virtualcell / vcell-solvers Goto Github PK

Background

Currently, there are broken builds of the VCell solvers on both Appveyor (windows) and TravisCI (Linux and Macos) - maintenance is required.

GitHub provides runners for all three of these platforms and is a natural choice to consolidate these builds under a common infrastructure (our 'vcell' repo uses GitHub build/deploy the rest of VCell).

Created a template with a matrix job for each of Ubuntu, Macos and Windows platforms, which:

1. checks out the vcell-solver repo.
2. initiates a TMATE action to allow debugging the installation of dependencies and the build steps (cmake)

Background

vcell-solvers is already used as a base image for vcell-batch docker image.
vcell-solvers should be used as a base image for the biosimulations docker image (with same Linux execution environment as server)

Both vcell-solvers and biosimulations containers need java and python (vcell-solvers may need python2).
biosimulations image was 2.5GB - first step was to create a small and complete base image with solvers, java and python, then focus on application dependencies in child containers.

use existing github action (prepared in issue #13) to configure Macos build/deploys of solvers. This involves configuring the Macos runner and configuring cmake accordingly to this new environment.

build base solvers for Docker

• FV solver (non-PETSc)
• Smoldyn
• nonspatial Stochastic
• NFSim
• Moving Boundary Solver

SimulationMessaging implements both a create method, and a getInstVar method, where getInstVar is quietly vulnerable to a nullptr SEGFAULT if create isn't called.

Per proper Singleton design, create should be removed, and it's logic transfered to getInstVar.

base solvers

• FV solver (non-PETSc)
• Smoldyn
• nonspatial Stochastic
• NFSim
• Moving Boundary Solver

Hy3S solvers (needs Fortran reconciled with LLVM toolchain)

• Hybrid_EM
• Hybrid_MIL
• Hybrid_MIL_Adaptive

Chombo solvers (difficult multi-step build)

• Chombo2D (without parallel)
• Chombo3D (without parallel)

subtasks

• #13
• #16
• #17
• #27
• build base solvers on Github for Macos platform
• virtualcell/vcell#1023
• #26
• build Hy3S solvers on Github for native Macos
• build Hy3S solvers on Github for Docker
• build Hy3S solvers on Github for native Linux
• build Hy3S solvers on Github for native Windows
• build Chombo solvers on Github for native Macos
• build Chombo solvers on Github for Docker
• build Chombo solvers on Github for native Linux
• build Chombo solvers on Github for native Windows

Motivation

Test coverage of most VCell solvers rely on integration testing and end to end testing with the math testing framework. However, solver unit tests would allow independent testing of solver components and provide a framework for debugging and extending the solvers.

Completion Criteria

• all solvers should have at least one unit test where results are compared with a typical output.

Tasks

• #24
• virtualcell/vcell#819. (Motivated Nonspatial Stochastic Unit Test)
• unit test for FiniteVolume solver (non-PETSc)
• unit test for Smoldyn solver
• unit test for NFSim
• unit test for Moving Boundary Solver
• unit test for Hy3S solvers (Hybrid_EM, Hybrid_MIL, Hybrid_MIL_Adaptive)
• unit test for Chombo2D solver
• unit test for Chombo3D solver

On a users Mac, the Reaction Diffusion solver used by VFrap (FiniteVolume_x64) cannot load a needed library which is shipped with VCell. This behavior is not reproducible on my dev machine, because my Mac 'trusts' VCell (not quarantined).

After some reading, it seems that recent Macos configuration don't always trust library paths specified with "@executable_path", it wants "@rpath" instead.

install_name_tool_macos.sh needs to be changed to update the path of executables or dynamic libraries using @rpath.

we'll need Sophia at UCHC to test our fix as I cannot reproduce it on my machine and on the Mac build machines in the cloud.

recent build of NFSim on Macos had runtime failures for some models. Rebuild NFSim on Macos paying special attention to memory safety.

upgrade MovingBoundary solver for C++14 and resurrect unit tests

building on new scaffold for build/deploy on Github (described in #13), implement a build/deploy for vcell solvers for Windows.

• FV solver (non-PETSc)
• Smoldyn
• nonspatial Stochastic
• NFSim
• Moving Boundary Solver

"forcing location index to be 1 instead of 0" is printed a huge number of times for some models.
biomodel_ 245262589 (from Kelvin's account).

building on new scaffold for build/deploy on Github (described in #13), implement a build/deploy for vcell solvers for Docker.

building on new scaffold for build/deploy on Github (described in #13), implement a build/deploy for vcell solvers for LInux.

• FV solver (non-PETSc)
• Smoldyn
• nonspatial Stochastic
• NFSim
• Moving Boundary Solver