FROM ubuntu:jammy-20260217

ENV DEBIAN_FRONTEND=noninteractive

RUN apt-get update && \
    apt-get install -y --no-install-recommends build-essential nvidia-cuda-toolkit && \
    rm -rf /var/lib/apt/lists/*

# Ensure nvcc from CUDA toolkit is in PATH
ENV PATH=/usr/local/cuda/bin:${PATH}
ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64:${LD_LIBRARY_PATH}

WORKDIR /workspace

COPY . /workspace

RUN set -eux; \
    make -f src/13-md/whole-code/makefile; \
    make -f src/13-md/force-only/makefile; \
    make -f src/13-md/cpp/makefile

CMD ["/bin/bash"]

# Exclude VCS and build artefacts
.git
.gitignore
build/
*.o
*.a
*.so
*.dll
*.dylib

# Node, Python caches (if any in repo)
__pycache__/
*.pyc

# CUDA build artefacts
*.ptx
*.cubin

# IDE files
.vscode/
.idea/
*.sublime-project
*.DS_Store

- Exact error message and exit code
  - Exact failure: "make: *** No rule to make target 'initialize.cu', needed by 'initialize.o'.  Stop."
  - Exit code: 2
  - Overall docker build step exit: 2 (as shown by: failed to complete: exit code: 2)

- Failing command/step
  - Step: [5/5] RUN set -eux;     make -f src/13-md/whole-code/makefile;     make -f src/13-md/force-only/makefile;     make -f src/13-md/cpp/makefile
  - Failing command within that step: make -f src/13-md/whole-code/makefile
  - The error occurs during the first make invocation

- Missing packages or files mentioned
  - The build is failing due to a missing Makefile rule for initialize.cu: No rule to make target 'initialize.cu', needed by 'initialize.o'.
  - This implies either the source file initialize.cu is missing or the Makefile does not provide a rule to build it.

- Version mismatch / environment details
  - Base image: ubuntu:jammy-20260217 (sha256: bf7bfa0b43e40076229eec59a254f539fc4803accc2bd9049ecee8bf2da3bd02)
  - The install step upgrades a large set of packages (gcc-12-base, libstdc++6, etc.) and installs many NVIDIA CUDA-related libraries/tools; logs show: “3 upgraded, 91 newly installed, 0 to remove and 8 not upgraded” with substantial archive fetch (about 1.5 GB). Also the system logs note CUDA/NVIDIA components (nvidia-cuda-toolkit, libnvidia-*, etc.).
  - A warning observed: UndefinedVar: Usage of undefined variable '$LD_LIBRARY_PATH' (line 11) in Dockerfile:17

- Note
  - The root cause appears to be a missing or mis-specified build rule for initialize.cu in the first Makefile, not a straightforward package/version mismatch, though the environment contains CUDA/NVIDIA tooling.

FROM ubuntu:jammy-20260217

ENV DEBIAN_FRONTEND=noninteractive

RUN apt-get update && \
    apt-get install -y --no-install-recommends build-essential nvidia-cuda-toolkit && \
    rm -rf /var/lib/apt/lists/*

# Ensure nvcc from CUDA toolkit is in PATH
ENV PATH=/usr/local/cuda/bin:${PATH}
ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64

WORKDIR /workspace

COPY . /workspace

RUN set -eux; \
    cd src/13-md/whole-code && make -f makefile; \
    cd ../../force-only && make -f makefile; \
    cd ../../cpp && make -f makefile

CMD ["/bin/bash"]

- Exact error message and exit code
  - ERROR: failed to build: failed to solve: process "/bin/sh -c set -eux;     cd src/13-md/whole-code && make -f makefile;     cd ../../force-only && make -f makefile;     cd ../../cpp && make -f makefile" did not complete successfully: exit code: 2
  - /bin/sh: 1: cd: can't cd to ../../force-only
  - /bin/sh: 1: cd: can't cd to ../../cpp

- Failing command/step
  - RUN set -eux;     cd src/13-md/whole-code && make -f makefile;     cd ../../force-only && make -f makefile;     cd ../../cpp && make -f makefile

- Missing packages or files mentioned
  - The errors indicate missing directories: ../../force-only and ../../cpp relative to src/13-md/whole-code (i.e., those paths do not exist in the build context at that point).

- Version mismatch info
  - Base image: ubuntu:jammy-20260217 (sha256:bf7bfa0b43e40076229eec59a254f539fc4803accc2bd9049ecee8bf2da3bd02)
  - No explicit version mismatch error; CUDA-related steps run compile (nvcc) successfully until the cd steps fail.

FROM ubuntu:jammy-20260217

ENV DEBIAN_FRONTEND=noninteractive

RUN apt-get update && \
    apt-get install -y --no-install-recommends build-essential nvidia-cuda-toolkit && \
    rm -rf /var/lib/apt/lists/*

# Ensure nvcc from CUDA toolkit is in PATH
ENV PATH=/usr/local/cuda/bin:${PATH}
ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64

WORKDIR /workspace

COPY . /workspace

RUN set -eux; \
    cd src/13-md/whole-code && make -f makefile; \
    cd ../force-only && make -f makefile; \
    cd ../cpp && make -f makefile

CMD ["/bin/bash"]