Replace Makefile build back end with SConstruct

[jtcooper10]

Replaces the Makefile scripts with corresponding SCons ones. The build artifacts should be roughly equivalent. Tested on Windows, still needs to be tested on Linux and Mac.

[BryanRumsey]

Examples failed on MacOS

Compiler

bryanrumsey@Bryans-MacBook-Pro stochss % g++ --version
Apple clang version 14.0.0 (clang-1400.0.29.201)
Target: arm64-apple-darwin21.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

Errors

scons: Entering directory `/var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_build_dxo110kt'
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
g++ -o /var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_build_dxo110kt/3DCylinderDemo_generated_model.o -c -std=c++14 -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/external/ANN/include /var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_build_dxo110kt/3DCylinderDemo_generated_model.cpp
g++ -o /var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_core/bryanrumsey/count_cores.o -c -std=c++14 -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/external/ANN/include /Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.cpp
g++ -o /var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_core/bryanrumsey/model.o -c -std=c++14 -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/external/ANN/include /Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.cpp
g++ -o /var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_core/bryanrumsey/NRMConstant_v5.o -c -std=c++14 -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/external/ANN/include /Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/NRMConstant_v5.cpp
g++ -o /var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_core/bryanrumsey/output.o -c -std=c++14 -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/external/ANN/include /Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp
/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp:37:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
        sprintf(filename,"output_%u.csv",current_step);
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp:111:13: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
            sprintf(filename, "output0_boundingBox.vtk");
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp:129:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
        sprintf(filename,"output%u.vtk", output_index++);
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
3 warnings generated.
g++ -o /var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_core/bryanrumsey/particle.o -c -std=c++14 -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/external/ANN/include /Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/particle.cpp
g++ -o /var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_core/bryanrumsey/pthread_barrier.o -c -std=c++14 -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/external/ANN/include /Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp
g++ -o /var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_core/bryanrumsey/read_lammps_input_file.o -c -std=c++14 -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include -I/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/external/ANN/include /Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.cpp
/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.cpp:97:14: error: use of undeclared identifier 'create_particle'
        me = create_particle(id);
             ^
/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.cpp:105:9: error: use of undeclared identifier 'add_particle'
        add_particle(me,system);
        ^
2 errors generated.
scons: *** [/var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_core/bryanrumsey/read_lammps_input_file.o] Error 1
scons: building terminated because of errors.

---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
File ~/SpatialPy/spatialpy/solvers/solver.py:492, in Solver.compile(self, debug, profile)
    491 try:
--> 492     result = subprocess.check_output(make_cmd, stderr=subprocess.STDOUT)
    493     if self.debug_level > 1:

File /opt/homebrew/Cellar/[email protected]/3.10.6_2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/subprocess.py:420, in check_output(timeout, *popenargs, **kwargs)
    418     kwargs['input'] = empty
--> 420 return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
    421            **kwargs).stdout

File /opt/homebrew/Cellar/[email protected]/3.10.6_2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/subprocess.py:524, in run(input, capture_output, timeout, check, *popenargs, **kwargs)
    523     if check and retcode:
--> 524         raise CalledProcessError(retcode, process.args,
    525                                  output=stdout, stderr=stderr)
    526 return CompletedProcess(process.args, retcode, stdout, stderr)

CalledProcessError: Command '['/opt/homebrew/opt/[email protected]/bin/python3.10', '-m', 'SCons', '-C/var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_build_dxo110kt', '-f/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/build/SConstruct', 'ROOT=/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine', 'ROOTINC=/Users/bryanrumsey/SpatialPy/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine', 'COREDIR=/var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_core/bryanrumsey', 'MODEL=/var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_build_dxo110kt/3DCylinderDemo_generated_model.cpp', 'BUILD=/var/folders/z4/bqpnd_kx7xg3s3c9jtz0pnfh0000gn/T/spatialpy_build_dxo110kt']' returned non-zero exit status 2.

During handling of the above exception, another exception occurred:

SimulationError                           Traceback (most recent call last)
File <timed exec>:1

File ~/SpatialPy/spatialpy/core/model.py:1055, in Model.run(self, number_of_trajectories, seed, timeout, number_of_threads, debug_level, debug, profile)
   1051 from spatialpy.solvers.solver import Solver # pylint: disable=import-outside-toplevel
   1053 sol = Solver(self, debug_level=debug_level)
-> 1055 return sol.run(number_of_trajectories=number_of_trajectories, seed=seed, timeout=timeout,
   1056                number_of_threads=number_of_threads, debug=debug, profile=profile)

File ~/SpatialPy/spatialpy/solvers/solver.py:547, in Solver.run(self, number_of_trajectories, seed, timeout, number_of_threads, debug, profile, verbose)
    545 # Check if compiled, call compile() if not.
    546 if not self.is_compiled:
--> 547     self.compile(debug=debug, profile=profile)
    549 # Execute the solver
    550 for run_ndx in range(number_of_trajectories):

File ~/SpatialPy/spatialpy/solvers/solver.py:500, in Solver.compile(self, debug, profile)
    498     except Exception:
    499         pass
--> 500     raise SimulationError(f"Compilation of solver failed, return_code={err.returncode}")
    501 except OSError as err:
    502     cmd = " ".join(make_cmd)

SimulationError: Compilation of solver failed, return_code=2

[briandrawert]

I also get the same error with:

$g++ --version
g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0