Fix and trim to 11.7 GB

2026-06-04 14:14:24 +08:00 · 2025-10-28 14:15:22 +01:00
parent d0216854d8
commit 94f0e4ac35
1 changed files with 68 additions and 59 deletions
--- a/docker/alphalink.dockerfile
+++ b/docker/alphalink.dockerfile
@@ -1,77 +1,87 @@
-# syntax=docker/dockerfile:1.4
+# syntax=docker/dockerfile:1.7
+ARG BASE_IMAGE=registry.git.embl.de/grp-cbbcs/abcdesktop-apps/base-image:ubuntu22-cuda-11-8
+FROM ${BASE_IMAGE}
 ARG CUDA=11.8.0
-FROM registry.git.embl.de/grp-cbbcs/abcdesktop-apps/base-image:ubuntu22-cuda-11-8
-ARG CUDA

 SHELL ["/bin/bash","-o","pipefail","-c"]

-# Minimal runtime deps (+ bzip2 for micromamba tar)
-# Note: Dropped cuda-command-line-tools-* to avoid duplicating CUDA with the torch cu118 wheel.
-# If you actually need the CUDA toolchain at runtime, add it back.
-RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
-      kalign tzdata wget ca-certificates bzip2 git openssh-client \
-  && rm -rf /var/lib/apt/lists/*
+# ---- prevent docs/locales from being installed (much faster than deleting later)
+RUN set -eux; \
+  echo 'path-exclude=/usr/share/man/*'             >  /etc/dpkg/dpkg.cfg.d/01_nodoc; \
+  echo 'path-exclude=/usr/share/doc/*'             >> /etc/dpkg/dpkg.cfg.d/01_nodoc; \
+  echo 'path-exclude=/usr/share/locale/*'          >> /etc/dpkg/dpkg.cfg.d/01_nodoc; \
+  echo 'path-include=/usr/share/locale/en*'        >> /etc/dpkg/dpkg.cfg.d/01_nodoc; \
+  printf 'Acquire::Languages "none";\n'            >  /etc/apt/apt.conf.d/99no-languages

-# micromamba bootstrap
-ENV MAMBA_ROOT_PREFIX=/opt/conda
+ENV TZ=Etc/UTC \
+    DEBIAN_FRONTEND=noninteractive
+
+# ---- base runtime deps (cached apt metadata with BuildKit mounts; no leftover lists)
+RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
+    --mount=type=cache,target=/var/lib/apt,sharing=locked \
+    set -eux; \
+    apt-get update; \
+    apt-get install -y --no-install-recommends tzdata wget ca-certificates bzip2 git openssh-client; \
+    rm -rf /var/lib/apt/lists/*
+
+# ---- micromamba bootstrap (pin to current 'latest' endpoint; change if you want a fixed version)
+ENV MAMBA_ROOT_PREFIX=/opt/conda \
+    MAMBA_NO_BANNER=1 \
+    CONDA_CHANNEL_PRIORITY=strict
 RUN set -eux; \
    wget -qO- https://micro.mamba.pm/api/micromamba/linux-64/latest \
      | tar -xvj -C /usr/local/bin --strip-components=1 bin/micromamba; \
    micromamba --help >/dev/null

-# faster dependency solve; strict priority
-ENV CONDA_CHANNEL_PRIORITY=strict
-
-# Create env at /opt/conda; no activation needed
-RUN micromamba install -y -p /opt/conda -c conda-forge -c bioconda \
-      python=3.10 openmm=8 pdbfixer=1.9 kalign2 \
-      importlib-metadata modelcif hmmer hhsuite pip \
-  && micromamba clean -y --all
+# ---- env creation (done in one layer; clean immediately)
+RUN set -eux; \
+    micromamba install -y -p /opt/conda -c conda-forge -c bioconda \
+        python=3.10 openmm=8 pdbfixer=1.9 kalign2 \
+        importlib-metadata modelcif hmmer hhsuite pip; \
+    micromamba clean -y --all

 ENV PATH=/opt/conda/bin:$PATH
 ENV LD_LIBRARY_PATH=/opt/conda/lib:/usr/local/nvidia/lib:/usr/local/nvidia/lib64
 ENV NVIDIA_DRIVER_CAPABILITIES=compute,utility

-# pip reliability defaults
+# ---- pip defaults
 ENV PIP_NO_CACHE_DIR=1 \
    PIP_DISABLE_PIP_VERSION_CHECK=1 \
-    PYTHONUNBUFFERED=1
+    PYTHONUNBUFFERED=1 \
+    PYTHONDONTWRITEBYTECODE=1

-# PyTorch via pip (CUDA 11.8) BEFORE Uni-Core (Fix A)
-# Torch from the PyTorch index; other deps from PyPI.
-RUN python -m pip install --upgrade pip \
- && python -m pip install \
-      torch==2.5.1+cu118 \
-      --index-url https://download.pytorch.org/whl/cu118 \
-      --extra-index-url https://pypi.org/simple
+# ---- PyTorch (CUDA 11.8) from PyTorch index
+ARG TORCH_VERSION=2.1.2
+ARG TORCH_CUDA=cu118
+ARG TORCH_INDEX_URL=https://download.pytorch.org/whl/${TORCH_CUDA}
+RUN set -eux; \
+    python -m pip install --upgrade pip; \
+    python -m pip install \
+        torch==${TORCH_VERSION}+${TORCH_CUDA} \
+        --index-url ${TORCH_INDEX_URL}

-# Python packages (after torch)
-# Optional: pin to SHAs for reproducibility instead of @main
-RUN python -m pip install \
-      git+https://github.com/dptech-corp/Uni-Core.git@main \
-      git+https://github.com/KosinskiLab/AlphaPulldown.git@main \
-      pytest
+# ---- project python deps (after torch)
+# NOTE: if you want reproducibility, pin to tags/SHAs instead of @main
+RUN set -eux; \
+    python -m pip install --no-build-isolation \
+        git+https://github.com/dptech-corp/Uni-Core.git@main; \
+    python -m pip install --no-build-isolation \
+        git+https://github.com/KosinskiLab/AlphaPulldown.git@main; \
+    python -m pip install pytest; \
+    # optional: strip tests, dist-info RECORDs, caches to shrink a bit
+    find /opt/conda -type d -name "__pycache__" -prune -exec rm -rf {} +; \
+    find /opt/conda -type f -name "*.pyc" -delete

-# Trim: drop build tools & caches
-RUN apt-get purge -y git openssh-client wget bzip2 \
- && apt-get autoremove -y && apt-get clean \
- && micromamba clean -y --all \
- && python - <<'PY'
-import os
-for root, dirs, files in os.walk("/opt/conda", topdown=False):
-    for f in files:
-        if f.endswith((".pyc",".pyo")):
-            try: os.remove(os.path.join(root,f))
-            except: pass
-    for d in list(dirs):
-        if d == "__pycache__":
-            try: os.rmdir(os.path.join(root,d))
-            except: pass
-PY
-RUN rm -rf /root/.cache /var/cache/apt/* /usr/share/man /usr/share/doc
-
-# Keep your abcdesktop labels/environment as needed
+# ---- trim build-time tools (kept until after git+pip installs)
+RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
+    --mount=type=cache,target=/var/lib/apt,sharing=locked \
+    set -eux; \
+    apt-get purge -y git openssh-client wget bzip2; \
+    apt-get autoremove -y; \
+    apt-get clean; \
+    rm -rf /var/lib/apt/lists/* /root/.cache

+# -------------- abcdesktop labels/env --------------
 LABEL oc.icon="alphafold.svg"
 LABEL oc.icondata="PD94bWwgdmVyc2lvbj0iMS4wIiBlbmNvZGluZz0iVVRGLTgiPz4KPCFET0NUWVBFIHN2ZyBQVUJMSUMgIi0vL1czQy8vRFREIFNWRyAxLjEvL0VOIiAiaHR0cDovL3d3dy53My5vcmcvR3JhcGhpY3MvU1ZHLzEuMS9EVEQvc3ZnMTEuZHRkSI[...]"
 LABEL oc.keyword="AlphaLink"
@@ -82,7 +92,6 @@ LABEL oc.template="abcdesktopio/oc.template.ubuntu.nvidia.22.04"
 LABEL oc.name="af1"
 LABEL oc.displayname="AlphaLink"
 LABEL oc.path="/usr/bin/konsole"
-#LABEL oc.args="--hold -e bash --rcfile"
 LABEL oc.type=app
 LABEL oc.showinview="dock"
 LABEL oc.rules="{\"homedir\":{\"default\":true}}"
@@ -91,14 +100,14 @@ LABEL oc.acl="{\"permit\":[\"all\"]}"
 RUN if [ -d /usr/share/icons ]   && [ -x /composer/safelinks.sh ]; then cd /usr/share/icons;   /composer/safelinks.sh; fi
 RUN if [ -d /usr/share/pixmaps ] && [ -x /composer/safelinks.sh ]; then cd /usr/share/pixmaps; /composer/safelinks.sh; fi

-ENV APPNAME="af1"
-ENV APPBIN="/usr/bin/konsole"
-ENV APP="/usr/bin/konsole"
+ENV APPNAME="af1" \
+    APPBIN="/usr/bin/konsole" \
+    APP="/usr/bin/konsole"

 RUN mkdir -p /run/user/ && chmod 777 /run/user
 RUN mkdir -p /etc/localaccount && for f in passwd shadow group gshadow; do \
      if [ -f /etc/$f ]; then cp /etc/$f /etc/localaccount; rm -f /etc/$f; ln -s /etc/localaccount/$f /etc/$f; fi; \
    done

-CMD ["/composer/appli-docker-entrypoint.sh"]
-# ENTRYPOINT ["bash"]
+# prefer abcdesktop entrypoint if present; otherwise bash
+CMD ["/bin/bash","-lc","if [ -x /composer/appli-docker-entrypoint.sh ]; then exec /composer/appli-docker-entrypoint.sh; else exec bash; fi"]