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pkg-scripts/python-3.10.7-0.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-$COOKIE.sh | |
| # TESTING=1 | |
| # SKIPTENSORFLOW=1 | |
| # ---------------------------------------------------------------- Preamble | |
| PKG=python | |
| VERSION=3.10.7 | |
| BUILD=0 | |
| PYTHONVER=${VERSION%.*} | |
| CUDADIR=/pkg/cuda-11.5.2-0 | |
| PREFIX=/pkg/$PKG-$VERSION-$BUILD | |
| if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$PKG-$VERSION-$BUILD ; fi | |
| PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin | |
| # set -xe | |
| set -e | |
| umask 022 | |
| BUILD_TMPDIR=/scratch/local2/$PKG-$VERSION-$BUILD.$USER.build.tmp | |
| 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_fucking_business...' >> .git/config | |
| echo '*' > .gitignore | |
| function piplist() { | |
| pip3 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() { | |
| # no-color is nice, but doesn't work when dependencies are installed, so (mis-)use a pipe | |
| pip3 install --no-color --compile --cache-dir=$HOME/.cache/pip --prefix=$PREFIX "${@+$@}" | cat | |
| piplist | |
| track $* | |
| } | |
| # ---------------------------------------- Build Python & support libraries | |
| ( | |
| # orig: https://www.python.org/ftp/python/3.10.7/Python-3.10.7.tgz | |
| BEEHIVE=https://beehive.molgen.mpg.de/1aea68575c0e97bc83ff8225977b0d46/Python-3.10.7.tgz | |
| test -e Python-$VERSION.tgz || 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 $PREFIX/bin/python | |
| python3 -m ensurepip | |
| pip3 install --prefix=$PREFIX -I pip | |
| ( # fix 'please update' noise from pip | |
| cd $PREFIX/lib/python*/site-packages | |
| sed -ne '/^#Epatch:pip/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose | |
| ) | |
| ) | |
| install setuptools==65.3.0 # see numba below | |
| piplist; track START | |
| # build various pythonbindings 'by hand', because pip installs do not deliver | |
| # header files and the like. | |
| # BTW: builds need meson | |
| install meson | |
| ( | |
| DBUS_PYTHON_VERSION=1.2.18 | |
| # https://files.pythonhosted.org/packages/b1/5c/ccfc167485806c1936f7d3ba97db6c448d0089c5746ba105b6eb22dba60e/dbus-python-1.2.18.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/468874f3bf61d1b7deac98bbe2cfd8ac/dbus-python-1.2.18.tar.gz | |
| test -e dbus-python-$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 $NPROC | |
| make install | |
| ) | |
| ( | |
| PYCAIRO_VERSION=1.21.0 | |
| # https://files.pythonhosted.org/packages/92/a4/506564f574fa74c90b98690e8ecc8dbae1629f31fcfe0be69de45d9e1605/pycairo-1.21.0.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/682238eaa8bd7032e36a20b6f53824d1/pycairo-1.21.0.tar.gz | |
| test -e pycairo-$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 \ | |
| .. | |
| ninja -j $NPROC | |
| ninja install | |
| ) | |
| ( | |
| PYGOBJECT3_VERSION=3.42.2 | |
| # https://files.pythonhosted.org/packages/fe/40/9afaeb8d3b453fb8596fcb6c7bc2b64e434868c91eda19955742778eff74/PyGObject-3.42.2.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/80ad843b2a49ccfcc30c6b756b755c09/PyGObject-3.42.2.tar.gz | |
| test -e PyGObject-$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 \ | |
| -Dtests=false \ | |
| .. | |
| ninja -j $NPROC | |
| ninja install | |
| ) | |
| piplist; track various pythonbindings | |
| # build support to use QT from python -- see www.riverbankcomputing.com | |
| ( # sip: tool to create Python bindings for C and C++ libraries. | |
| SIP_VERSION=6.6.2 | |
| # https://files.pythonhosted.org/packages/5b/cb/c27c925ae07bd03a2597fa1db17bfc2a4ac57da61aeb90f8ec98ffbb975b/sip-6.6.2.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/620eb75a8b22fb6af9c6044aa015782d/sip-6.6.2.tar.gz | |
| test -e sip-$SIP_VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d sip-$SIP_VERSION || tar -xf sip-$SIP_VERSION.tar.gz | |
| cd sip-$SIP_VERSION | |
| sed -ne '/^#Epatch:sip1/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose | |
| sed -ne '/^#Epatch:sip2/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose | |
| python3 setup.py build | |
| python3 setup.py install --skip-build --optimize=1 | |
| ) | |
| # QT bindings need some python modules to build | |
| install PyQt5-sip | |
| install PyQt-builder | |
| ( | |
| PYQT_VERSION=5.15.7 | |
| # orig: https://files.pythonhosted.org/packages/e1/57/2023316578646e1adab903caab714708422f83a57f97eb34a5d13510f4e1/PyQt5-5.15.7.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/ae2c68e38b9b36fdf5f932419353a2b3/PyQt5-5.15.7.tar.gz | |
| test -e PyQt5-$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 $PREFIX/lib/python*/site-packages/PyQt5/uic/port_v2 | |
| ) | |
| ( | |
| QSCINTILLA_VERSION=2.13.4.dev2206171421 | |
| # orig: https://www.riverbankcomputing.com/static/Downloads/QScintilla/${PKGVERSION}/QScintilla_src-${PKGVERSION}.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/d196ebd441f40474dd7732d4d492de69/QScintilla_src-2.13.4.dev2206171421.tar.gz | |
| test -e QScintilla_src-$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 $NPROC | |
| make install | |
| ) | |
| piplist; track qt-support-riverbankcomputing | |
| # -------------------------------------------------------- Install packages | |
| # Install the psychotic diva first | |
| install numpy==1.23.2 | |
| install Cython | |
| # libxml2-python from pypi isn't up to date, cause lxml seems to be the favored binding | |
| # do this early, not that some dependency tries it on its own. | |
| # (btw. libxslt-python isn't ported to python3) | |
| ( | |
| LIBXML2_VERSION=2.9.12 | |
| # orig: http://xmlsoft.org/sources/libxml2-${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-$LIBXML2_VERSION/python | |
| python3 setup.py build | |
| python3 setup.py install | |
| ) | |
| piplist; track legacy-libxml2 | |
| # 'numba' the cuda enabled numpy, yeahhhh! | |
| ( | |
| NUMBA_VERSION=0.56.2 | |
| # orig: https://files.pythonhosted.org/packages/d9/fa/4905b6ca79084ecf47c543121e317a9dc4b69183343f9c07c3e78bd7e2a1/numba-0.56.2.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/669778a8dbc772e908d8d9e76131d453/numba-0.56.2.tar.gz | |
| test -e numba-$NUMBA_VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d numba-$NUMBA_VERSION || tar -xf numba-$NUMBA_VERSION.tar.gz | |
| cd numba-$NUMBA_VERSION | |
| # the old setup tools are used in the tests, not in the package! | |
| sed -i -e '/setuptools<60/ d' setup.py | |
| # let pip handle the build, this seems to be the new 'way to go' | |
| install . | |
| ) | |
| piplist; track numba | |
| # 'distributed' doesn't like the 'new' tornado 6.2 -- reason: a deprecation warning makes the CI choke (geht's noch?) | |
| ( | |
| DISTRIBUTED_VERSION=2022.9.0 | |
| # orig: https://files.pythonhosted.org/packages/df/46/e8ef41f8dfd553327b6a12f4ab78d9351b54299596fe5b8b165ba40b1550/distributed-2022.9.0.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/335d718f1ba331ee8e85e40e564559a1/distributed-2022.9.0.tar.gz | |
| test -e distributed-$DISTRIBUTED_VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d distributed-$DISTRIBUTED_VERSION || tar -xf distributed-$DISTRIBUTED_VERSION.tar.gz | |
| cd distributed-$DISTRIBUTED_VERSION | |
| sed -i -e '/tornado/ s/.*/tornado/' requirements.txt | |
| sed -i -e '/tornado/ s/.*/tornado/' distributed.egg-info/requires.txt | |
| install . | |
| ) | |
| piplist; track distributed and tornado | |
| PACKAGES=$(sed -e s/#.*$// <<- __PKGLIST__ | |
| protobuf==3.19.4 # tensorflow likes to have an slightly older one [< 3.20], no conflict with this | |
| ipython[all] | |
| SciPy Matplotlib pandas SymPy nose statsmodels | |
| pysam | |
| seaborn | |
| scikit-learn | |
| Mako | |
| cutadapt # Helpdesk 01/24/18 16:19, Sabrina Krakau | |
| pygobject # Helpdesk 03/26/18 14:19, Virginie Stanisla | |
| blink1 # Blink1-lib 07/04/18 12:00, Niclas Hofmann | |
| umi-tools | |
| sphinx | |
| recommonmark | |
| fastcluster | |
| pydot | |
| pygraphviz | |
| deeptools | |
| HTSeq | |
| keras | |
| keras_preprocessing # tensorflow ... | |
| MotifScan # Alena 30.8.2018 | |
| MAmotif | |
| hic2cool # Helpdesk Robert Schoepflin 17.09.2018 | |
| snakemake | |
| virtualenv # Donald | |
| odfpy # Donald | |
| Dumper # Thomas | |
| igraph | |
| louvain # monocle3 prep for Helene | |
| selenium # 19.7.19 Kreitler -> https://webxray.org/ | |
| gmpy # From viper context, Helpdesk Laura Glaser 9.8.2019 | |
| torch | |
| torchvision | |
| plotly | |
| pyOpenCL | |
| docopt | |
| distro | |
| ply | |
| threadpoolctl | |
| HiCMatrix | |
| pybedtools | |
| gffutils | |
| python-bioformats | |
| jupyterlab | |
| jupyterlab-git # request Peter Arndt | |
| igv_jupyterlab # Matthias Lienhard HD 01-04-2020 | |
| igv-jupyter | |
| scour # https://github.molgen.mpg.de/mariux64/pkg-scripts/issues/98 | |
| multiqc | |
| pybind11 | |
| svgwrite | |
| pyomo | |
| bioservices | |
| pairtools | |
| SharedArray | |
| pyabc # dependency for stochkit, HD 20.07.20 Gemma Noviello | |
| petab | |
| tadtool # HD 26.01.21 Michael Robson | |
| pyperf # Paul sep-20 | |
| helen # HD, a dependency from a request by helene | |
| umap # HD, used by Matthias Lienhard | |
| MACS3 | |
| biopython # HD 2021-07-23 Magalhaes/Hnisz alphafold related -- cool that we have missed biopython so far, LOL | |
| dm-tree | |
| dm-haiku | |
| flatbuffers | |
| contextlib2 | |
| ml_collections | |
| # additions/fixups since 3.9 | |
| 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 | |
| napari[pyqt5] | |
| napari-czifile2 | |
| CrossMap | |
| cooltools # cause trouble with numba/nupy versions -- Maria Valieva 17.7.2019 | |
| scanpy | |
| __PKGLIST__ | |
| ) | |
| for PKG in $PACKAGES; do | |
| install $PKG | |
| done | |
| 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 $PREFIX/share/jupyter/lab/settings # try to defeat a silly error in jupyter labextension install | |
| # --------------------------------------------------- Install misc packages | |
| ( | |
| BOOST_VERSION=(1.80.0 1_80_0) | |
| PKGCFLAGS="-O2 -fPIC" | |
| # orig: https://dl.bintray.com/boostorg/release/1.75.0/source/boost_1_75_0.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de//38813f6feb40387dfe90160debd71251/boost_1_75_0.tar.gz | |
| # orig: https://boostorg.jfrog.io/artifactory/main/release/1.80.0/source/boost_1_80_0.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/077f074743ea7b0cb49c6ed43953ae95/boost_1_80_0.tar.gz | |
| test -e boost_${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=2022.1 | |
| PYTHON_LIBNAME=boost_python${PYTHONVER/./} | |
| # orig: https://github.com/inducer/pycuda/archive/v2020.1.tar.gz | |
| # BEEHIVE=https://beehive.molgen.mpg.de/580562d7af4d3249c5b42a1df8d428a0/pycuda-2020.1.tar.gz | |
| # orig: https://files.pythonhosted.org/packages/2d/1f/48a3a5b2c715345e7af1e09361100bd98c3d72b4025371692ab233f523d3/pycuda-2022.1.tar.gz # maybe those very long URLs compensate for other (shorter) things ... | |
| BEEHIVE="https://beehive.molgen.mpg.de/2fad5a15db4153d825822eba7cb25f25/pycuda-2022.1.tar.gz" | |
| test -e pycuda-${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 | |
| python3 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 | |
| python3 setup.py build | |
| python3 setup.py install --prefix $PREFIX | |
| ) | |
| ( | |
| # orig: https://github.com/nboley/idr/archive/2.0.3/idr-2.0.3.tar.gz # HD: Tobias Zehnder, 18.3.21 | |
| BEEHIVE=https://beehive.molgen.mpg.de/1bec61b526bb1dcf92a5ab99c27852d0/idr-2.0.3.tar.gz | |
| test -e idr-2.0.3.tar.gz || wget -nv $BEEHIVE | |
| test -d idr-2.0.3 || tar -xf idr-2.0.3.tar.gz | |
| cd idr-2.0.3 | |
| python3 setup.py build | |
| python3 setup.py install --prefix $PREFIX | |
| ) | |
| ( | |
| # orig: https://github.com/stacked-git/stgit/archive/v1.0/stgit-1.0.tar.gz # Paul mariux64/pkg-scripts/issues/152 | |
| BEEHIVE=https://beehive.molgen.mpg.de/b20ab5a197fc3a141f4b00c5859c0a3b/stgit-1.0.tar.gz | |
| test -e stgit-1.0.tar.gz || wget -nv $BEEHIVE | |
| test -d stgit-1.0 || tar -xf stgit-1.0.tar.gz | |
| cd stgit-1.0 | |
| python3 setup.py build | |
| python3 setup.py install --prefix $PREFIX | |
| ) | |
| ( | |
| # https://github.com/brentp/bwa-meth/archive/refs/tags/v0.2.5.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/33a4c416760dd67e77f17e07791527e2/bwa-meth-0.2.5.tar.gz | |
| test -e bwa-meth-0.2.5.tar.gz || wget -nv $BEEHIVE | |
| test -d bwa-meth-0.2.5 || tar -xf bwa-meth-0.2.5.tar.gz | |
| cd bwa-meth-0.2.5 | |
| python3 setup.py build | |
| python3 setup.py install --prefix $PREFIX | |
| ) | |
| piplist; track misc packages | |
| # ------------------------------------------------ finally build tensorflaw | |
| install wheel # to build our tf-wheel (i.e. zip archive) | |
| ( | |
| test -n "$SKIPTENSORFLOW" && exit | |
| TFVERSION=2.10.0 | |
| NCCLSHORTVERSION=$(pkg-config nccl --modversion | grep -Po '\d+\.\d+') | |
| . /pkg/bazel-5.1.0-0/profile | |
| # orig: https://github.com/tensorflow/tensorflow/archive/refs/tags/v2.10.0.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/7ceb5277d482f10d2df8644deb412061/tensorflow-2.10.0.tar.gz | |
| test -e tensorflow-${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=${PREFIX}/bin/python3 | |
| export USE_DEFAULT_PYTHON_LIB_PATH=1 | |
| export TF_NEED_JEMALLOC=1 | |
| export TF_NEED_KAFKA=0 | |
| export TF_NEED_OPENCL_SYCL=0 | |
| export TF_NEED_AWS=0 | |
| export TF_NEED_GCP=0 | |
| export TF_NEED_HDFS=0 | |
| export TF_NEED_S3=0 | |
| export TF_ENABLE_XLA=1 | |
| export TF_NEED_GDR=0 | |
| export TF_NEED_VERBS=0 | |
| export TF_NEED_OPENCL=0 | |
| export TF_NEED_MPI=0 | |
| export TF_NEED_TENSORRT=0 | |
| export TF_NEED_NGRAPH=0 | |
| export TF_NEED_IGNITE=0 | |
| export TF_NEED_ROCM=0 | |
| export TF_SET_ANDROID_WORKSPACE=0 | |
| export TF_DOWNLOAD_CLANG=0 | |
| export TF_NCCL_VERSION=${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 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') | |
| 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,compute_86 | |
| # stay compatible with the cluster machines | |
| export CC_OPT_FLAGS="-march=nehalem" | |
| export TF_NEED_CUDA=1 | |
| export BAZEL_ARGS="--config=mkl -c opt" | |
| ./configure | |
| bazel build \ | |
| --cxxopt="-march=nehalem" \ | |
| --copt="-march=nehalem" \ | |
| --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 ??? 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 | |
| python3 setup.py build | |
| python3 setup.py 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 | |
| # But don't care about r2py, a further dependence into R is not wanted! | |
| echo "# START load test." | |
| python3 -c 'help("modules")' > /dev/null | |
| echo "# END load test (passed)." | |
| echo "# running pip check" | |
| pip3 check | |
| # I guess it makes sense that files can be read by all users ... | |
| echo "# check for unreadable files" | |
| cd $PREFIX | |
| find \! -perm -004 -exec chmod -c a+r {} + | |
| 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 ) | |
| # https://riverbankcomputing.com/hg/sip/raw-rev/1430b279a3c9 -> sip-fix-exceptions.patch | |
| #Epatch:sip1 Fixed the handling of exceptions that sub-class C++ exceptions. | |
| #Epatch:sip1 diff -r 6eff81a15822 -r 1430b279a3c9 sipbuild/generator/parser/rules.py | |
| #Epatch:sip1 --- a/sipbuild/generator/parser/rules.py Fri Jun 17 14:25:16 2022 +0100 | |
| #Epatch:sip1 +++ b/sipbuild/generator/parser/rules.py Sun Jun 26 10:01:41 2022 +0100 | |
| #Epatch:sip1 @@ -2293,6 +2293,7 @@ | |
| #Epatch:sip1 | |
| #Epatch:sip1 if len(p) == 4: | |
| #Epatch:sip1 base = p[2] | |
| #Epatch:sip1 + base.make_absolute() | |
| #Epatch:sip1 | |
| #Epatch:sip1 # See if it is a project-defined exception. | |
| #Epatch:sip1 for xd in p.parser.pm.spec.exceptions: | |
| # https://riverbankcomputing.com/hg/sip/raw-rev/323d39a2d602 -> sip-fix-template-values.patch | |
| #Epatch:sip2 Fixed the instantiation of template values. | |
| #Epatch:sip2 diff -r 1430b279a3c9 -r 323d39a2d602 sipbuild/generator/parser/instantiations.py | |
| #Epatch:sip2 --- a/sipbuild/generator/parser/instantiations.py Sun Jun 26 10:01:41 2022 +0100 | |
| #Epatch:sip2 +++ b/sipbuild/generator/parser/instantiations.py Sun Jul 17 09:41:16 2022 +0100 | |
| #Epatch:sip2 @@ -434,7 +434,8 @@ | |
| #Epatch:sip2 proto_name = proto_value.value.result.definition | |
| #Epatch:sip2 | |
| #Epatch:sip2 if proto_name.is_simple: | |
| #Epatch:sip2 - i_name = ScopedName.parse(template_string(proto_name, expansions)) | |
| #Epatch:sip2 + i_name = ScopedName.parse( | |
| #Epatch:sip2 + template_string(proto_name.base_name, expansions)) | |
| #Epatch:sip2 i_result = Argument(type=ArgumentType.DEFINED, definition=i_name) | |
| #Epatch:sip2 i_fcall = FunctionCall(result=i_result, | |
| #Epatch:sip2 args=proto_value.value.args) | |
| # -------------------------------------------------------- This is the end. | |