Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, openCARP uses a vMAJOR.PATCH versioning scheme. We increase the

• MAJOR version when we add functionality, and the
• PATCH version when we make backwards compatible bug fixes

Unreleased

Added

• Sinus node cell models of Fabbri (2017) and Severi (2012) et al. + AC-cAMP-PKA signalling cascade based on Behar et al. (2016) (thanks @moritz.linder)
• Update to new stimulus definition (experiments, regression tests and carputils functions) (thanks @moritz.linder)
• openCARP Docker image is now built for architectures arm64 and amd64
• New operations for igbops (intX_t and t_maxX)
• Bipole mode for igbapd
• igbtools can be piped together (reading/writing stdin and stdout)
• Documentation about running openCARP simulations on HPC systems in user manual
• Three onboarding tutorials for single cell using openCARP JupyterLab included

Changed

• Simplified the petsc interface (#352)
• Reduced Docker image size by 50% (!242)
• Remove declaration-only header files from CMakeLists
• Use current meshtool version
• Time integration for tension models (#357)
• Moved MLIR test jobs to CI test stage
• Use regression test references specified in git submodule also for Ginkgo and MLIR (!263)

Fixed

• The deps Docker image was never updated (!242)
• Support for EasyML heav() and sign() with MLIR (!260)

Known issues

• Some regression tests are failing when using Ginkgo as the numerical backend (#151)

[16.0] - 2024-08-19

Added

• Pig model based on Gaur & Vigmond et al. (2021) (thanks @moritz.linder)
• Support for max function in MLIR builds
• Support for SUNDIALS v6 and v7
• Update C++ standard to 17
• Update LLVM to 18
• MLIR noground_bidom benchmarks (thanks @huppe) to xbat (formerly Continuous Benchmarking)
• Add FindSUNDIALS.cmake to support cases where SUNDIALS doesn't provide CMake configuration file
• A link to make_dynamic_model.sh is created in the bin folder during CMake builds
• More verbose error message when statefile does not match IMP
• Flag to enable OHara model modifications as suggested by Michael Clerx (thanks @jorge.sanchez)

Fixed

• sv_dump in MLIR+DLO build where extra "0" lines were output
• Conversion of transmembrane charge into concentration (#356)
• Reference to stimulus file format for bench
• Fixed gvec output for plugins.

Changed

• Docker image archives are not stored on the web server anymore, only in the Docker registry.
• CI artifacts are kept for 12 hours instead of 2
• Removed duplicate Steward model (Stewart still exists)
• Changed the initial value of APD90 for restitution curve calculation to work with less depolarized ionic models (thanks @jorge.sanchez)
• Change in OpenMP activation: the option USE_OPENMP can now take three different values:
  • UTILS (default): OpenMP is activated for igbutils and meshtool
  • OFF: OpenMP is deactivated
  • ON: OpenMP is activated globally
  • Note: this changes the default behavior (before, OpenMP was deactivated by default).
• Compiler optimization level set to zero for param (issues with Ubuntu 24.04, gcc 13.2.0, glibc 2.39)

[15.0] - 2024-03-18

Added

• More detailed information on how stimulus currents are treated in chapter 3 of the manual
• Regression test for stress models
• Option to calculate cell surface to cell volume ratio (convert stimulus current to concentration change) (thanks @ml0401)
• Regression test for the feature above (thanks @ml0401)
• Generic build target defines below for ionic models introduced. By default all targets for a given model are built, define model specific macros to only generate code for specific targets, e.g. ALIEVPANFILOV_MLIR_CPU_GENERATED. Cleaner build logs (#243, !184, thanks @huppe)
  • CPU_GENERATED
  • MLIR_CPU_GENERATED
  • MLIR_ROCM_GENERATED
  • MLIR_CUDA_GENERATED
• CI job to keep generated IMP sources (physics/limpet/src/imps_src) in sync with .model files (on master)
• CI job to warn if IMP sources (physics/limpet/src/imps_src) are out of sync with .model files (on non-master branches)
• Support for non-activating nodes when using prepacing
• Regression test for non-existing imp regions (#332, thanks @tomas.stary)
• Documentation for MLIR tests (thanks @huppe)
• Modifications to OHara model suggested by Michael Clerx (flag CLERX)

Fixed

• Stress model variables Ca_i renamed to Cai (thanks @jorge.sanchez)
• Calling of python and shell scripts for dynamic model building now supported with AppImage after extraction
• Bugs related to IMP data layout optimisation (DLO) (thanks @huppe)
• The deps Docker image is now built on branches when Dockerfile-deps is modified
• Correctly convert math function pow to corresponding vector math library function call for MLIR code (thanks @huppe)
• Fixed buildinfo output
• Fixed Vm_clamp and GND_ex pulse forms
• Fixed HodgkinHuxley.model
• Bug when dumping state variables in DLO builds (thanks @huppe)
• Enable build in source folders which are not a repository (#351)

Changed

• State vector extension in bench when validation flag is set true (e.g. OHara.Cai -> OHara.Cai.bin) (thanks @ml0401)

[14.0] - 2023-12-07

Added

• latest tag pointing to the most current release (#334)

Changed

• The documentation of bench commands in the PDF manual is now autogenerated from bench --help
• Improved documentation for MLIR builds (thanks @vincent.loechner)
• Major rewrite of LIMPET moving from C to C++ (thanks @Raphael)
• Deprecated -buildinfo argument, now the build info is printed by default
• igbapd: linear interpolation of AP start
• State structure data layout optimization of ionic models (thanks @Raphael)
• Do --stim-assign preprocessing in bench only once and not per timestep

Fixed

• ISAC_Hu model was missing some parentheses
• Missing initialization of pointers to parameter structures in ION_IF.h
• Include units in PDF and online parameter help
• make_dynamic_model.sh works with CMake based compilation for CVODE and DEBUG (#330)
• Compatibility with SUNDIALS v6
• Checkpointing when data layout optimization (DLO) was enabled (thanks @Raphael)
• Dynamic models (#310)
• Incorrect memory copies and memory initialization on GPU when using multiple regions
• --stim-assign in bench didn't work (#338, thanks @sophiaohnms)
• Stim species assignment for multiple species with non-equal ratios
• Linear solver name changed from const char* to std::string to prevent name corruption.

[13.0] - 2023-05-25

Added

• Elec matrix integration: Added output of element and region info in case of NaN matrix entries. This help with spotting errors in the tissue parametrization (e.g zero fibers or conductivities, deteriorated elements).
• Ionic models: Added support for AMD code generation with MLIR. Ionic models can now be compiled and ran on AMD GPUs.
• Compilation of multiple versions of a given ionic model in the same build (see docs/BUILD_WITH_MLIR.md)
• --target option to select execution platform in bench (see docs/BUILD_WITH_MLIR.md)
• User manual: Cite carphelp and give an example of usage
• CI job building openCARP using the provided Makefile

Changed

• Elec matrix integration: Optimized choice of integration order.
• CMake process in physics/limpet refactored for readability
• GPU models can now access data correctly with -DENABLE_MLIR_CODEGEN=DATA_LAYOUT_OPTIMIZATION
• Use overlay2 as DOCKER_DRIVER in CI pipelines

Fixed

• Fixed a number of compiler warnings. Now builds clean with clang15.
• Build process based on plain Makefile.

Known issues

• Some regression tests are failing when using Ginkgo as the numerical backend (#151)

[12.0] - 2022-12-19

Added

• New macOS package, compatible with Apple Silicon Macs.
• Tomek ionic model.
• Pre-commit hook to generate CITATION.cff from codemeta.json
• Added Ginkgo numerical backend (use CMake option ENABLE_GINKGO)
• Added the printout of all parameters with --output-setup option
• Optimized CPU and GPU code generation for ionic models using MLIR compiler infrastructure (use CMake option ENABLE_MLIR_CODEGEN, see docs/BUILD_WITH_MLIR).

Changed

• macOS precompiled packages now contain MPICH, shipped with PETSc, like the Linux packages.
• Continuous Benchmarking can now be run on any branch (commit hash passed to Continuous Benchmarking trigger)
• Abstraction of interface to numerical backend (vectors etc.)
• Release step consists of two steps (manual tag pre-vX.Y and automatic tag vX.Y) now to include specific DOI in metadata in repo
• Steward model renamed to Stewart (fixing a typo in the name)

Fixed

• cleaned up stim.crct.type and stimulus.stimtype to only contain available stimulus types.
• --initial flag in example 01/02B

Known issues

• Some regression tests are failing when using Ginkgo as the numerical backend (#151)

[11.0] - 2022-07-18

Added

• Control over output domain for (phie, phie_i, and vm) via -dataout_i and -dataout_e.
• Dedicated, asynchronous IO processes via -num_io_nodes.
• Support for arctan, atan, sin, floor functions in .model and CellML files
• CI pipeline extended by Continuous Benchmarking via Megware's framework
• Modify package generation and include paths in make_dynamic_model.sh to make it usable in precompiled packages (rpm, deb, pkg and AppImage).

Fixed

• When using cmake to build openCARP with external tools, openMP is disabled in meshtool if it is disabled for openCARP
• Right-handed coordinate system also for 2D elements in SF::get_transformed_pts() (thanks @jk)
• Maintenance on tutorials (thanks @joshuasteyer, @jk)
• CMake aborted when libgfortran wasn't found (thanks @teo.puig)
• Fix include path hints in make_dynamic_model.sh for the case where openCARP is compiled from sources

[10.0] - 2022-05-30

Added

• EasyML2mmt.py to faciliatate conversion from .model to .cellml via .mmt, see example 01/11 for detailed instructions
• Documentation on monodmain and bidomain boundary conditions (sections 3.2 and 3.3 of the manual)
• Performance stats output for ionics (ODE_stats.dat) and IO (IO_stats.dat) in sim output dir

Changed

• The AppImage package now contains some helper scripts: one to extract openCARP binaries from the AppImage, the other one to install carputils.
• In the postinstall phase of cmake, symbolic links created for MPI executables in /usr/local/bin could potentially interfer with an existing installation. These symbolic links were removed and the path to the MPI executable is now configured in carputils settings.
• openCARP Docker image is now based on Ubuntu 20.04
• bench --imp-info now also shows plugin metadata
• Metadata lines in .model files do not need to end with a semicolon anymore
• Added _build/physics/limpet to make_dynamic_model.sh include directories to be compatible with CMake-based installations

Fixed

• square(X) and cube(X) in .model files were causing error during code generation when using the Rosenbrock method
• make_dynamic_model.sh: Skip tests on contents of my_switches.def if it does not exist in install directory
• Fix the inclusion of MPI executables in Linux precompiled packages
• Fix documentation pipeline to include Stim structure.
• Fix error when trying to recompile openCARP after adding a new ionic model
• Ionic model metadata fields were cut if they contained a colon
• Made ionic model metadata fields consistent
• Compilation on macOS with M1 processor
• Changed xmltree.etree.getchildren() to list(xmltree.etree) for Python3.9 compatibility
• Better support for exponential notation in CellML files

[9.0] - 2022-02-22

Added

• Implementation for --stim-species and --stim-ratios parameters in bench
• Option for OpenMP support in CMake (-DUSE_OPENMP=ON)

Changed

• Names of ionic models and plugins. See physics/limpet/models/README.md for details of the naming scheme and a mapping from old to new names. Additionally, variables were named consistenly across all available ionic models and plugins.
• bench: consistently no output of progress to terminal if using --fout irrespective of wheter --validate is being used or not.
• model files: changed pow(x,2) and pow(x,3) to square(X) and cube(X), respectively.
• Ensure fibre vectors have unit length (https://git.opencarp.org/openCARP/openCARP/-/merge_requests/73)
• Courtemanche.model now considers dynamically changing intracellular potassium concentration as in the original publication

Fixed

• Add missing link to hydra_pmi_proxy in /usr/local/bin in postinstall phase for MPICH
• Kurata et al. ionic model
• mesher fiber generation for off-center meshes (https://git.opencarp.org/openCARP/openCARP/-/issues/132)
• Loading of external IMPs when openCARP is built with -DNDEBUG flag

[8.2] - 2021-12-18

Added

• Add CI jobs for testing (on schedule) and releasing openCARP Spack package when a new version is released.
• Added libjpeg as a dependency in CPack for being able to install pillow python package
• Documentation for the installation of openCARP via Spack.
• Optional building igbdft, required FFTW3 library
• --buildinfo flag for bench
• Added autotester pipeline
• Added AppImage building and release

[8.1] - 2021-10-01

Fixed

• Fixed bench not starting when tracing is used.
• Fixed trace output granularity.

[8.0] - 2021-09-23

Added

• Added trace functionality.
• Added human readable interpretations of PETSc solver divergence errors.
• Automatically add dropdown entries on webpage (parameters, doxygen, test reports) for release versions.

Fixed

• Many fixes and improvements.

[7.0] - 2021-06-29

Added

• Pathmanathan & Gray cell model for test cases with analytical solution
• Loewe-Lutz-Fabbri-Severi cell model (human sinus node)
• Extended documentation on gvec[] parameters
• A filename given as parameter can now be given with its extension
• Warning in header to not change auto-generated files in simulator
• Numerical schemes as chapter 29 of the user manual

Changed

• Default PETSc linear solver options set more sensibly.
• limpet/common.py module renamed to limpet/limpetcommon.py for better compatibility with other common modules
• Ionic model code is only re-generated in the CMake compilation when changes are present (determined per model)
• Types of some parameters of type string but corresponding to file names to RFile/WFile
• carp.prm was renamed to openCARP.prm as well as the auto-generated files in simulator

Fixed

• Adjustments per node were only applied to the first node of the mesh.

[6.0] - 2021-05-17

Added

• illumination ionics interface and IchR2 model supporting it
• Bench parameter --start-out to control first output time step
• dump_vtx option for stimuli

Fixed

• Archiving of releases in the RADAR repository
• mesher fix for 2D mesh lon files.
• many fixes throughout the codebase.
• CI fixes.

[5.0] - 2021-01-20

Fixed

• CVODE related fixes.

Added

• Added EasyML function rand01(): random number in range [0,1]
• Header to restitution*.dat files generated by bench (starting with '# ')
• Added stim[].ptcl.stimlist to specify list of stimulation times.
• Documentation on units for currents on the single cell level.

[4.0] - 2020-09-29

Fixed

• Several fixes to FEM integration.

Added

• External projects (carputils, examples, and meshtool) in the packages.
• Added support for Prism and Pyramid element types.
• Added support for per-element conductivity scaling.
• Added support for element renumbering and element-based input data.

Changed

• Restructured docker files, merged user-version and developer-version docker images.

[3.2] - 2020-07-13

Added

• mMS ionic model.
• Increased robustness of im_param option by applying whitespace removal to option string.
• CI improvements.

Fixed

• Fixed write_statef option not working.
• Fixed dynamic model building workflow.

[3.1] - 2020-06-18

Added

• MacOS installer.

[3.0] - 2020-06-17

Added

• Support for heterogenous electrode strength scaling via stimulus[].vtx_fcn (legacy stim) and stim[].elec.vtx_fcn (new stim format).

Fixed

• Fixes to igbapd. It is now more consistent in its output handling.

Changed

• Exposed more state vars in COURTEMANCHE model.
• CI updates.
• Reworked index and indexed data reading.

[2.0] - 2020-05-09

Added

• Python3 support complete.
• Added support for different (i.e. non-PETSc) matrix and solver implementations.
• KDtree partitioner is faster and requires less memory.

Fixed

• Fixed MacCannell_Fb_plug and I_KATP models.
• Laplace solver only requires extracellular mesh.
• Many fixes and optimizations to the cmake building and packaging workflow.

Changed

• CONTRIBUTORS.md is now CONTRIBUTORS.yml, which will also be used to generate the metadata for archives of the releases.
• Exposed TT2.Gto limpet variable.
• Build-time code generation now uses python3.

[1.2] - 2020-03-17

Fixed

• adjust_MIIF_variable now tells the user what adjustment went wrong.

Added

• Added gridout_p for partitioning output.

Removed

• Removed some unsupported simulator parameters.

Changed

• Further improved python3 compatibility.
• Improved message output for gridout.

[1.1] - 2020-03-05

Fixed

• Dynamic ionic model loading was fixed.

Changed

• Many python scripts are now python3 compatible. The transition is not complete yet.

[1.0] - 2020-03-03

• Initial public release