This pulls in the work from the following tickets #3077 #3078 #3079 #2087

Continuous testa and coverage pass https://chaste.cs.ox.ac.uk/buildbot/Nightly%20Coverage/coverage1573/

Hello there, I am new to the community.

I was trying to execute the first run case following the tutorial web-page. The building step succeeded without troubles, however, the compilation of Continuous failed, showing up the following error message

Chaste/mesh/src/reader/VtkMeshReader.cpp:106:40: error: ‘virtual void vtkUnstructuredGrid::GetCellTypes(vtkCellTypes*)’ is deprecated: Please use GetDistinctCellTypesArray() instead. [-Werror=deprecated-declarations] mpVtkUnstructuredGrid->GetCellTypes(cell_types);

The VTK version I have installed is the following 9.1, Looking after your comments I salute you.

Edit: If prompted I can edit the file that the compiler complains about but I'm afraid more trouble can appear... What current versions are you using?

I just tried to download Chaste. The page that pops up (https://www.cs.ox.ac.uk/chaste/download.html) has a section at the bottom stating:

"Redirect to GitHub Please see the tagged release on GitHub and download from there. Thank you."

I get a 404 on the link it provides. I think the correct link is: https://github.com/Chaste/Chaste/releases/tag/release_2019.1

I am trying to run the demos written in the joss paper using the pre-built docker image and the command

docker run -it --init --rm -v chaste_data:/home/chaste chaste/chaste-docker:2019.1

Inside this container, the environment variable CHASTE_SRC is called CHASTE_SRC_DIR instead, and the output directory is called testoutput instead of test_summary as you write in the paper.

It would be good if you could tag one docker image that had the exact same folder structure and environment variables as you describe in the paper.

By the way, everything seems to run fine using the correct folders.

Summary

This adds support for boost 1.78 to Chaste for ticket 3094.

Passing Tests

• [x] Continuous
• [x] Nightly
• [x] Parallel

Failing Tests

• ~~TestArchivingHelperClasses~~ (Fixed)
• ~~TestArchivingHelperClassesParallel~~ (Fixed)

Additional Testing

Boost 1.75

• [x] Continuous
• [x] Nightly
• [x] Parallel

Boost 1.76

• [x] Continuous
• [x] Nightly
• [x] Parallel

Boost 1.77

• [x] Continuous
• [x] Nightly
• [x] Parallel

Notes

• TestGenerateSteadyStateCrypt in Weekly test pack currently passes for intel, but fails for gcc regardless of boost version. All other Weekly tests pass for gcc.

This class finds the steady state behaviour of an action potential model. This is done by using linear regression on the state variables when it looks like we have exponential decay.

TestSteadyStateExtrapolationRunner.hpp provides an example which uses this class.

Apparently its not possible to link to another user project from within a separate user project. The problem appears when trying to build using cmake. However, this isn't a issue while using scons. I am facing this problem for my user project "ApPredict_GP" (https://github.com/sanmitraghosh/ApPredict_GP) which uses some of "ApPredict" (https://github.com/Chaste/ApPredict) code.

Summary

This issue addresses the following legacy tickets:

• 3061 - Support Boost 1.75
• 3073 - Support Boost 1.76
• 3074 - Support Boost 1.77
• 3094 - [BBR WP2] Support Boost 1.78

Support for these boost versions has been added in PR #27.

This archive was causing Portability_3_Wed (Boost 1.66 and CVODE=OFF) to fail. Archive has been recreated with Boost 1.58 (oldest tested) and CVODE=OFF.

Description

This upgrades the minimum version of chaste_codegen to 0.9.10 for Sundials 6.0 support.

Context

• This change is related to Chaste ticket #3084
• The chaste_codegen project has been updated to generate Chaste code that supports Sundials 6.0.

Types of changes

• [ ] Bug fix (non-breaking change which fixes an issue)
• [x] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to change)

Testing

• [ ] Testing is done automatically and codecov shows test coverage
• [ ] This cannot be tested automatically
• [x] This can be tested automatically, but requires Sundials 6.0.0 to be installed. It has been tested manually in a chaste-docker container. The following tests all passed:
  • Continuous
  • Nightly
  • Codegen
  • project_ApPredict
  • Weekly (except TestGenerateSteadyStateCrypt, which already fails)

Description

• These changes are for Chaste ticket #3084 to add support for Sundials 6.0.0 which requires a newly introduced SUNContext object.
• A CvodeContextManager Singleton has been added to manage a shared SUNContext object with thread_local storage.
• Pragmas have been added where required to account for the changes in Sundials library function calls.
• Tolerance for TestMonodomainProblem -> TestOutputDoesNotDependOnPrintTimestep was adjusted from 3e-3 to 4e-3, in line with observed results from parallel execution using the new solver.

Context

• Relevant updates have been made to boilerplate code and reference models in chaste_codegen. These are required to pass Codegen tests.

Types of changes

• [ ] Bug fix (non-breaking change which fixes an issue)
• [x] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to change)

Documentation checklist

• [x] I have updated all documentation in the code where necessary.
• [x] I have checked spelling in all (new) comments and documentation.
• [ ] I have added a note to RELEASE.md if relevant (new feature, breaking change, or notable bug fix).
• [ ] I have updated version & citation.txt & citation.cff version.

Testing

• [ ] Testing is done automatically and codecov shows test coverage
• [ ] This cannot be tested automatically
• [x] This can be tested automatically, but requires Sundials 6.0.0 to be installed. It has been tested manually in a chaste-docker container. The following tests all passed:
  • Continuous
  • Codegen
  • project_ApPredict
  • Nightly
  • Weekly (except TestGenerateSteadyStateCrypt, which already fails)
  • Parallel (required adjusting tolerance for TestOutputDoesNotDependOnPrintTimestep)

I am running a cell simulation with a node-based off-vertex model.

I set some nodes and run my simulation for 10 hours with a cell cycle uniform 1 hour.

After some time I get this failed test error: The point provided is outside all of the boxes

From this block of code:

template<unsigned DIM>
unsigned DistributedBoxCollection<DIM>::CalculateContainingBox(c_vector<double, DIM>& rLocation)
{
    // The node must lie inside the boundary of the box collection
    for (unsigned i=0; i<DIM; i++)
    {
        if ((rLocation[i] < mDomainSize(2*i)) || !(rLocation[i] < mDomainSize(2*i+1)))
        {
            EXCEPTION("The point provided is outside all of the boxes");
        }
    }

When I run the same test for shorter periods of time, the error goes away.

I think this means that the box does not increase as the population increases.

Is this the case?

TL/DR;

My main question: how can I adjust how much memory I allow Chaste to use?

I would like to increase this amount as I have 32GB of RAM and I think Chaste kills simulations well before it uses all of what's available.

Longer version

I am running some off-lattice node-based cell models.

My cell populations divide and run for some $N$ cell cycles and I generally end up with a few hundred cells.

This usually means that my simulation stop time is approximately 7 (I think the units are hours), where each cell cycle is uniform around 1.

When I try to run my simulations past 7 or so, I get errors saying my simulation threw an exception.

I am not sure how to gauge what is happening, but I wanted to start by exploring the memory case first.

Also, I have 8 cores that I can multi-thread to 16, is there any way I can parallelise multiple runs of a model?

For AP portal it would be quite useful if some information could be output to progress_status.txt about the fact that the CellML file is being converted. This does take a bit of time, so it would be nice to be bale to give feedback to portal users, otherwise they may wrongly assume the simulation has failed to start.

Add some member variables to change properties of Halo Nodes in Cylindrical2dMesh. #3089 Also change bounded cylindrical meshes to only have 1 ghost image node for each boundary edge, as more stable #3078

Dear developers.

I'm having some problems with the installation of chaste. My Ubuntu version is 20.04 LTS and I installed it using the Ubuntu package as described in "https://chaste.cs.ox.ac.uk/trac/wiki/InstallGuides/UbuntuPackage". I installed Chaste using the Ubuntu package as described in "" and did not encounter any errors at this step. Then I compiled as described in "https://chaste.cs.ox.ac.uk/trac/wiki/ChasteGuides/CmakeFirstRun" and in the configuration step I got the following message： "-- Configuring done -- Generating done -- Build files have been written to: /path/to/chaste_build " without any errors. But when I perform the build step, I type "make -j4 Continuous" and I get the following error：

[email protected]:~/chaste/chaste_build$ make -j4 Continuous Scanning dependencies of target timekeeper Scanning dependencies of target testglobal Scanning dependencies of target testmesh Scanning dependencies of target testode [ 0%] Building CXX object global/CMakeFiles/timekeeper.dir/src/timekeeper.cpp.o [ 0%] Building CXX object global/test/CMakeFiles/testglobal.dir/ForTestArchiving.cpp.o [ 0%] Building CXX object mesh/test/CMakeFiles/testmesh.dir/data/inputs/gen2Dele.cpp.o [ 0%] Building CXX object ode/test/CMakeFiles/testode.dir/odes/ParameterisedCvode.cpp.o [ 1%] Linking CXX executable timekeeper [ 1%] Built target timekeeper Scanning dependencies of target testpde [ 1%] Building CXX object pde/test/CMakeFiles/testpde.dir/pdes/SimpleUniformSourceParabolicPde.cpp.o [ 1%] Linking CXX static library libtestmesh.a [ 1%] Built target testmesh Scanning dependencies of target testcell_based [ 1%] Building CXX object cell_based/test/CMakeFiles/testcell_based.dir/simulation/OffLatticeSimulationWithMyStoppingEvent.cpp.o In file included from /usr/lib/petscdir/petsc3.12/x86_64-linux-gnu-real/include/petscis.h:7, from /usr/lib/petscdir/petsc3.12/x86_64-linux-gnu-real/include/petscvec.h:9, from /home/gwqsz/chaste/Chaste_source_code/pde/src/problem/AbstractLinearParabolicPde.hpp:46, from /home/gwqsz/chaste/Chaste_source_code/pde/test/pdes/SimpleUniformSourceParabolicPde.hpp:42, from /home/gwqsz/chaste/Chaste_source_code/pde/test/pdes/SimpleUniformSourceParabolicPde.cpp:36: /usr/lib/petscdir/petsc3.12/x86_64-linux-gnu-real/include/petscsys.h:169:6: error: #error "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version" 169 | # error "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version" | ^~~~~ In file included from /usr/lib/petscdir/petsc3.12/x86_64-linux-gnu-real/include/petscis.h:7, from /usr/lib/petscdir/petsc3.12/x86_64-linux-gnu-real/include/petscvec.h:9, from /home/gwqsz/chaste/Chaste_source_code/cell_based/src/cell/properties/CellVecData.hpp:44, from /home/gwqsz/chaste/Chaste_source_code/cell_based/src/cell/Cell.hpp:49, from /home/gwqsz/chaste/Chaste_source_code/cell_based/src/population/AbstractCellPopulation.hpp:39, from /home/gwqsz/chaste/Chaste_source_code/cell_based/src/population/killers/AbstractCellKiller.hpp:39, from /home/gwqsz/chaste/Chaste_source_code/cell_based/src/simulation/AbstractCellBasedSimulation.hpp:45, from /home/gwqsz/chaste/Chaste_source_code/cell_based/src/simulation/OffLatticeSimulation.hpp:39, from /home/gwqsz/chaste/Chaste_source_code/cell_based/test/simulation/OffLatticeSimulationWithMyStoppingEvent.hpp:39, from /home/gwqsz/chaste/Chaste_source_code/cell_based/test/simulation/OffLatticeSimulationWithMyStoppingEvent.cpp:36: /usr/lib/petscdir/petsc3.12/x86_64-linux-gnu-real/include/petscsys.h:169:6: error: #error "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version" 169 | # error "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version" | ^~~~~ In file included from /home/gwqsz/chaste/Chaste_source_code/mesh/src/reader/GenericMeshReader.hpp:47, from /home/gwqsz/chaste/Chaste_source_code/mesh/src/common/AbstractTetrahedralMesh.hpp:54, from /home/gwqsz/chaste/Chaste_source_code/mesh/src/common/TetrahedralMesh.hpp:49, from /home/gwqsz/chaste/Chaste_source_code/cell_based/src/population/AbstractCellPopulation.hpp:59, from /home/gwqsz/chaste/Chaste_source_code/cell_based/src/population/killers/AbstractCellKiller.hpp:39, from /home/gwqsz/chaste/Chaste_source_code/cell_based/src/simulation/AbstractCellBasedSimulation.hpp:45, from /home/gwqsz/chaste/Chaste_source_code/cell_based/src/simulation/OffLatticeSimulation.hpp:39, from /home/gwqsz/chaste/Chaste_source_code/cell_based/test/simulation/OffLatticeSimulationWithMyStoppingEvent.hpp:39, from /home/gwqsz/chaste/Chaste_source_code/cell_based/test/simulation/OffLatticeSimulationWithMyStoppingEvent.cpp:36: /home/gwqsz/chaste/Chaste_source_code/mesh/src/reader/VtkMeshReader.hpp:55:10: fatal error: vtkDataArray.h: No such file or directory 55 | #include <vtkDataArray.h> | ^~~~~~~~~~~~~~~~ compilation terminated. make[3]: *** [cell_based/test/CMakeFiles/testcell_based.dir/build.make:63: cell_based/test/CMakeFiles/testcell_based.dir/simulation/OffLatticeSimulationWithMyStoppingEvent.cpp.o] Error 1 make[2]: *** [CMakeFiles/Makefile2:11184: cell_based/test/CMakeFiles/testcell_based.dir/all] Error 2 make[2]: *** Waiting for unfinished jobs.... [ 1%] Building CXX object ode/test/CMakeFiles/testode.dir/odes/ParameterisedOde.cpp.o [ 1%] Linking CXX static library libtestglobal.a [ 1%] Built target testglobal make[3]: *** [pde/test/CMakeFiles/testpde.dir/build.make:63: **pde/test/CMakeFiles/testpde.dir/pdes/SimpleUniformSourceParabolicPde.cpp.o] Error 1 make[2]: *** [CMakeFiles/Makefile2:7748: pde/test/CMakeFiles/testpde.dir/all] Error 2 [ 1%] Linking CXX static library libtestode.a [ 1%] Built target testode make[1]: *** [CMakeFiles/Makefile2:1037: CMakeFiles/Continuous.dir/rule] Error 2 make: *** [Makefile:314: Continuous] Error 2**

I am a beginner and I really need your help. Many thanks, Guo Weiqi