Furen Xiao
5e525c07c8
This commit introduces a new script, `setup_impact_konfai.sh`, which facilitates a one-time setup for the IMPACT registration pipeline (impact-reg-konfai). The script builds a self-contained shim that includes: - A glibc 2.35 loader and libraries extracted from the niftyreg:2.1.1-ubuntu Docker image. - A self-contained LibTorch 2.8.0 (cu128) library. - A wrapper script that runs the stock elastix-impact binary through the glibc 2.35 loader with the appropriate library paths. The setup ensures compatibility with hosts that do not meet the required glibc and LibTorch versions, allowing the pipeline to function correctly. The script also verifies the installation and provides usage instructions.
110 lines
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5 KiB
Bash
110 lines
No EOL
5 KiB
Bash
#!/usr/bin/env bash
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# One-time host setup for the IMPACT registration pipeline (impact-reg-konfai).
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#
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# The stock elastix-impact 1.0.0 binary (vboussot/ImpactElastix) needs
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# glibc >= 2.35 and links LibTorch 2.8.0. This host (Ubuntu 20.04, glibc 2.31,
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# env torch 2.14) satisfies neither, so this script builds a self-contained
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# shim at ~/.cache/konfai/elastix-impact-shim:
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# * glibc 2.35 loader + libs, extracted from the niftyreg:2.1.1-ubuntu image
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# (ubuntu 22.04 base) -- docker is needed ONLY for this one-time copy;
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# * LibTorch 2.8.0 cu128, self-contained (its own CUDA runtime), from
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# download.pytorch.org;
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# * a wrapper bin/elastix that runs the stock binary through the glibc 2.35
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# loader with the LibTorch 2.8.0 library path (ignoring the inherited
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# LD_LIBRARY_PATH, so the env's torch 2.14 cannot leak in).
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# The pipeline selects the shim via KONFAI_ELASTIX_DIR
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# (src/registration_pipelines.py::_impact_elastix_root).
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#
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# Run from the repo root, inside the conda env:
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# source /opt/conda/etc/profile.d/conda.sh && conda activate longitudinal-313
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# pip install impact-reg-konfai # the CLI itself
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# bash scripts/setup_impact_konfai.sh # this script
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#
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# First `register` afterwards auto-downloads from HF/GitHub: the preset app
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# (VBoussot/ImpactReg), the feature models (VBoussot/impact-torchscript-models)
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# and, on hosts that CAN run the stock binary directly, the binary itself.
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set -euo pipefail
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KONFAI_CACHE="${KONFAI_CACHE:-$HOME/.cache/konfai}"
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SHIM="$KONFAI_CACHE/elastix-impact-shim"
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STOCK="$KONFAI_CACHE/elastix-impact"
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GLIBC_SRC_DIR="${GLIBC_SRC_DIR:-glibc-2.35}"
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GLIBC_IMG="${GLIBC_IMG:-niftyreg:2.1.1-ubuntu}"
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LT_VER="2.8.0"
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LT_DIR="libtorch-${LT_VER}-cu128"
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LT_URL="https://download.pytorch.org/libtorch/cu128/libtorch-shared-with-deps-${LT_VER}%2Bcu128.zip"
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echo "[1/5] stock elastix-impact binary (package auto-install)"
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if [ ! -x "$STOCK/bin/elastix" ]; then
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python - <<'PY'
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from pathlib import Path
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from impact_reg_konfai.models.elastix_install import (
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ELASTIX_CACHE, get_elastix_bin, install_elastix_impact)
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if not get_elastix_bin(ELASTIX_CACHE).exists():
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# flavor auto-detected (cu128 on this host); downloads + extracts the zip
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install_elastix_impact(ELASTIX_CACHE, force_cuda=False, force_cpu=False)
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PY
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fi
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[ -x "$STOCK/bin/elastix" ] || { echo "stock binary missing: $STOCK/bin/elastix"; exit 1; }
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echo "[2/5] glibc 2.35 from $GLIBC_IMG (docker, one-time)"
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if [ ! -x "$KONFAI_CACHE/$GLIBC_SRC_DIR/ld-linux-x86-64.so.2" ]; then
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docker run --rm --entrypoint sh -v "$KONFAI_CACHE":/dest "$GLIBC_IMG" -c \
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"rm -rf /dest/$GLIBC_SRC_DIR && mkdir -p /dest/$GLIBC_SRC_DIR && \
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cp -a /lib/x86_64-linux-gnu/. /dest/$GLIBC_SRC_DIR/ && \
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cp -a /usr/lib/x86_64-linux-gnu/libstdc++.so.6* /dest/$GLIBC_SRC_DIR/ 2>/dev/null || true"
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fi
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echo "[3/5] LibTorch ${LT_VER} cu128 (self-contained)"
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if [ ! -f "$SHIM/lib/$LT_DIR/libtorch/lib/libc10.so" ]; then
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mkdir -p "$SHIM/lib"
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curl -L --fail -o "$KONFAI_CACHE/$LT_DIR.zip" "$LT_URL"
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unzip -q "$KONFAI_CACHE/$LT_DIR.zip" -d "$SHIM/lib/$LT_DIR"
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rm "$KONFAI_CACHE/$LT_DIR.zip"
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fi
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# the with-deps zip carries the CUDA libs under hashed names; expose the public
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# soname elastix links directly
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LT_LIB="$SHIM/lib/$LT_DIR/libtorch/lib"
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CUDART="$(ls "$LT_LIB"/libcudart-*.so.12 | head -1)"
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ln -sf "$(basename "$CUDART")" "$LT_LIB/libcudart.so.12"
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echo "[4/5] shim layout + wrapper"
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mkdir -p "$SHIM/bin"
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cp "$STOCK/bin/elastix" "$SHIM/bin/elastix-real"
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[ -d "$STOCK/lib" ] && cp -a "$STOCK/lib/." "$SHIM/lib/"
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[ -d "$KONFAI_CACHE/$GLIBC_SRC_DIR" ] && cp -a "$KONFAI_CACHE/$GLIBC_SRC_DIR" "$SHIM/lib/$GLIBC_SRC_DIR"
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cat > "$SHIM/bin/elastix" <<'WRAP'
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#!/bin/sh
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# elastix-impact 1.0.0 shim: the host glibc (2.31) is too old for the binary
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# (built against glibc 2.35) and the binary expects LibTorch 2.8.0, which the
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# conda env's torch (2.14) does not provide. Run it through the bundled
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# glibc 2.35 loader with the bundled self-contained LibTorch 2.8.0 (cu128).
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ROOT="$(cd "$(dirname "$0")/.." && pwd)"
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LT="$ROOT/lib/libtorch-2.8.0-cu128/libtorch/lib"
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GLIBC="$ROOT/lib/glibc-2.35"
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exec env -u LD_LIBRARY_PATH -u LD_PRELOAD \
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"$GLIBC/ld-linux-x86-64.so.2" \
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--library-path "$LT:$ROOT/lib:$GLIBC" \
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"$ROOT/bin/elastix-real" "$@"
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WRAP
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chmod +x "$SHIM/bin/elastix"
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echo "[5/5] verify"
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KONFAI_ELASTIX_DIR="$SHIM" python - <<'PY'
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import os
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from pathlib import Path
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from impact_reg_konfai.models.elastix_install import get_elastix_bin, loader_env, try_elastix
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import subprocess
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root = Path(os.environ["KONFAI_ELASTIX_DIR"])
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try_elastix(root)
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r = subprocess.run([str(get_elastix_bin(root).resolve()), "--extended-version"],
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capture_output=True, text=True, env=loader_env(root))
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assert r.returncode == 0, r.stderr
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print(r.stdout.splitlines()[0] if r.stdout else "elastix OK")
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print("elastix-impact shim OK:", root)
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PY
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echo
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echo "Done. The impact pipeline picks the shim up automatically"
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echo "(src/registration_pipelines.py::_impact_elastix_root), e.g.:"
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echo " python scripts/bench_registration.py --pipelines impact --n-cases 2" |