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pkg-scripts/python-3.11.7-1.build.sh
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| #!/bin/bash | |
| # ------------------------------------------------------------------- Debug | |
| COOKIE=$(mcookie|cut -c-8); grep -v V_GREP_ME $0 > /dev/shm/runme-$COOKIE.sh ; sleep 0.3; exec bash /dev/shm/runme-$COOKIE.sh | |
| # TESTING=1 | |
| # SKIPTENSORFLOW=1 | |
| # ---------------------------------------------------------------- Preamble | |
| PKG=python | |
| VERSION=3.11.7 | |
| BUILD=1 | |
| PYTHONVER=${VERSION%.*} | |
| CUDADIR=/pkg/cuda-11.8.0-0 | |
| PREFIX=/pkg/$PKG-$VERSION-$BUILD | |
| if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$PKG-$VERSION-$BUILD ; fi | |
| PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin | |
| set -e | |
| umask 022 | |
| BUILD_TMPDIR=/scratch/local2/$PKG-$VERSION-$BUILD.$USER.build.tmp | |
| # keep pip's download cache when testing | |
| test -z "$TESTING" && test -d $BUILD_TMPDIR && ( chmod -R u+rwx $BUILD_TMPDIR || true ; rm -rf $BUILD_TMPDIR ) | |
| mkdir -p $BUILD_TMPDIR/home/.cache/pip | |
| mkdir -p $BUILD_TMPDIR/home/.local | |
| # copy script to an accessible location | |
| cp $0 $BUILD_TMPDIR; ME="$BUILD_TMPDIR/$(basename $0)" | |
| export TMPDIR=$BUILD_TMPDIR | |
| export HOME=$BUILD_TMPDIR/home | |
| exec </dev/null | |
| mkdir -p $PREFIX | |
| cat >$PREFIX/profile <<-EOF | |
| . $CUDADIR/profile | |
| PATH=$PREFIX/bin:\$PATH | |
| export LD_LIBRARY_PATH=$PREFIX/lib\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH | |
| PKG_CONFIG_PATH=$PREFIX/lib/pkgconfig\${PKG_CONFIG_PATH:+:}\$PKG_CONFIG_PATH | |
| export PKG_CONFIG_PATH | |
| if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH ; fi | |
| EOF | |
| . $PREFIX/profile | |
| NPROC=$(( $(nproc) * 4 / 5 + 1 )) | |
| export MAKEFLAGS="-j $NPROC" | |
| BUILDDIR=$PREFIX/build | |
| mkdir -p $BUILDDIR | |
| cd $BUILDDIR | |
| # -------------------------------------- Use git to track package evolution | |
| test -d .git && rm -rf .git | |
| git init -q; echo -e '[user]\n name = none\n email = of_your_business...' >> .git/config | |
| echo '*' > .gitignore | |
| function piplist() { | |
| pip list | awk '{ printf("%-36s %s\n", $1,$2) }' | grep -v '\----' > GameOfVersions | |
| } | |
| function track() { | |
| if [ -d .git ]; then | |
| if git add -f GameOfVersions; then | |
| git commit -q -n -m "Package: '$*'" || /bin/true | |
| fi | |
| fi | |
| } | |
| function install() { | |
| echo "# ::INST:: # '${@+$@}'" | |
| # no-color is nice, but doesn't work when dependencies are installed, so (mis-)use a pipe | |
| pip install --no-color --compile --cache-dir=$HOME/.cache/pip --prefix=$PREFIX "${@+$@}" | cat | |
| piplist | |
| track $* | |
| } | |
| # ---------------------------------------- Build Python & support libraries | |
| ( | |
| # orig: https://www.python.org/ftp/python/3.11.7/Python-3.11.7.tgz | |
| BEEHIVE=https://beehive.molgen.mpg.de/ef61f81ec82c490484219c7f0ec96783/Python-3.11.7.tgz | |
| test -e Python-$VERSION.tar.xz || wget -nv $BEEHIVE | |
| test -d Python-$VERSION || tar -xf Python-$VERSION.tgz | |
| cd Python-$VERSION | |
| # BerkeleyDB, the undead ... | |
| # Newer libgdbm_compat.so versions pull libgdbm.so on their own, our libgdbm_compat.so is older ... | |
| # So, let setup.py create '-lgdbm -lgdbm_compat' instead of a sole '-lgdbm_compat' | |
| # verbatim: ndbm_libs = ['gdbm_compat'] => ndbm_libs = ['gdbm','gdbm_compat'] | |
| sed -i -e "/ndbm_libs = / s/_compat'/','gdbm_compat'/" setup.py | |
| # leave further hints in the log | |
| sed -i -e '/db_setup_debug = False/ s/False/True/' \ | |
| -e '/dbm_setup_debug = False/ s/False/True/' setup.py | |
| # These may come handy if the Python build needs exclusive stuff from $PREFIX | |
| # INCLUDEDIR=$PREFIX/include \ | |
| # LIBDIR=$PREFIX/lib \ | |
| LDFLAGS="-Wl,-rpath=$PREFIX/lib" \ | |
| ./configure \ | |
| --prefix=$PREFIX \ | |
| --enable-shared | |
| make -j $NPROC | |
| make install | |
| # it might come to happen that something down the line may just call 'python', defuse ... | |
| test -e $PREFIX/bin/python || ln -s python3 $PREFIX/bin/python | |
| python -m ensurepip | |
| pip3 install --prefix=$PREFIX -I pip | |
| ( # fix 'please update' noise from pip | |
| cd $PREFIX/lib/python*/site-packages | |
| sed -ne '/^#Epatch:pip/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose | |
| ) | |
| # libblosc2 installs in $PREFIX/lib64, I hate to do this ... | |
| ln -s lib $PREFIX/lib64 | |
| ) | |
| install setuptools | |
| piplist; track START | |
| # build various pythonbindings 'by hand', because pip installs do not deliver | |
| # header files and the like. | |
| # BTW: builds need meson | |
| install meson | |
| ( | |
| DBUS_PYTHON_VERSION=1.3.2 | |
| # PyPi | |
| # https://files.pythonhosted.org/packages/c1/d3/6be85a9c772d6ebba0cc3ab37390dd6620006dcced758667e0217fb13307/dbus-python-1.3.2.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/33be8a4a766e1c7c9a377b8f934ce21a/dbus-python-1.3.2.tar.gz | |
| test -e dbus-python-$DBUS_PYTHON_VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d dbus-python-$DBUS_PYTHON_VERSION || tar -xf dbus-python-$DBUS_PYTHON_VERSION.tar.gz | |
| cd dbus-python-$DBUS_PYTHON_VERSION | |
| ./configure --prefix=$PREFIX | |
| make -j $NPROC | |
| make install | |
| ) | |
| ( | |
| PYCAIRO_VERSION=1.23.0 | |
| # PyPi | |
| # https://files.pythonhosted.org/packages/69/ca/9e9fa2e8be0876a9bbf046a1be7ee33e61d4fdfbd1fd25c76c1bdfddf8c4/pycairo-1.23.0.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/7a3729d21659098e1b9a411b62e88966/pycairo-1.23.0.tar.gz | |
| test -e pycairo-$PYCAIRO_VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d pycairo-$PYCAIRO_VERSION || tar -xf pycairo-$PYCAIRO_VERSION.tar.gz | |
| cd pycairo-$PYCAIRO_VERSION | |
| mkdir -p meson-build | |
| cd meson-build | |
| meson setup \ | |
| --prefix=$PREFIX \ | |
| --buildtype=release \ | |
| -Dpython=$PREFIX/bin/python \ | |
| -Dtests=false \ | |
| .. | |
| ninja -j $NPROC | |
| ninja install | |
| ) | |
| ( | |
| PYGOBJECT3_VERSION=3.44.1 | |
| # https://files.pythonhosted.org/packages/07/73/a034fc1bcd6d402d6f72ff618c093f91ac6921f968cc19806b6a1b1b19c8/PyGObject-3.44.0.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/959259478566b24316edaa18da6e0eaa/PyGObject-3.44.1.tar.gz | |
| test -e PyGObject-$PYGOBJECT3_VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d PyGObject-$PYGOBJECT3_VERSION || tar -xf PyGObject-$PYGOBJECT3_VERSION.tar.gz | |
| cd PyGObject-$PYGOBJECT3_VERSION | |
| mkdir -p meson-build | |
| cd meson-build | |
| meson setup \ | |
| --prefix=$PREFIX \ | |
| --buildtype=release \ | |
| -Dpython=$PREFIX/bin/python \ | |
| -Dtests=false \ | |
| .. | |
| ninja -j $NPROC | |
| ninja install | |
| ) | |
| piplist; track various pythonbindings | |
| # build support to use QT from python -- see www.riverbankcomputing.com | |
| ( # sip: tool to create Python bindings for C and C++ libraries. | |
| SIP_VERSION=6.7.7 | |
| # https://files.pythonhosted.org/packages/5b/cb/c27c925ae07bd03a2597fa1db17bfc2a4ac57da61aeb90f8ec98ffbb975b/sip-6.6.2.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/a131efd79649d31ee11601b19d1e3784/sip-6.7.7.tar.gz | |
| test -e sip-$SIP_VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d sip-$SIP_VERSION || tar -xf sip-$SIP_VERSION.tar.gz | |
| cd sip-$SIP_VERSION | |
| pip install . | |
| ) | |
| # QT bindings need some python modules to build | |
| install PyQt5-sip | |
| install PyQt-builder | |
| ( | |
| PYQT_VERSION=5.15.9 | |
| # orig: https://files.pythonhosted.org/packages/5c/46/b4b6eae1e24d9432905ef1d4e7c28b6610e28252527cdc38f2a75997d8b5/PyQt5-5.15.9.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/9d97fc06b7ae75e654e946c49e07ff12/PyQt5-5.15.9.tar.gz | |
| test -e PyQt5-$PYQT_VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d PyQt5-$PYQT_VERSION || tar -xf PyQt5-$PYQT_VERSION.tar.gz | |
| cd PyQt5-$PYQT_VERSION | |
| sip-build \ | |
| --confirm-license \ | |
| --no-make \ | |
| --api-dir $PREFIX/share/qsci/api/python \ | |
| --dbus $PREFIX/include/dbus-1.0 \ | |
| --no-designer-plugin \ | |
| --no-qml-plugin \ | |
| --jobs $NPROC | |
| cd build | |
| make -j $NPROC | |
| make install | |
| # Remove unused py2 version of uic modules | |
| rm -r $PREFIX/lib/python*/site-packages/PyQt5/uic/port_v2 | |
| ) | |
| ( | |
| QSCINTILLA_VERSION=2.13.4 # no 2.14 in sight ... | |
| # orig: https://www.riverbankcomputing.com/static/Downloads/QScintilla/2.13.4/QScintilla_src-2.13.4.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/4f83a4a4ad7da40eae80ad23f9fb18f2/QScintilla_src-2.13.4.tar.gz | |
| test -e QScintilla_src-$QSCINTILLA_VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d QScintilla_src-$QSCINTILLA_VERSION || tar -xf QScintilla_src-$QSCINTILLA_VERSION.tar.gz | |
| cd QScintilla_src-$QSCINTILLA_VERSION | |
| cd Python | |
| cp -vp pyproject-qt5.toml pyproject.toml | |
| sip-build \ | |
| --no-make \ | |
| --qsci-features-dir ../src/features \ | |
| --qsci-include-dir ../src \ | |
| --qsci-library-dir ../src \ | |
| --api-dir $PREFIX/share/qsci/api/python \ | |
| --jobs $NPROC | |
| cd build | |
| make -j $NPROC | |
| make install | |
| ) | |
| ( | |
| set -x | |
| PYQTWEBENGINE_VERSION=5.15.6 | |
| #orpg: https://pypi.org/project/PyQtWebEngine/#files | |
| BEEHIVE="https://beehive.molgen.mpg.de/d1e548617de149ba8142a32c1eb9f994/PyQtWebEngine-5.15.6.tar.gz" | |
| test -e PyQtWebEngine-${PYQTWEBENGINE_VERSION}.tar.gz || wget -nv $BEEHIVE | |
| test -d PyQtWebEngine-${PYQTWEBENGINE_VERSION} || tar -xf PyQtWebEngine-${PYQTWEBENGINE_VERSION}.tar.gz | |
| cd PyQtWebEngine-${PYQTWEBENGINE_VERSION} | |
| sip-build \ | |
| --no-make \ | |
| --api-dir ${PREFIX}/share/qsci/api/python \ | |
| --jobs $NPROC | |
| cd build | |
| make -j $NPROC | |
| make install | |
| ) | |
| piplist; track qt-support-riverbankcomputing | |
| # -------------------------------------------------------- Install packages | |
| install Cython | |
| # libxml2-python from pypi isn't up to date, cause lxml seems to be the favored binding | |
| # do this early, not that some dependency tries it on its own. | |
| # (btw. libxslt-python isn't ported to python3) | |
| ( | |
| LIBXML2_VERSION=2.9.12 | |
| # orig: http://xmlsoft.org/sources/libxml2-${PKGVERSION}.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/f433a39be087a9f0b197eb2307ad9f75/libxml2-2.9.12.tar.gz | |
| test -e libxml2-$LIBXML2_VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d libxml2-$LIBXML2_VERSION || tar -xf libxml2-$LIBXML2_VERSION.tar.gz libxml2-$LIBXML2_VERSION/python | |
| cd libxml2-$LIBXML2_VERSION/python | |
| pip install . | |
| ) | |
| piplist; track legacy-libxml2 | |
| # Install the most 'sensitive' packages first | |
| install numpy==1.25.2 | |
| install numba==0.58.1 | |
| install wheel | |
| # python-javabridge, problems with python 3.11 and recent cython, thus | |
| # regenerate C bindings from *pxd, *pyx -- so must use github, and wheel | |
| ( | |
| # use the fork from cellprofiler, as used in pypi | |
| git clone https://github.com/CellProfiler/python-javabridge | |
| cd python-javabridge | |
| git checkout v4.0.3 | |
| sed -ne '/^#Epatch:javabridge/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose | |
| pip install . | |
| ) | |
| PACKAGES=$(sed -e s/#.*$// <<- __PKGLIST__ | |
| igraph==0.10.8 # louvain | |
| keras==2.14.0 # tensorflow 2.14.1 | |
| ml-dtypes==0.2.0 # tensorflow, dm-haiku, jax, tensorstore | |
| pytest==6.2.5 | |
| pytest-asyncio==0.19.0 # to get rid of a deprecation warning in 0.20.3, -> 0.19.0 | |
| urllib3==2.0.7 | |
| ipython[all] | |
| wrapt==1.14.1 # tensorflow vs. snakemake, snakemake 8.1.1 insists somehow on 1.16.0 | |
| snakemake==7.32.4 # December 2024 brougt snakemake 8++ | |
| triton=2.1.0 # pytorch | |
| Pillow | |
| protobuf | |
| onnx | |
| Sphinx | |
| jedi | |
| black[d] # onnx wants it, but does not install it ... | |
| flask | |
| SciPy | |
| pandas | |
| SymPy | |
| nose | |
| statsmodels | |
| pysam | |
| seaborn | |
| scikit-learn | |
| Mako | |
| cutadapt # Helpdesk 01/24/18 16:19, S. K. | |
| pygobject # Helpdesk 03/26/18 14:19, V. S. | |
| blink1 # Blink1-lib 07/04/18 12:00, N. H. | |
| hvplot # ont/nextflow pipelines | |
| pyarrow # ont/nextflow pipelines | |
| umi-tools | |
| recommonmark | |
| fastcluster | |
| pydot | |
| pygraphviz | |
| deeptools | |
| HTSeq | |
| keras_preprocessing # tensorflow ... | |
| MotifScan # A.B. 30.8.2018 | |
| MAmotif | |
| hic2cool # Helpdesk R. S. 17.09.2018 | |
| virtualenv # Donald | |
| odfpy # Donald | |
| Dumper # Thomas | |
| louvain # monocle3 prep for H. K. | |
| selenium # 19.7.19 T.K. -> https://webxray.org/ | |
| plotly | |
| pyOpenCL | |
| docopt | |
| distro | |
| ply | |
| threadpoolctl | |
| HiCMatrix # 17.1 -> https://github.com/deeptools/HiCMatrix/issues/47 | |
| pybedtools | |
| gffutils | |
| jupyter | |
| jupyterlab | |
| jupyterlab-git # request P. A. | |
| igv_jupyterlab # M. L. HD 01-04-2020 | |
| igv-notebook | |
| scour # https://github.molgen.mpg.de/mariux64/pkg-scripts/issues/98 | |
| multiqc | |
| pybind11 | |
| svgwrite | |
| pyomo | |
| bioservices | |
| SharedArray | |
| pyabc # dependency for stochkit, HD 20.07.20 G. N. | |
| petab | |
| tadtool # HD 26.01.21 M. R. | |
| pyperf # Paul sep-20 | |
| umap # HD, used by M. L. | |
| MACS3 | |
| biopython # HD 2021-07-23 Magalhaes/Hnisz alphafold related -- cool that we have missed biopython so far, LOL | |
| # prevent dm-haiku from fetching 'brand-new' stuff, thus avoiding further havoc | |
| tensorstore==0.1.45 # tensorflow | |
| orbax-checkpoint==0.4.4 # tensorflow | |
| dm-tree | |
| dm-haiku | |
| flatbuffers | |
| contextlib2 | |
| ml_collections | |
| python-bioformats==4.0.6 # 4.0.7 would pull up too much other packages | |
| # additions/fixups since 3.9 | |
| spyder | |
| spyder-kernels | |
| papermill # turns jupyter notebooks into scripts [sic!] used by P.A. [who else, *grin*] | |
| opencv-python | |
| scikit-image | |
| git-cola | |
| cffi-glpk # uses /usr/lib/libglpk.so.40, see if I can get it linked statically - kreitler | |
| czifile | |
| # watch https://pypi.org/project/napari/#history | |
| napari[pyqt5]==0.4.19rc7 # 0.4.18 would turn into a psychotic downgrader via numpydoc ... | |
| napari-czifile2 | |
| bx-python | |
| # CrossMap - coredumps by help[modules] because of a '__init__.py' in site_packages, fix is below | |
| leidenalg | |
| scanpy # this is a MESS, you might always have broken/ugly plots ... | |
| asciidoc | |
| # additions/fixups since 3.10 | |
| aicspylibczi | |
| filetype | |
| gmpy2 | |
| shap | |
| xgboost | |
| UpSetPlot | |
| hypothesis | |
| # nf-core / epi2me related | |
| dominate | |
| libsass | |
| sigfig | |
| whatshap | |
| Truvari | |
| nanopack | |
| __PKGLIST__ | |
| ) | |
| for PKG in $PACKAGES; do | |
| install $PKG | |
| done | |
| # build CrossMap from git, https://github.com/liguowang/CrossMap/issues/67 | |
| ( | |
| git clone https://github.com/liguowang/CrossMap | |
| cd CrossMap | |
| git rm src/__init__.py | |
| git commit -a -m 'remove badly placed src/__init__.py' | |
| pip install . --prefix=$PREFIX | |
| piplist; track CrossMap | |
| ) | |
| # remove unneeded dependency, and save the current pillow, then go for pyimagej, nerve ... | |
| ( | |
| LABELING_VERSION=0.1.13 | |
| # https://files.pythonhosted.org/packages/71/b0/c3c3c6931850c05e548c0a8cfadb8e6d8c5bd5ad18dce90ad4c909db5867/labeling-0.1.13.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/6da91e43f9864e9f4d4acb252eb486eb/labeling-0.1.13.tar.gz | |
| test -e labeling-${LABELING_VERSION}.tar.gz || wget -nv $BEEHIVE | |
| test -d labeling-${LABELING_VERSION} || tar -xf labeling-${LABELING_VERSION}.tar.gz | |
| cd labeling-${LABELING_VERSION} | |
| # not needed (tests work...) | |
| sed -i -e '/pillow/ s/<10//' ./setup.py | |
| sed -i -e '/pillow/ s/<10//' ./labeling.egg-info/requires.txt | |
| pip install . --prefix=$PREFIX | |
| piplist; track labeling==${LABELING_VERSION} | |
| ) | |
| install pyimagej # Microscopy | |
| # create a wrapper that sets JAVA_HOME | |
| mv -v $PREFIX/bin/imagej $PREFIX/bin/imagej.dist | |
| cat << EOF > $PREFIX/bin/imagej | |
| #! /bin/bash | |
| export JAVA_HOME=/pkg/openjdk-21.0.0.35-0 | |
| exec $PREFIX/bin/imagej.dist "\${@+\$@}" | |
| EOF | |
| chmod +x $PREFIX/bin/imagej | |
| # torch bundled with a recent CUDA-Toolkit | |
| install torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cu118 | |
| install pyopengl # Tk binding creates an error, so remove it (Expects Tk Togl installation...) | |
| rm -rf ${PREFIX}/lib/python$PYTHONVER/site-packages/OpenGL/Tk | |
| mkdir -vp $PREFIX/share/jupyter/lab/settings # try to defeat a silly error in jupyter labextension install | |
| # --------------------------------------------------- Install misc packages | |
| # these mostly bigger packages require either wheel, other treatments, | |
| # or java. | |
| # GYP is a Meta-Build system: a build system that generates other build systems. https://gyp.gsrc.io/ | |
| ( | |
| set -x | |
| GYP_VERSION=20230301_c6d8b9f7 | |
| # orig: https://mirror.netcologne.de/slackware/slackware64-current/source/d/gyp/ | |
| BEEHIVE=https://beehive.molgen.mpg.de/ba0357be23ca55555714261afccc7aab/gyp-20230301_c6d8b9f7.tar.xz | |
| test -e gyp-${GYP_VERSION}.tar.xz || wget -nv $BEEHIVE | |
| test -d gyp-${GYP_VERSION} || tar -xf gyp-${GYP_VERSION}.tar.xz | |
| cd gyp-${GYP_VERSION} | |
| sed -ne '/^#Epatch:gyp/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose | |
| pip install . | |
| ) | |
| piplist; track gyp | |
| ( | |
| BOOST_VERSION=(1.80.0 1_80_0) | |
| PKGCFLAGS="-O2 -fPIC" | |
| # orig: https://boostorg.jfrog.io/artifactory/main/release/1.80.0/source/boost_1_80_0.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/077f074743ea7b0cb49c6ed43953ae95/boost_1_80_0.tar.gz | |
| test -e boost_${BOOST_VERSION[1]}.tar.gz || wget -nv $BEEHIVE | |
| test -d boost-${BOOST_VERSION[0]} || mkdir boost-${BOOST_VERSION[0]} && tar -xf boost_${BOOST_VERSION[1]}.tar.gz -C boost-${BOOST_VERSION[0]} --strip-components=1 | |
| cd boost-${BOOST_VERSION[0]} | |
| sed -e "/using python/ s|;|: ${PREFIX}/include/python${PYTHONVER} ;|" \ | |
| -i bootstrap.sh | |
| ./bootstrap.sh \ | |
| --with-toolset=gcc \ | |
| --with-icu \ | |
| --with-python=$PREFIX/bin/python3 \ | |
| --with-libraries=python,thread || exit 1 | |
| ./b2 \ | |
| -j $NPROC \ | |
| --layout=system \ | |
| --build-dir=build-python3 \ | |
| --prefix=$PREFIX \ | |
| --libdir=$PREFIX/lib \ | |
| --build-type=minimal \ | |
| toolset=gcc \ | |
| variant=release \ | |
| debug-symbols=off \ | |
| link=shared \ | |
| threading=multi \ | |
| runtime-link=shared \ | |
| python=$PYTHONVER \ | |
| cflags="$PKGCFLAGS" \ | |
| cxxflags="$PKGCFLAGS" \ | |
| install || exit 1 | |
| ) | |
| ( | |
| PYCUDAVERS=2023.1 | |
| PYTHON_LIBNAME=boost_python${PYTHONVER/./} | |
| # orig: https://files.pythonhosted.org/packages/dd/b2/e30282f3286ddad05ef44548fa5c306a179ed3baceefa699af078e49ce6e/pycuda-2023.1.tar.gz | |
| BEEHIVE="https://beehive.molgen.mpg.de/3193e66e54242ac634825b14944295ac/pycuda-2023.1.tar.gz" | |
| test -e pycuda-${PYCUDAVERS}.tar.gz || wget -nv $BEEHIVE | |
| test -d pycuda-${PYCUDAVERS} || tar -xf pycuda-${PYCUDAVERS}.tar.gz | |
| cd pycuda-${PYCUDAVERS} | |
| test -e siteconf.py && rm siteconf.py | |
| python configure.py \ | |
| --cuda-enable-gl \ | |
| --cuda-root=$CUDADIR \ | |
| --no-use-shipped-boost \ | |
| --boost-python-libname=$PYTHON_LIBNAME \ | |
| --boost-inc-dir=$PREFIX/include \ | |
| --boost-lib-dir=$PREFIX/lib \ | |
| --cudadrv-lib-dir='${CUDA_ROOT}/lib,${CUDA_ROOT}/lib/stubs' \ | |
| --cudart-lib-dir='${CUDA_ROOT}/lib,${CUDA_ROOT}/lib/stubs' \ | |
| --curand-lib-dir='${CUDA_ROOT}/lib,${CUDA_ROOT}/lib/stubs' \ | |
| --ldflags=-L$PREFIX/lib | |
| pip install . --prefix=$PREFIX | |
| ) | |
| piplist; track pycuda | |
| ( | |
| # install from git to get .so files in case | |
| pip install git+https://github.com/open2c/pairtools.git@v1.0.2 --prefix=$PREFIX | |
| pip install git+https://github.com/brentp/bwa-meth.git@v0.2.7 --prefix=$PREFIX | |
| # versions > 1.5 will not work with pip install github | |
| pip install git+https://github.com/stacked-git/stgit.git@v1.5 --prefix=$PREFIX | |
| ) | |
| piplist; track pairtools bwa-meth stgit | |
| ( | |
| IDR_VERSION=2.0.3 | |
| # orig: https://github.com/nboley/idr/archive/2.0.3/idr-2.0.3.tar.gz # HD: T. Z., 18.3.21 | |
| BEEHIVE=https://beehive.molgen.mpg.de/1bec61b526bb1dcf92a5ab99c27852d0/idr-2.0.3.tar.gz | |
| test -e idr-${IDR_VERSION}.tar.gz || wget -nv $BEEHIVE | |
| test -d idr-${IDR_VERSION} || tar -xf idr-${IDR_VERSION}.tar.gz | |
| cd idr-${IDR_VERSION} | |
| pip install . --prefix=$PREFIX | |
| ) | |
| piplist; track IDR | |
| # ------------------------------------------------ finally build tensorflaw | |
| ( | |
| test -n "$SKIPTENSORFLOW" && exit | |
| TFVERSION=2.14.1 | |
| NCCLSHORTVERSION=$(pkg-config nccl --modversion | grep -Po '\d+\.\d+') | |
| # Need newer JRE to handle --add-opens=java.base/java.lang=ALL-UNNAMED, and bazel >= 6.1 | |
| # Also: "error -- unsupported GNU version! gcc versions later than 11 are not supported! The | |
| # nvcc flag '-allow-unsupported-compiler' can be used to override this version check" | |
| . /pkg/openjdk-21.0.0.35-0/profile | |
| . /pkg/bazel-6.2.1-0/profile | |
| . /pkg/gcc-10.3.0-0/profile | |
| pkggcc=/pkg/gcc-10.3.0-0/bin | |
| # orig: https://github.com/tensorflow/tensorflow/archive/refs/tags/v2.14.1.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/c7ba144a4b1b0a6d5fea5ecd274172d3/tensorflow-2.14.1.tar.gz | |
| test -e tensorflow-${TFVERSION}.tar.gz || wget -nv $BEEHIVE | |
| test -d tensorflow-${TFVERSION} || tar -xf tensorflow-${TFVERSION}.tar.gz | |
| cd tensorflow-${TFVERSION} | |
| #vars for config | |
| export PYTHON_BIN_PATH=${PREFIX}/bin/python3 | |
| export USE_DEFAULT_PYTHON_LIB_PATH=1 | |
| export TF_PYTHON_VERSION=3.11 | |
| export TF_NEED_JEMALLOC=1 | |
| export TF_NEED_KAFKA=0 | |
| export TF_NEED_OPENCL_SYCL=0 | |
| export TF_NEED_AWS=0 | |
| export TF_NEED_GCP=0 | |
| export TF_NEED_HDFS=0 | |
| export TF_NEED_S3=0 | |
| export TF_ENABLE_XLA=1 | |
| export TF_NEED_GDR=0 | |
| export TF_NEED_VERBS=0 | |
| export TF_NEED_OPENCL=0 | |
| export TF_NEED_MPI=0 | |
| export TF_NEED_TENSORRT=0 | |
| export TF_NEED_NGRAPH=0 | |
| export TF_NEED_IGNITE=0 | |
| export TF_NEED_ROCM=0 | |
| export TF_SET_ANDROID_WORKSPACE=0 | |
| export TF_DOWNLOAD_CLANG=0 | |
| export TF_NCCL_VERSION=${NCCLSHORTVERSION} | |
| export TF_IGNORE_MAX_BAZEL_VERSION=1 | |
| export NCCL_INSTALL_PATH=${CUDADIR} | |
| export CC=gcc | |
| export CXX=g++ | |
| # export GCC_HOST_COMPILER_PATH=/usr/bin/${CC} | |
| # export HOST_C_COMPILER=/usr/bin/${CC} | |
| # export HOST_CXX_COMPILER=/usr/bin/${CXX} | |
| export GCC_HOST_COMPILER_PATH=$pkggcc/${CC} | |
| export HOST_C_COMPILER=$pkggcc/${CC} | |
| export HOST_CXX_COMPILER=$pkggcc/${CXX} | |
| export TF_CUDA_CLANG=0 | |
| export CLANG_CUDA_COMPILER_PATH=/usr/bin/clang | |
| export TF_CUDA_PATHS=${CUDADIR},${CUDADIR}/extras/CUPTI,${CUDADIR}/nvvm | |
| export TF_CUDA_VERSION=$(${CUDADIR}/bin/nvcc --version | sed -n 's/^.*release \(.*\),.*/\1/p') # -> '11.8' | |
| export TF_CUDNN_VERSION=$(sed -n 's/^#define CUDNN_MAJOR\s*\(.*\).*/\1/p' ${CUDADIR}/include/cudnn_version.h) | |
| # hardware older than sm_52 is said to be unsupported, compute_86 denotes an emulation | |
| export TF_CUDA_COMPUTE_CAPABILITIES=sm_52,sm_53,sm_60,sm_61,sm_62,sm_70,sm_72,sm_75,sm_80,sm_86,sm_87,sm_89,sm_90,compute_90 | |
| # stay compatible with the cluster machines | |
| # https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html | |
| export CC_OPT_FLAGS="-march=broadwell" # or haswell to be safe ? no more nehalem | |
| export TF_NEED_CUDA=1 | |
| export BAZEL_ARGS="--config=mkl -c opt" | |
| # avoid: Auto-Configuration Warning: 'TMP' environment variable is not set, using 'C:\Windows\Temp' as default :/ | |
| export TMP=$BUILD_TMPDIR/tf_tmp | |
| mkdir -p $TMP | |
| ./configure | |
| bazel build \ | |
| --cxxopt="-march=broadwell" \ | |
| --copt="-march=broadwell" \ | |
| --noshow_loading_progress \ | |
| --noshow_progress \ | |
| --color="no" \ | |
| //tensorflow:libtensorflow.so \ | |
| //tensorflow:libtensorflow_cc.so \ | |
| //tensorflow:install_headers \ | |
| //tensorflow/tools/pip_package:build_pip_package | |
| bazel shutdown # otherwise it hogs in cwd | |
| # create a _clean/decent_ python package from so far created debris | |
| test -d tensorflow-pip && rm -r tensorflow-pip | |
| mkdir tensorflow-pip | |
| ./bazel-bin/tensorflow/tools/pip_package/build_pip_package --src ${BUILDDIR}/tensorflow-pip | |
| cd ${BUILDDIR} | |
| # ... cope with the weird symlink-structure placed in bazels' build-TMPDIR (-h) (tell me why ?) | |
| test -e tensorflow-pip.tar && rm tensorflow-pip.tar | |
| tar -chf tensorflow-pip.tar tensorflow-pip | |
| # and perform a regular install | |
| test -d tensorflow-pip && rm -r tensorflow-pip | |
| tar -xf tensorflow-pip.tar | |
| cd ${BUILDDIR}/tensorflow-pip | |
| pip install . --prefix=$PREFIX | |
| ) | |
| piplist; track tensorflow | |
| # tidy up a bit | |
| if [ -d $PREFIX/man/man1 ]; then | |
| mv -v $PREFIX/man/man1/* $PREFIX/share/man/man1 || true | |
| rm -rf $PREFIX/man | |
| fi | |
| # ------------------------------------------------------------ Sanity check | |
| # load all packages, see warnings and spot installation errors | |
| echo "# START load test." | |
| export NUMEXPR_MAX_THREADS=1 | |
| python -c 'help("modules")' | |
| echo "# END load test (passed)." | |
| echo "# running pip check" | |
| pip check | |
| # I guess it makes sense that files can be read by all users ... | |
| echo "# check for unreadable files" | |
| cd $PREFIX | |
| for D in bin etc include lib share; do | |
| find $D \! -perm -004 -exec chmod -c a+r {} + | |
| done | |
| echo "For Deeper checks:" | |
| echo "cd ${BUILDDIR} ; git log --patch | grep ^[\+\-][^\+\-]" | |
| exit | |
| # -------------------------------------------------------- Included patches | |
| #Epatch:pip # Operation 'Forever young', disable version-check per default. | |
| #Epatch:pip # The option needs to be kept, because some tools make use of | |
| #Epatch:pip # it and would cause pip to fail. | |
| #Epatch:pip --- a/pip/_internal/cli/cmdoptions.py 2022-08-09 17:29:15.853442948 +0200 | |
| #Epatch:pip +++ b/pip/_internal/cli/cmdoptions.py 2022-08-10 10:31:35.124945154 +0200 | |
| #Epatch:pip @@ -892,7 +892,6 @@ | |
| #Epatch:pip dest="disable_pip_version_check", | |
| #Epatch:pip action="store_true", | |
| #Epatch:pip - default=False, | |
| #Epatch:pip - help="Don't periodically check PyPI to determine whether a new version " | |
| #Epatch:pip - "of pip is available for download. Implied with --no-index.", | |
| #Epatch:pip + default=True, | |
| #Epatch:pip + help="Ignore this option, the version check IS disabled.", | |
| #Epatch:pip ) | |
| #Epatch:gyp --- a/pylib/gyp/generator/cmake.py | |
| #Epatch:gyp +++ b/pylib/gyp/generator/cmake.py | |
| #Epatch:gyp @@ -41,7 +41,7 @@ | |
| #Epatch:gyp try: | |
| #Epatch:gyp # maketrans moved to str in python3. | |
| #Epatch:gyp + _maketrans = str.maketrans | |
| #Epatch:gyp +except NameError: | |
| #Epatch:gyp _maketrans = string.maketrans | |
| #Epatch:gyp -except NameError: | |
| #Epatch:gyp - _maketrans = str.maketrans | |
| #Epatch:gyp generator_default_variables = { | |
| #Epatch:gyp 'EXECUTABLE_PREFIX': '', | |
| #Epatch:gyp @@ -283,2 +283,2 @@ | |
| #Epatch:gyp if int(action.get('process_outputs_as_sources', False)): | |
| #Epatch:gyp - extra_sources.extend(zip(cmake_outputs, outputs)) | |
| #Epatch:gyp + extra_sources.extend(list(zip(cmake_outputs, outputs))) | |
| #Epatch:gyp @@ -988,6 +988,6 @@ | |
| #Epatch:gyp # XCode settings | |
| #Epatch:gyp xcode_settings = config.get('xcode_settings', {}) | |
| #Epatch:gyp - for xcode_setting, xcode_value in xcode_settings.viewitems(): | |
| #Epatch:gyp + for xcode_setting, xcode_value in xcode_settings.items(): | |
| #Epatch:gyp SetTargetProperty(output, cmake_target_name, | |
| #Epatch:gyp "XCODE_ATTRIBUTE_%s" % xcode_setting, xcode_value, | |
| #Epatch:gyp '' if isinstance(xcode_value, str) else ' ') | |
| #Epatch:gyp diff --git a/pylib/gyp/input.py b/pylib/gyp/input.py | |
| #Epatch:gyp index 4c12891..2bea334 100644 | |
| #Epatch:gyp --- a/pylib/gyp/input.py | |
| #Epatch:gyp +++ b/pylib/gyp/input.py | |
| #Epatch:gyp @@ -1183,7 +1183,7 @@ | |
| #Epatch:gyp if variable_name in variables: | |
| #Epatch:gyp # If the variable is already set, don't set it. | |
| #Epatch:gyp continue | |
| #Epatch:gyp - if the_dict_key is 'variables' and variable_name in the_dict: | |
| #Epatch:gyp + if the_dict_key == 'variables' and variable_name in the_dict: | |
| #Epatch:gyp # If the variable is set without a % in the_dict, and the_dict is a | |
| #Epatch:gyp # variables dict (making |variables| a varaibles sub-dict of a | |
| #Epatch:gyp # variables dict), use the_dict's definition. | |
| #Epatch:javabridge diff --git a/_javabridge_nomac.pyx b/_javabridge_nomac.pyx | |
| #Epatch:javabridge index 9f28939..c437db0 100644 | |
| #Epatch:javabridge --- a/_javabridge_nomac.pyx | |
| #Epatch:javabridge +++ b/_javabridge_nomac.pyx | |
| #Epatch:javabridge @@ -16,30 +16,30 @@ cdef extern from "jni.h": | |
| #Epatch:javabridge jint (*AttachCurrentThreadAsDaemon)(JavaVM *vm, void *penv, void *args) nogil | |
| #Epatch:javabridge jint JNI_CreateJavaVM(JavaVM **pvm, void **penv, void *args) nogil | |
| #Epatch:javabridge | |
| #Epatch:javabridge -cdef int MacStartVM(JavaVM **pvm, JavaVMInitArgs *pVMArgs, char *class_name) nogil: | |
| #Epatch:javabridge +cdef extern int MacStartVM(JavaVM **pvm, JavaVMInitArgs *pVMArgs, char *class_name) nogil: | |
| #Epatch:javabridge return -1 | |
| #Epatch:javabridge | |
| #Epatch:javabridge -cdef void StopVM(JavaVM *vm) nogil: | |
| #Epatch:javabridge +cdef extern void StopVM(JavaVM *vm) nogil: | |
| #Epatch:javabridge vm[0].DestroyJavaVM(vm) | |
| #Epatch:javabridge | |
| #Epatch:javabridge -cdef void MacRunLoopInit() nogil: | |
| #Epatch:javabridge +cdef extern void MacRunLoopInit() nogil: | |
| #Epatch:javabridge pass | |
| #Epatch:javabridge | |
| #Epatch:javabridge -cdef void MacRunLoopRun() nogil: | |
| #Epatch:javabridge +cdef extern void MacRunLoopRun() nogil: | |
| #Epatch:javabridge pass | |
| #Epatch:javabridge | |
| #Epatch:javabridge -cdef void MacRunLoopStop() nogil: | |
| #Epatch:javabridge +cdef extern void MacRunLoopStop() nogil: | |
| #Epatch:javabridge pass | |
| #Epatch:javabridge | |
| #Epatch:javabridge -cdef void MacRunLoopReset() nogil: | |
| #Epatch:javabridge +cdef extern void MacRunLoopReset() nogil: | |
| #Epatch:javabridge pass | |
| #Epatch:javabridge | |
| #Epatch:javabridge -cdef int MacIsMainThread() nogil: | |
| #Epatch:javabridge +cdef extern int MacIsMainThread() nogil: | |
| #Epatch:javabridge return 0 | |
| #Epatch:javabridge | |
| #Epatch:javabridge -cdef void MacRunLoopRunInMode(double timeout) nogil: | |
| #Epatch:javabridge +cdef extern void MacRunLoopRunInMode(double timeout) nogil: | |
| #Epatch:javabridge pass | |
| #Epatch:javabridge | |
| #Epatch:javabridge -cdef int CreateJavaVM(JavaVM **pvm, void **pEnv, void *args) nogil: | |
| #Epatch:javabridge +cdef extern int CreateJavaVM(JavaVM **pvm, void **pEnv, void *args) nogil: | |
| #Epatch:javabridge return JNI_CreateJavaVM(pvm, pEnv, args) | |
| #Epatch:javabridge | |
| #Epatch:javabridge diff --git a/_javabridge_mac.pyx b/_javabridge_mac.pyx | |
| #Epatch:javabridge index 2e3c524..daed790 100644 | |
| #Epatch:javabridge --- a/_javabridge_mac.pyx | |
| #Epatch:javabridge +++ b/_javabridge_mac.pyx | |
| #Epatch:javabridge @@ -31,11 +31,11 @@ cdef extern from "mac_javabridge_utils.h": | |
| #Epatch:javabridge int MacIsMainThread() nogil | |
| #Epatch:javabridge void MacRunLoopRunInMode(double) nogil | |
| #Epatch:javabridge | |
| #Epatch:javabridge -cdef void StopVM(JavaVM *vm): | |
| #Epatch:javabridge +cdef extern void StopVM(JavaVM *vm): | |
| #Epatch:javabridge MacStopVM() | |
| #Epatch:javabridge | |
| #Epatch:javabridge # | |
| #Epatch:javabridge # Unused stub in Mac | |
| #Epatch:javabridge # | |
| #Epatch:javabridge -cdef int CreateJavaVM(JavaVM **pvm, void **pEnv, void *args): | |
| #Epatch:javabridge +cdef extern int CreateJavaVM(JavaVM **pvm, void **pEnv, void *args): | |
| #Epatch:javabridge return -1 | |
| # -------------------------------------------------------- This is the end. | |