • Random123 will be the default random number generator in NEURON and most of the random number distributions implementations will be replaced by those in the C++ standard library, while a few will be discontinued. See #1330 for follow-up and questions.

Bug Fixes

  • Fix for #335: Return proper exit code in hoc execution #1633
  • Build on Ubuntu21.10 WSL: escape special characters (#1862)

Improvements / Other Changes

  • Support for using mallinfo2() (#1805)
  • HOC domain for Sphinx 5.0.1

Upgrade Steps

  • If your MOD files contain VERBATIM blocks you may need to refer to the aforementioned C++ migration guide and make minor changes to prepare for the upcoming 9.0.0 release. Remaining compatible with 8.2.0 and older versions is typically straightforward.

For the complete list of features and bug fixes, see the list in GitHub Issue #1879

NEURON 8.1

8.1.0

Release Date : 25-03-2022

What's New

  • Python wheels

    • Support for ARM (Aarch64) Platform wheels via CircleCI - Python 3.6 to 3.10 (#1676)
    • Apple M1 Platform wheels - Python 3.8 to 3.10 (#1649)
    • NVIDIA GPU enabled wheels
      • First iteration released under a separate package: neuron-gpu
        • Must use NVHPC 21.1 SDK when you compile your MOD files (#1657)
    • Improved CoreNEURON support (#1705)
      • Use vendor compilers like Intel, Cray or NVHPC for better performance when you compile MOD files using nrnivmodl.
    • Support for HPE MPT MPI library (#1498)
    • Linux wheels are now manylinux2014 (#1365)

  • MacOS universal2 package installer now available - Python 3.8 to 3.10

  • CoreNEURON

    • Tight integration for both in-memory and as well as file transfer mode
    • Extend CoreNEURON POINTER transfer to any RANGE variable in a NRN_THREAD (#1622)
    • Support for BEFORE/AFTER constructs in MOD file (#1581)

  • RXD

    • SaveState support added (#1586)
    • Dynamic extracellular tortuosity and volume fraction (#1260)
    • 3D support for importing multiple morphologies and for moving imported morphologies (#1147)

  • Dedicated CI repository nrn-build-ci to check builds on different distributions. Check this if you have build issues.

  • Documentation

    • Integrated various documentation & tutorials from neuron.yale.edu website to the readthedocs (#1674)
    • Added training videos, guides and a list of NEURON publications
    • CoreNEURON: usage, MOD files compatibility/migration, profiling and (GPU) performance benchmarking
    • RxD programmer's reference expanded and rewritten (#1680)
    • Propose changes directly from ReadTheDocs - click on Edit on GitHub

Breaking Changes

  • Models using _NrnThread in a VERBATIM block will fail now. Change it to NrnThread.See #1609.
  • Minimum CMake version supported is now 3.15.0 (#1408)
  • Python2 and Python3.5 support dropped
  • Legacy internal readline source code is removed, must have Readline installed (#1371)
  • Python wheels are now manylinux2014 (#1365)

Deprecations

  • NEURON is being migrated to a C++ codebase and beginning with the next release MOD files will be converted to C++ instead of C. This might break compatibility with some legacy MOD files containing VERBATIM blocks. We will update the NEURON documentation describing how one can make MOD files compatible with this change.
  • Python 3.6 Is End-of-Life - drop support after 8.1 release (#1651)

Bug Fixes

  • Can use ParallelContext.mpiabort_on_error(0) to say do not call to MPI_Abort on error (#1567)
  • OpenMPI initialisation crash: argv[argc] should be null. (#1682)
  • Avoid segfault if error during construction of POINT_PROCESS (#1627)
  • Fixes a 1D/3D voxelization problem where frusta are outside the 3D grid. (#1227)
  • Allow for two point (single section) SWC somas (#1144)
  • Fix for current response in 3D reaction-diffusion simulations (#1721)
  • rxdmath.abs no longer raises an exception (#1545)
  • Fixes for 3D reaction-diffusion grid alignment edge cases (#1471, #1227)
  • Update coreneuron : gpu bugfix for the BBP models (#1374)
  • Fix UndefinedBehaviourSanitizer errors. (#1518)
  • import3d_gui bugfix for HOC classes and top-level (#1159)

Improvements / Other Changes

  • Documentation
    • sphinx jupyter notebooks integration via nbsphinx (#1684)
    • Update CoreNEURON documentation. (#1650)
    • Building python wheels & managing NEURON Docker Images (#1469)
    • Short tutorial on using the profiler interface (#1453)
    • docs: Updated several rxd tutorials (#1061)
    • docs: WSL & Linux Python Wheel (#1496)
    • Update GPU profiling documentation (#1538)
  • Testing and coverage
    • Integration of tqperf model for CI and CoreNEURON testing (#1556)
    • Add olfactory bulb mode as external test (#1541)
    • Add reduced dentate model tests (#1515)
    • Add BBP channel-benchmark to CTest suite. (#1439)
    • Make neuronsimulator/nrntest part of the CI (#1429)
  • Refactorings
    • Move codebase to CPP (#763)
    • Remove all code related to NRN_REALTIME and NRN_DAQ (#1401)
    • Drop legacy hash implementations: nrnhash (#1403)
    • Remove absolute paths from generated code for ccache builds (#1574)
    • Using std::unordered_map as Gid2PreSyn/Int2TarList (#1568)
    • nrnivmodl succeeds when there are no mod files (#1583)
    • Fix UndefinedBehaviourSanitizer errors. (#1518)
    • Remove copy of readline (#1396)
    • Remove multisend specific for BlueGene (DMA) (#1294)
  • Improvements
    • Possible to prefer python from $PATH when building from source with CMake #1659
    • User can use MPI_LIB_NRN_PATH to provide MPI library on linux platform (#1172)
    • MPI Multisend available in NEURON by default (#1537)
    • modlunit: Add CHARGE keyword and map it to VALENCE. (#1508)
    • Allow user to specify dialog popup location. (#1487)
    • Allow python section.disconnect(). (#1451)
    • Implement BBSaveState for Python cells (#1355)
    • macos build_wheels: add /usr/x11 to CMAKE_PREFIX_PATH (#1565)
    • Add NRN_NMODL_CXX_FLAGS to facilitate cross compilation (#1174)
  • RXD
    • Faster convergence rate for surface voxel partial volume estimation (#1555)
    • Internal API for saving/restoring 3D voxelization (#1476)
    • Prevent RxD keeping objects alive (#1270, #1103, #1072)
    • Improved assignment of 3D voxels to segments (#1149)

Upgrade Steps

  • Linux wheels are now manylinux2014: upgrade your pip
  • Legacy internal readline source code is removed: install readline on your system
  • Python2 and Python3.5 support dropped: migrate to Python 3.7+ (3.6 is deprecated)

For the complete list of features and bug fixes, see Commits going into 8.1.0 in GitHub Issue #1719

NEURON 8.0

8.0.2

Release Date : 02-02-2022

Bug Fixes

Python 3.10 bugfixes for RXD and Windows, more details in GitHub PR #1614

8.0.1

Release Date : 28-01-2022

What's New

  • Python 3.10 support & wheels

Bug Fixes

For the complete list of bug fixes, see the list in GitHub PR #1603

Improvements / Other Changes

  • Introduce a Sphinx HOC domain for NEURON documentation

8.0.0

Release Date : 30-04-2021

What's New

  • Dynamic selection of legacy vs modern units using HOC/Python API (default : modern)
  • Faster reaction-diffusion support
  • Initial GPU support using integration of CoreNEURON
  • Binary installer for new Apple M1 platform
  • Binary wheel distribution for Python 3.9 and Python 2.7
  • Release of NMODL version 0.3 (available as python wheel)
  • Versioned documentation available via nrn.readthedocs.io
  • CMake as a primary build system for NEURON and Interviews

Breaking Changes

  • h.Section now interprets positional arguments as name, cell. Previously positional arguments were interpreted in the other order. (Calling it with keyword arguments is unchanged.)
  • For 3d reaction-diffusion simulations, the voxelization and segment mapping algorithms have been adjusted, especially around the soma. Voxel indices and sometimes counts will change from previous versions.

Deprecations

  • Five functions in the neuron module: neuron.init, neuron.run, neuron.psection, neuron.xopen, and neuron.quit.
  • Autotools build is deprecated and will be removed in the next release. Use CMake instead.
  • Python 2 and Python 3.5 support is deprecated and will be removed in the next release. Use Python >= 3.6

Bug Fixes

For the complete list of bug fixes, see the list on the GitHub here.

Improvements / Other Changes

  • Allow for two point (single section) SWC somas
  • GitHub Actions and Azure as primary CI systems. Travis CI removed.
  • GitHub Releases provides full source tarballs, binary installers and python wheels.
  • Improved testing and CI infrastructure including GPUs
  • nrn-build-ci repository test nightly builds for Ubuntu 18.04, Ubuntu 20.04, Fedora 32, Fedora 33, CentOS7, CentOS8, Debian Buster (10) and macOS 10.15 platforms.
  • Improved integration of CoreNEURON
  • Support for recent numpy version
  • Various build improvements on Linux, MacOS and HPC platforms
  • Documentation from various repositories is consolidated under nrn repository
  • New releases via Spack and Easybuild package managers
  • Fix deadlock when compiling NEURON with AVX-512
  • Add backward-cpp for better backtraces
  • NEURON_MODULE_OPTIONS environment variable to pass in nrniv options before neuron import

Upgrade Steps

Existing models should work without any changes. In order to upgrade NEURON version you can:

  • Use python wheels provided for Linux or Mac OS platform
  • Use binary installer provided for windows
  • Install from source, preferably using CMake build system
  • For new version, it's always a good idea to start over from scratch with nrnivmodl (deleting existing directory like x86_64)

See Installation section under nrn.readthedocs.io/. In the very rare case that numerical differences exist, check selection of legacy vs modern units.

Contributors

See the list of contributors on respective GitHub projects:

Feedback / Help