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

  • 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

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 (thank @huppe)
  • Fixed buildinfo output.
  • Fixed Vm_clamp and GND_ex pulse forms.
  • Fixed HodgkinHuxley.model.

Changed

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

Known issues

  • Some regression tests are failing when using Ginkgo as the numerical backend (#151)
  • State vector access can fail when building with data layout optimization (#330)

[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

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