pyminichem 0.1.2

Torch-based Python bindings for the minichem Fortran chemistry solver.

pyminichem

pyminichem is a standalone Python package and Torch-based C++ wrapper around the Fortran mini_chem code base. The repository follows the same broad layout used by pydisort, pyharp, and kintera:

• src/: native C, C++, and wrapper code
• python/: Python package, pybind11 bindings, and packaged resources
• patches/: upstream minichem patch set
• tests/: C++ and Python validation

The build flow is:

1. Fetch upstream mini_chem with CMake.
2. Apply the same mini_ch_i_dlsode.f90 patch used by canoe.
3. Link the patched Fortran implementation into a thin C shim.
4. Wrap that shim in a Torch-based C++ API.
5. Expose the C++ API to Python with pybind11.

Build

CPU build

Use the default GNU toolchain for the CPU-only path:

cmake -S . -B build-cpu -DBUILD_TESTS=ON
cmake --build build-cpu -j
ctest --test-dir build-cpu -R '^test_minichem.release$' --output-on-failure

If you want the editable Python package to use the CPU build, copy the native library into the package locations and reinstall:

cp build-cpu/lib/libpyminichem_release.so build/lib/libpyminichem_release.so
cp build-cpu/lib/libpyminichem_release.so python/lib/libpyminichem_release.so
python -m pip install -e .

CUDA/OpenACC build with NVHPC

The working CUDA path in this repo uses the NVIDIA HPC SDK toolchain:

cmake -S . -B build-nvhpc \
  -DBUILD_TESTS=OFF \
  -DCUDA=ON \
  -DCMAKE_C_COMPILER=nvc \
  -DCMAKE_CXX_COMPILER=nvc++ \
  -DCMAKE_Fortran_COMPILER=nvfortran

cmake --build build-nvhpc -j

To make the editable Python package use the NVHPC/CUDA build:

cp build-nvhpc/lib/libpyminichem_release.so build/lib/libpyminichem_release.so
cp build-nvhpc/lib/libpyminichem_release.so python/lib/libpyminichem_release.so
python -m pip install -e .

Test

Python tests

After installing the editable package:

pytest tests

GPU smoke test

Run the live CUDA test from a directory outside the repo root, so Python imports the editable package instead of treating the top-level pyminichem/ repo directory as a namespace package:

cd /tmp
python - <<'PY'
import torch
import pyminichem

print('cuda_enabled', pyminichem.cuda_enabled())
print('torch_cuda_available', torch.cuda.is_available())
print('device_count', torch.cuda.device_count())

base_vmr = torch.tensor(
    [[0.0, 0.9975, 0.001074, 0.0, 0.0, 0.0, 0.0, 0.00059024, 0.0, 0.00014159, 0.0, 0.0]],
    dtype=torch.float64,
)

outputs = []
for dev in [0, 1]:
    device = f'cuda:{dev}'
    mc = pyminichem.MiniChem()
    mc.initialize()
    temp = torch.tensor([1500.0], dtype=torch.float64, device=device)
    pres = torch.tensor([1.0e5], dtype=torch.float64, device=device)
    vmr = base_vmr.to(device)
    out = mc.forward(temp, pres, vmr, 60.0)
    torch.cuda.synchronize(dev)
    out_cpu = out.detach().cpu()
    outputs.append(out_cpu)
    print('device', dev, 'out_device', out.device, 'shape', tuple(out.shape))
    print('finite', bool(torch.isfinite(out).all().item()), 'sum', float(out_cpu.sum().item()))

if len(outputs) == 2:
    diff = (outputs[0] - outputs[1]).abs().max().item()
    print('max_abs_diff_between_gpu0_gpu1', diff)
PY

Expected behavior for the current working NVHPC build:

• cuda_enabled True
• torch_cuda_available True
• device_count 2 on this machine
• finite output tensors on both cuda:0 and cuda:1
• max_abs_diff_between_gpu0_gpu1 0.0 for the smoke test above

NVIDIA HPC SDK

For the CUDA/OpenACC build, install the NVIDIA HPC SDK from NVIDIA's official Linux x86_64 packages:

1. Download the SDK tarball from the NVIDIA HPC SDK download page.
2. Extract the archive.
3. Run the installer.
4. Add the compiler bin directory to PATH.

Official references:

• OpenACC getting started guide: https://docs.nvidia.com/hpc-sdk/archive/25.3/compilers/openacc-gs/index.html
• NVIDIA HPC SDK download page: https://developer.nvidia.com/hpc-sdk

Typical installation flow:

wget <official-nvhpc-tarball-url>
tar -xpf nvhpc_<version>_Linux_x86_64_cuda_multi.tar.gz
cd nvhpc_<version>_Linux_x86_64_cuda_multi
sudo ./install

The default install location is typically:

/opt/nvidia/hpc_sdk/Linux_x86_64/<version>/compilers/bin

Add the compilers to your shell environment:

export NVHPC=/opt/nvidia/hpc_sdk
export PATH=$NVHPC/Linux_x86_64/<version>/compilers/bin:$PATH

Verify the installation with:

nvfortran --version
nvc++ --version
nvaccelinfo

Notes:

• Replace <version> with the installed SDK version, for example 25.3.
• nvaccelinfo is NVIDIA's recommended check that the driver and GPU-facing toolchain are visible.
• The default /opt installation path usually requires sudo.