Cmake issues/documentation

[JaroCamphuijsen]

When trying to build this model with Biocellion v3.1 framework.
Using:
gcc version 9.3.0 (Ubuntu 9.3.0-10ubuntu2)

I run into the following errors:

While compiling straight after cloning this repo:

model_routine_grid.cpp:141:6: error: no declaration matches ‘void ModelRoutine::updateIfSubgridKappaDomainBdry(int, int, const VIdx&, const VIdx&, const UBAgentData&, const UBEnv&, double&)’
  141 | void ModelRoutine::updateIfSubgridKappaDomainBdry( const S32 pdeIdx, const S32 dim, const VIdx& vIdx, const VIdx& ifSubgridVOffset, const UBAgentData& ubAgentData, const UBEnv& ubEnv, REAL& kappa ) {/* for boundary condition */

and

model_routine_grid.cpp:313:6: error: no declaration matches ‘void ModelRoutine::updatePDEBufferGridKappaDomainBdry(int, int, const VIdx&, const VIdx&, double&)’
  313 | void ModelRoutine::updatePDEBufferGridKappaDomainBdry( const S32 pdeIdx, const S32 dim, const VIdx& startVIdx, const VIdx& pdeBufferBoxVSize, REAL& kappa ) {/* for boundary condition */

After commenting out the above two erroneous methods:

cd tetra/; cgal_create_CMakeLists -s tetra; cmake -DCMAKE_BUILD_TYPE=Release -DCGAL_CXX_FLAGS="-v -shared -fPIC"; make;
/bin/sh: 1: cgal_create_CMakeLists: not found
CMake Warning:
  No source or binary directory provided.  Both will be assumed to be the
  same as the current working directory, but note that this warning will
  become a fatal error in future CMake releases.


CMake Error: The source directory "/home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/tetra" does not appear to contain CMakeLists.txt.
Specify --help for usage, or press the help button on the CMake GUI.
make[1]: Entering directory '/home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/tetra'
make[1]: *** No targets specified and no makefile found.  Stop.
make[1]: Leaving directory '/home/jaroknor/NLeSC/InSilicoMeat/Biocellion/Biocellion-3.1/biocellion-3.1/biocellion-user/ABM-microcarriers/tetra'
make: *** [Makefile:28: tetra/CMakeFiles/tetra.dir/tetra.cpp.o] Error 2

The latter is due to a missing CGAL installation.

After installing CGAL, it has the cgal_create_CMakeLists script.

Next error in line is possibly due to gcc version:

g++ -std=c++11 -shared  -Wl,-soname,libmodel.DP.SPAGENT.so -o libmodel.DP.SPAGENT.so interface_config.o interface_agent.o interface_mech_intrct.o interface_grid.o interface_output.o model_routine_config.o model_routine_grid.o model_routine_agent.o model_routine_mech_intrct.o model_routine_output.o interface_check.o  tetra/CMakeFiles/tetra.dir/tetra.cpp.o -lgmp
/usr/bin/ld: tetra/CMakeFiles/tetra.dir/tetra.cpp.o: relocation R_X86_64_TPOFF32 against symbol `_ZGVZN4CGAL30Triangulation_data_structure_3INS_37Triangulation_hierarchy_vertex_base_3INS_37Triangulation_vertex_base_with_info_3INS_7Point_3INS_5EpickEEES4_NS_27Triangulation_vertex_base_3IS4_NS_30Triangulation_ds_vertex_base_3INS0_INS2_IS5_S4_NS6_IS4_NS7_IvEEEEEENS_28Triangulation_ds_cell_base_3IvEENS_14Sequential_tagEEEEEEEEEEESC_SD_E21_insert_in_small_holeIN5boost9container12small_vectorINS_8internal11CC_iteratorINS_17Compact_containerINSB_ISJ_EENS_7DefaultESS_SS_EELb0EEELm32EvvEENSN_ISt4pairISU_iELm32EvvEEEENSP_INSQ_INS1_INS2_IS5_S4_NS6_IS4_NS7_ISJ_EEEEEEEESS_SS_SS_EELb0EEERKT_RKT0_E21vertex_pair_facet_map' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: tetra/CMakeFiles/tetra.dir/tetra.cpp.o: relocation R_X86_64_PC32 against symbol `_ZZN4CGAL26get_static_error_behaviourEvE16_error_behaviour' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make: *** [Makefile:25: libmodel.DP.SPAGENT.so] Error 1

[JaroCamphuijsen]

Solution to the last error shown above:

In

ABM-microcarriers/Makefile

Line 28 in 22d8263

cd tetra/; cgal_create_CMakeLists -s tetra; cmake -DCMAKE_BUILD_TYPE=Release -DCGAL_CXX_FLAGS="-v -shared -fPIC"; make;

-DCGAL_CXX_FLAGS should be -DCMAKE_CXX_FLAGS

See TheCMMC/Utilities-Tetra#4