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Add documentation for debug builds and heap analysis (#687)
* Instructions to build cctbx with debug symbols * Steps for heap analysis in gdb-heap with example data and Dockerfile
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| # Fedora 30 image with gdb-heap and cctbx for debugging heap memory | ||
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| FROM fedora:30 | ||
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| # Install basic utilities, devel packages, debuginfo packages, and gdb-heap | ||
| RUN dnf install -y make which dnf-plugins-core && \ | ||
| dnf install -y python3-devel glibc-devel glib2-devel openssl-devel && \ | ||
| dnf debuginfo-install -y python3 glibc ncurses-libs readline openssl-libs zlib glib2 && \ | ||
| dnf install -y gdb-heap | ||
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| # Pull in some gdb-heap changes on personal fork | ||
| RUN dnf install -y git && \ | ||
| cd /usr/share/gdb-heap/ && \ | ||
| rm heap/*.py && \ | ||
| git init && \ | ||
| git remote add origin https://github.com/dwpaley/gdb-heap && \ | ||
| git fetch origin && \ | ||
| git checkout origin/master | ||
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| # CCTBX system dependencies and directory structure | ||
| RUN dnf install -y mesa-libGL-devel | ||
| RUN mkdir /img | ||
| RUN mkdir /mc3 | ||
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| # Conda | ||
| RUN cd /mc3 && \ | ||
| curl -LO https://repo.anaconda.com/miniconda/Miniconda3-py37_4.10.3-Linux-x86_64.sh && \ | ||
| /bin/sh Miniconda3-*.sh -b -u -p /mc3 | ||
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| # Bootstrap.py and conda yml file | ||
| RUN cd /img && \ | ||
| curl -LO https://raw.githubusercontent.com/cctbx/cctbx_project/master/xfel/conda_envs/psana_environment.yml && \ | ||
| curl -LO https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py | ||
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| # Set up conda_base environment using mamba | ||
| RUN cd /img && \ | ||
| source /mc3/etc/profile.d/conda.sh && \ | ||
| conda activate base && \ | ||
| conda install mamba -c conda-forge -y && \ | ||
| mamba env create -f psana_environment.yml -p $PWD/conda_base | ||
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| # Get sources and build | ||
| RUN cd /img && \ | ||
| source /mc3/etc/profile.d/conda.sh && \ | ||
| conda activate $PWD/conda_base && \ | ||
| python bootstrap.py \ | ||
| --builder=xfel \ | ||
| --use_conda=$PWD/conda_base \ | ||
| --nproc=12 \ | ||
| --python=37 \ | ||
| --build-dir=build_debug \ | ||
| --config-flags="--build=debug" \ | ||
| hot update build | ||
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| # Modify conda installation to use system python with debug symbols | ||
| RUN ln -sf /usr/bin/python3 /img/conda_base/bin/python3.7 |
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