Sundials 7.1.1 #17
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Sundials 7.1.1 #17
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…ity with Sundials 7.1.1 - Updated call signatures - Require explicit context provided to create Variables - Added exports - Updated cmake method to find Sundials - Updated README with testing information and additional requirements that were not explicit - Added conda environment.yml file - Added Github workflow for testing - Fixed sizes of ratio vectors in tests
Try making the tests fail for older sundials Updated README with additional info about managing dependencies via conda Fixed name of executable in CLI help
Remove additional use of deprecated cvode_direct.h
Define RCONST in RedoxReg_Rate.cpp Added CLI option for output file Update Github workflow docs step to use new dev script
…e (was causing test failure when run with coverage) Updated trDynaPS driver FullTest to cause failure for older sundials Updated README with minimum tested version of sundials (5.7.0) Fix forward declaration of CalcData Export static class variables for Windows compat Add decimals to test Emap to prevent windows warnings about conversion to double Try using os compilers for valgrind workflow jobs since conda-forge libraries do not include debug symbols
…(DynaPS test disable for failing with default params)
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Disabled unused module ssPS Clean up leaked condition instance in DynaPS getResults
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These changes should not modify the calculated results and no internal constants have been modified. In addition to supporting Sundials 7.1.1 changes were also made to support development and improve utility:
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…on-pointer Re-enabled tests for RedoxReg module, fixed order of KINSol operations, & added test for RedoxReg output as this module is not currently called via the CLI
Added comment about enabling RedoxReg in trDynaPS driver
…m**2 && CO2 in ppm) Stripped input file down to just used parameters Set test input PAR to 2000 umol/s/m**2 (470 W/m**2)
…arams that should be exact reguardless of system/sundials version Add flag for stopping after first failure that is disabled by default Add flag for preserving test outputs
…ault to allow for creation of Variables instances without providing a context Use shared pointer to manage sundials contexts
Declare dummy SUNGetErrMsg inline Define SUN_COMM_NULL if not defined for older versions of sundials
… before module mode (FindSUNDIALS) and update FindSUNDIALS.cmake to use the same names as the most recent version of Sundials
Make MPI optional to allow build w/ or w/o MPI (Sundials will only link MPI as needed)
Install built Sundials W/ MPI in conda environment
…extension Add methods for reading files into Variables that can be used by the python extension Add debug messages for duplicate input parameters and for absent EnzymeAct when useC3 is true
Add missing headers Fix minor compilation errors & warnings w/ MSVC
…d without the library
Add missing flag for installing the Python extension
…irectory without install Update README with info on the Python package Don't re-use CVode solver memory between driver calls
yufenghe22
approved these changes
Dec 19, 2024
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I merged the cvode_7.1.1 to my working branch SoybeanParameterization. When testing on biocluster, the cmake and compilation were successful. I was also able to repeat my previous results using my own scripts that link to the libEPhotosynthesis.so. A result example is shown below:
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Update to be compatible with latest version of Sundials library (currently 7.1.1).