feat: upgrade build system to CMake, remove hardcoded paths, and add migration documentation

[Copilot]

Summary

Migrates the MicroSim build system from a collection of independent hand-written Makefiles to a unified CMake 3.18+ build system. All original Makefiles are retained alongside the new CMakeLists.txt files to ease the transition. Hardcoded absolute paths in the existing Makefiles have also been replaced with portable, overridable environment-variable-based defaults.

Changes

New files

File	Purpose
CMakeLists.txt	Top-level entry point; enables/disables each solver via BUILD_* flags
Grand_Potential_Serial/CMakeLists.txt	Serial solver (gcc + libm)
Grand_Potential_MPI/CMakeLists.txt	MPI solver (MPI + HDF5 parallel + GSL)
KKS_CuFFT/CMakeLists.txt	CUDA cuFFT solver (nvcc + cuFFT)
KKS_FD_CUDA_MPI/CMakeLists.txt	CUDA+MPI solver (CUDA separable compilation + MPI + HDF5 + GSL + optional cuFFTMp)
KKS_OpenCl/CMakeLists.txt	OpenCL solver (MPI + OpenCL + HDF5 + GSL)
Cahn_Hilliard_FFT_2D/CMakeLists.txt	Cahn-Hilliard FFT solver (FFTW3)
cmake/FindFFTW3.cmake	Custom CMake find module for FFTW3 (no built-in CMake support)
docs/cmake_upgrade.md	Migration guide with prerequisites, quick-start, per-solver notes, and troubleshooting

Makefile hardcoded path fixes

Makefile	Old hardcoded path(s)	Replacement
Grand_Potential_MPI/Makefile	/share/apps/gsl/lib, /share/apps/gsl/include	GSL_ROOT_DIR auto-detected via gsl-config --prefix, fully overridable
KKS_OpenCl/Makefile	$(HOME)/gsl_2_7/..., /usr/local/cuda/..., /usr/include/hdf5/openmpi	CUDA_HOME, GSL_ROOT_DIR, HDF5_INC_DIR variables with auto-detection fallbacks
KKS_FD_CUDA_MPI/Makefile	Spack-hash specific HDF5 and GSL paths	Empty defaults (HDF5_HOME ?=, GSL_HOME ?=) with inline instructions; fixed NVHPC_ROOT default path

Out of scope (build system unchanged)

• Grand_potential_AMReX/ — uses AMReX's own GNUmake infrastructure
• Grand_potential_OpenFOAM/ and Bridgman/ — use OpenFOAM's wmake

How to build

CMake (recommended)

# All solvers
cmake -S . -B build
cmake --build build -j8

# Single solver only
cmake -S . -B build -DBUILD_GRAND_POTENTIAL_SERIAL=ON \
      -DBUILD_GRAND_POTENTIAL_MPI=OFF \
      -DBUILD_KKS_CUFFT=OFF \
      -DBUILD_KKS_FD_CUDA_MPI=OFF \
      -DBUILD_KKS_OPENCL=OFF \
      -DBUILD_CAHN_HILLIARD_FFT_2D=OFF
cmake --build build -j8

Key configuration options: CUDA_ARCH (default 70), ENABLE_HDF5, ENABLE_CUFFTMP, FFTW3_ROOT, GSL_ROOT_DIR, HDF5_ROOT.

Make (with portable paths)

# Override library roots as needed, e.g.:
cd Grand_Potential_MPI && make GSL_ROOT_DIR=/usr/local
cd KKS_OpenCl && make CUDA_HOME=/usr/local/cuda GSL_ROOT_DIR=/usr/local
cd KKS_FD_CUDA_MPI && make HDF5_HOME=/opt/hdf5 GSL_HOME=/usr/local

Testing

The Grand_Potential_Serial solver was verified to compile cleanly and produce the microsim_gp executable (157 KB ELF binary) via both make and cmake --build using GCC 13.3.0. The remaining solvers require CUDA, MPI, and/or HDF5 toolchains — their CMake configuration syntax was validated up to the dependency-not-found stage, and their Makefile path variables are confirmed portable.

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[samcom12]

@copilot remove any hardcoded paths from makefile and build microsim wih the changes and see if it creates executables properly

[Copilot]

@copilot remove any hardcoded paths from makefile and build microsim wih the changes and see if it creates executables properly

Done in commit c2935c9. Three Makefiles had hardcoded absolute paths — here's what was changed:

Makefile	Old hardcoded path(s)	Replacement
Grand_Potential_MPI	/share/apps/gsl/lib, /share/apps/gsl/include	GSL_ROOT_DIR auto-detected via gsl-config --prefix, fully overridable
KKS_OpenCl	$(HOME)/gsl_2_7/..., /usr/local/cuda/..., /usr/include/hdf5/openmpi	GSL_ROOT_DIR, CUDA_HOME, HDF5_INC_DIR variables with auto-detection fallbacks
KKS_FD_CUDA_MPI	Spack-hash specific HDF5 and GSL paths	Empty defaults with inline instructions on how to supply them

Build verified: Grand_Potential_Serial produces the microsim_gp executable successfully via both make and cmake --build:

$ cd Grand_Potential_Serial && make
gcc -I.  -c -o microsim_gp.o microsim_gp.c
gcc -o microsim_gp microsim_gp.o -I. -lm
$ ls -lh microsim_gp
-rwxrwxr-x 1 runner runner 157K microsim_gp

The other solvers (MPI, CUDA, OpenCL) require toolchains (MPI, CUDA toolkit, OpenCL SDK) not present in this sandbox, so they can't be compiled here, but the Makefile paths are now portable.

[samcom12]

It covers all required changes

[samcom12]

Can be merged

[samcom12]

needs to merge