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pkg-scripts/python-3.9.12-0.build.sh
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| #! /bin/bash | |
| # COOKIE=$(mcookie|cut -c-8); grep -v V_GREP_ME $0 > /dev/shm/runme-$COOKIE.sh ; sleep 0.3; exec bash /dev/shm/runme-$COOKIE.sh | |
| # TESTING=1 | |
| PKG=python | |
| VERSION=3.9.12 | |
| BUILD=0 | |
| PYTHONVER=${VERSION%.*} | |
| CUDADIR=/pkg/cuda-11.1.1-0 | |
| PREFIX=/pkg/$PKG-$VERSION-$BUILD | |
| if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$PKG-$VERSION-$BUILD ; fi | |
| PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin | |
| set -xe | |
| umask 022 | |
| BUILD_TMPDIR=/scratch/local2/$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 $NPROC" | |
| # bookkeeping, spots package downgrades | |
| PIPMETADIR=$PREFIX/share/pipmeta | |
| mkdir -p $PIPMETADIR | |
| BUILDDIR=$PREFIX/build | |
| mkdir -p $BUILDDIR | |
| cd $BUILDDIR | |
| # if false; then ######### DEBUG_BASE DEBUG_TF | |
| #URL=https://www.python.org/ftp/python/$VERSION/Python-$VERSION.tar.xz | |
| URL="https://beehive.molgen.mpg.de/4b5fda03e3fbfceca833c997d501bcca/Python-3.9.12.tar.xz" | |
| test -e Python-$VERSION.tar.xz || wget -nv $URL | |
| test -d Python-$VERSION || tar -xf Python-$VERSION.tar.xz | |
| cd Python-$VERSION | |
| LDFLAGS="-Wl,-rpath=$PREFIX/lib" \ | |
| ./configure \ | |
| --prefix=$PREFIX \ | |
| --enable-shared | |
| make -j $NPROC | |
| # make test # || true # 'test_socket' seems to run for ever | |
| 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 | |
| ( # sip: tool to create Python bindings for C and C++ libraries., v6 is out, but not so popular at the moment | |
| cd $BUILDDIR | |
| SIP_VERSION=4.19.24 | |
| # orig: https://www.riverbankcomputing.com/static/Downloads/sip/$SIP_VERSION/sip-$SIP_VERSION.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/595e9ad6bb0a4b3a6ea92c163a05d19c/sip-4.19.24.tar.gz | |
| test -e sip-$SIP_VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d sip-$SIP_VERSION || tar -xf sip-$SIP_VERSION.tar.gz | |
| cd sip-$SIP_VERSION | |
| #### ATTN! | |
| #### python meanders between /python${PYTHONVER} and /python${PYTHONVER}m | |
| python3 configure.py \ | |
| -b $PREFIX/bin \ | |
| -d $PREFIX/lib/python$PYTHONVER/site-packages \ | |
| -e $PREFIX/include/python${PYTHONVER} \ | |
| -v $PREFIX/share/sip \ | |
| --sip-module=sip | |
| # well, right here share/sip is spoilage, but maybe some packages will use the decent sip later on ... | |
| mkdir -p $PREFIX/share/sip | |
| make -j $NPROC | |
| make install | |
| ) | |
| ( # now for the private (sic!) version required by newer PyQt | |
| cd $BUILDDIR | |
| SIP_VERSION=4.19.24 | |
| mkdir -p private_sip | |
| cd private_sip | |
| # orig: https://www.riverbankcomputing.com/static/Downloads/sip/$SIP_VERSION/sip-$SIP_VERSION.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/595e9ad6bb0a4b3a6ea92c163a05d19c/sip-4.19.24.tar.gz | |
| test -e sip-$SIP_VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d sip-$SIP_VERSION || tar -xf sip-$SIP_VERSION.tar.gz | |
| cd sip-$SIP_VERSION | |
| # note $PREFIX/share/sip/PyQt5 is mandatory | |
| python3 configure.py \ | |
| -d $PREFIX/lib/python$PYTHONVER/site-packages \ | |
| -v $PREFIX/share/sip/PyQt5 \ | |
| --no-tools \ | |
| --sip-module=PyQt5.sip | |
| mkdir -p $PREFIX/share/sip/PyQt5 | |
| make -j $NPROC | |
| # The resulting sip.so in site-packages/PyQt5 differs indeed a bit (grep for PyQt5) | |
| make install | |
| ) | |
| ( | |
| cd $BUILDDIR | |
| PYQT_VERSION=5.15.2 | |
| # orig: https://files.pythonhosted.org/packages/28/6c/640e3f5c734c296a7193079a86842a789edb7988dca39eab44579088a1d1/PyQt5-5.15.2.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/b94576e9e013210dc5aba061913e4bd4/PyQt5-5.15.2.tar.gz | |
| test -e PyQt5-$PYQT_VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d PyQt5-$PYQT_VERSION || tar -xf PyQt5-$PYQT_VERSION.tar.gz | |
| cd PyQt5-$PYQT_VERSION | |
| #### ATTN! | |
| #### python meanders between /python${PYTHONVER} and /python${PYTHONVER}m | |
| # export QTDIR=/usr/local/qt5 | |
| python3 configure.py \ | |
| -b $PREFIX/bin \ | |
| -d $PREFIX/lib/python$PYTHONVER/site-packages \ | |
| -n $PREFIX/share/qsci \ | |
| -q /usr/local/qt5/bin/qmake \ | |
| -v $PREFIX/share/sip/PyQt5 \ | |
| --sip-incdir=$PREFIX/include/python${PYTHONVER} \ | |
| --confirm-license \ | |
| --no-qml-plugin \ | |
| --no-designer-plugin \ | |
| --no-dist-info \ | |
| --verbose | |
| make -j $NPROC | |
| make install | |
| ) | |
| ( | |
| cd $BUILDDIR | |
| QSCINTILLA_VERSION=2.11.6 | |
| # orig: https://www.riverbankcomputing.com/static/Downloads/QScintilla/$QSCINTILLA_VERSION/QScintilla-$QSCINTILLA_VERSION.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/343cd0c2c8b425518df2e51eb994fbc6/QScintilla-2.11.6.tar.gz | |
| test -e QScintilla-$QSCINTILLA_VERSION.tar.gz || wget -nv $BEEHIVE | |
| test -d QScintilla-$QSCINTILLA_VERSION || tar -xf QScintilla-$QSCINTILLA_VERSION.tar.gz | |
| cd QScintilla-$QSCINTILLA_VERSION | |
| cd Python | |
| # apidir follows PyQt, not Qt (default is: QT_INSTALL_DATA/qsci) | |
| python3 configure.py \ | |
| --pyqt=PyQt5 \ | |
| --qmake=/usr/local/qt5/bin/qmake \ | |
| --apidir=$PREFIX/share/qsci \ | |
| --no-dist-info | |
| make -j $NPROC | |
| make install | |
| ) | |
| # fi ######### DEBUG_BASE (1) | |
| # cd $BUILDDIR | |
| python3 -m ensurepip | |
| pip3 install --prefix=$PREFIX -I pip | |
| ( # fix 'please update' noise from pip | |
| cd $PREFIX/lib/python$PYTHONVER/site-packages | |
| sed -ne '/^#Epatch:pip/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose | |
| ) | |
| pip3 list > $PIPMETADIR/pip3list_initial | |
| # ATTN: numpy=1.21.x is out but not everybody like it already (e.g. SciPy ...) | |
| pip3 install --prefix=$PREFIX numpy==1.20.3 | |
| pip3 install --prefix=$PREFIX ipython[all] | |
| # install the basic ballpark ... | |
| # numpy holds no ref to *_MAX_THREADS, albeit it's an issue, fix via profile? | |
| # still persisting: NUMEXPR_MAX_THREADS issue caused by numexpr.utils (braindead defaults from this dependency) | |
| pip3 install --prefix=$PREFIX SciPy Matplotlib pandas SymPy nose statsmodels | |
| # clean up some dirt that statsmodels placed also into $PREFIX | |
| rm -vf $PREFIX/LICENSE.txt | |
| rm -vf $PREFIX/setup.cfg | |
| pip3 install --prefix=$PREFIX 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. (btw. libxslt-python isn't ported to python3) | |
| ( | |
| . ${PREFIX}/profile | |
| LIBXML2_VERSION=2.9.12 | |
| # orig: http://xmlsoft.org/sources/libxml2-${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-$LIBXML2_VERSION/python | |
| python3 setup.py build | |
| python3 setup.py install | |
| ) | |
| pip3 install --prefix=$PREFIX pysam | |
| pip3 install --prefix=$PREFIX seaborn | |
| pip3 install --prefix=$PREFIX scikit-learn | |
| #pip3 install --prefix=$PREFIX metaseq # fails (Latest commit fa875d1 on Jan 10, 2017) | |
| pip3 install --prefix=$PREFIX Mako | |
| pip3 install --prefix=$PREFIX meson # required in mariux | |
| pip3 install --prefix=$PREFIX cutadapt # Helpdesk 01/24/18 16:19, Sabrina Krakau | |
| pip3 install --prefix=$PREFIX pygobject # Helpdesk 03/26/18 14:19, Virginie Stanisla | |
| pip3 install --prefix=$PREFIX blink1 # Blink1-lib 07/04/18 12:00, Niclas Hofmann | |
| pip3 install --prefix=$PREFIX umi-tools | |
| pip3 install --prefix=$PREFIX sphinx | |
| pip3 install --prefix=$PREFIX recommonmark | |
| pip3 install --prefix=$PREFIX fastcluster | |
| pip3 install --prefix=$PREFIX pydot | |
| pip3 install --prefix=$PREFIX pygraphviz | |
| pip3 install --prefix=$PREFIX deeptools | |
| pip3 install --prefix=$PREFIX HTSeq | |
| pip3 install --prefix=$PREFIX keras | |
| pip3 install --prefix=$PREFIX keras_preprocessing # tensorflow ... | |
| pip3 install --prefix=$PREFIX MotifScan # Alena 30.8.2018 | |
| pip3 install --prefix=$PREFIX MAmotif | |
| pip3 install --prefix=$PREFIX hic2cool # Helpdesk Robert Schoepflin 17.09.2018 | |
| #pip3 install --prefix=$PREFIX hifive # only python 2.7+ | |
| pip3 install --prefix=$PREFIX snakemake | |
| pip3 install --prefix=$PREFIX virtualenv # Donald | |
| pip3 install --prefix=$PREFIX odfpy # Donald | |
| pip3 install --prefix=$PREFIX Dumper # Thomas | |
| pip3 install --prefix=$PREFIX igraph | |
| pip3 install --prefix=$PREFIX louvain # monocle3 prep for Helene | |
| pip3 install --prefix=$PREFIX selenium # 19.7.19 Kreitler -> https://webxray.org/ | |
| pip3 install --prefix=$PREFIX cooltools # Maria Valieva 17.7.2019 | |
| pip3 install --prefix=$PREFIX gmpy # From viper context (Helpdesk Laura Glaser 9.8.2019) | |
| pip3 install --prefix=$PREFIX torch | |
| pip3 install --prefix=$PREFIX torchvision | |
| pip3 install --prefix=$PREFIX plotly | |
| pip3 install --prefix=$PREFIX pyOpenCL | |
| pip3 install --prefix=$PREFIX docopt | |
| pip3 install --prefix=$PREFIX dbus-python | |
| pip3 install --prefix=$PREFIX distro | |
| pip3 install --prefix=$PREFIX ply | |
| pip3 install --prefix=$PREFIX threadpoolctl | |
| pip3 install --prefix=$PREFIX pyopengl | |
| # creates error, so remove it | |
| rm -rf ${PREFIX}/lib/python$PYTHONVER/site-packages/OpenGL/Tk | |
| # pip3 install --prefix=$PREFIX HiCExplorer # Would be a nice to have, but it likes to downgrade too much, pick some cherries | |
| pip3 install --prefix=$PREFIX HiCMatrix | |
| pip3 install --prefix=$PREFIX pybedtools | |
| pip3 install --prefix=$PREFIX gffutils | |
| pip3 install --prefix=$PREFIX --no-deps "pyGenomeTracks" # example produces plots, so give it a chance, otherwise it's just a dumbfucked downgrader | |
| pip3 install --prefix=$PREFIX python-bioformats | |
| pip3 install --prefix=$PREFIX jupyterlab # request Peter Arndt | |
| pip3 install --prefix=$PREFIX jupyterlab-git | |
| pip3 install --prefix=$PREFIX igv_jupyterlab # Matthias Lienhard HD 01-04-2020 | |
| pip3 install --prefix=$PREFIX igv-jupyter | |
| mkdir -vp $PREFIX/share/jupyter/lab/settings # try to defeat a silly error in jupyter labextension install | |
| pip3 install --prefix=$PREFIX scour # https://github.molgen.mpg.de/mariux64/pkg-scripts/issues/98 | |
| pip3 install --prefix=$PREFIX multiqc | |
| pip3 install --prefix=$PREFIX thonny # nice little ide, kreitler | |
| pip3 install --prefix=$PREFIX pybind11 | |
| pip3 install --prefix=$PREFIX svgwrite | |
| pip3 install --prefix=$PREFIX pyomo | |
| pip3 install --prefix=$PREFIX jsbsim # kreitler, hobby | |
| pip3 install --prefix=$PREFIX bioservices | |
| pip3 install --prefix=$PREFIX pairtools | |
| pip3 install --prefix=$PREFIX SharedArray | |
| pip3 install --prefix=$PREFIX pyabc # dependency for stochkit, HD 20.07.20 Gemma Noviello | |
| pip3 install --prefix=$PREFIX petab | |
| pip3 install --prefix=$PREFIX tadtool # HD 26.01.21 Michael Robson | |
| # pip3 install --prefix=$PREFIX perf # fails, issue from Paul sep-20, no clue... | |
| # pip3 install --prefix=$PREFIX glpk-py # kreitler, fails, wants setuptools_scm, do I want setuptools_scm? | |
| pip3 install --prefix=$PREFIX helen # HD, a dependency from a request by helene :) | |
| pip3 install --prefix=$PREFIX umap # HD, used by Matthias Lienhard | |
| pip3 install --prefix=$PREFIX macs2 # HD, Alessa Ringel, Tobias Zehnder, old python2 version broke after glibc update | |
| pip3 install --prefix=$PREFIX macs3 | |
| pip3 install --prefix=$PREFIX biopython # HD 2021-07-23 Magalhaes/Hnisz alphafold related (cool that we have missed biopython so far, LOL) | |
| pip3 install --prefix=$PREFIX dm-tree | |
| pip3 install --prefix=$PREFIX dm-haiku | |
| # pip3 install --prefix=$PREFIX jaxlib # these should be build from source, otherwise it will have trouble finding the right cuda | |
| # pip3 install --prefix=$PREFIX jax | |
| pip3 install --prefix=$PREFIX flatbuffers | |
| pip3 install --prefix=$PREFIX contextlib2 | |
| pip3 install --prefix=$PREFIX ml_collections | |
| pip3 install --prefix=$PREFIX wheel # wheel is evil, but jaxlib needs it, and tf would pull it anyway | |
| # fi ######### DEBUG_BASE (2) | |
| # cd $BUILDDIR | |
| # jax/jaxlib | |
| ( | |
| . ${PREFIX}/profile | |
| . /pkg/bazel-4.1.0-0/profile | |
| cd $BUILDDIR | |
| # orig: https://github.com/google/jax/archive/refs/tags/jaxlib-v0.1.71.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/10b3082f32e4088a139b8a5b9591ea9f/jax-jaxlib-v0.1.71.tar.gz | |
| test -e jax-jaxlib-v0.1.71.tar.gz || wget -nv $BEEHIVE | |
| test -d jax-jaxlib-v0.1.71 || tar -xf jax-jaxlib-v0.1.71.tar.gz | |
| cd jax-jaxlib-v0.1.71 | |
| test -d dist && rm -f dist/* | |
| export JAX_CUDA_VERSION=11.1 # just to give a '+cuda111' in the wheel name | |
| python3 build/build.py \ | |
| --target_cpu_features native \ | |
| --enable_cuda \ | |
| --cuda_path /pkg/cuda-11.1.1-0 \ | |
| --cuda_version 11.1 \ | |
| --cudnn_path /pkg/cuda-11.1.1-0 \ | |
| --cudnn_version 8.0.4 \ | |
| --noenable_tpu | |
| # result looks like dist/jaxlib-0.1.71-cp39-none-manylinux2010_x86_64.whl | |
| pip3 install --prefix=$PREFIX ./dist/*.whl | |
| # this brings the jax package | |
| pip3 install --prefix=$PREFIX . | |
| ) | |
| # boost for pycuda | |
| ( | |
| . ${PREFIX}/profile | |
| BOOST_VERSION=(1.75.0 1_75_0) | |
| PKGCFLAGS="-O2 -fPIC" | |
| cd $BUILDDIR | |
| # orig: https://dl.bintray.com/boostorg/release/1.75.0/source/boost_1_75_0.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de//38813f6feb40387dfe90160debd71251/boost_1_75_0.tar.gz | |
| test -e boost_${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-${BOOST_VERSION[0]} --strip-components=1 | |
| #### ATTN! | |
| #### python meanders between /python${PYTHONVER} and /python${PYTHONVER}m | |
| cd boost-${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 | |
| ) | |
| # use pycuda git version to get GL support | |
| ( | |
| PYCUDAVERS=2020.1 | |
| PYTHON_LIBNAME=boost_python${PYTHONVER/./} | |
| . ${PREFIX}/profile | |
| cd $BUILDDIR | |
| # future build might try this one | |
| # https://github.com/inducer/pycuda/archive/refs/tags/v2021.1.tar.gz | |
| # orig: https://github.com/inducer/pycuda/archive/v2020.1.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/580562d7af4d3249c5b42a1df8d428a0/pycuda-2020.1.tar.gz | |
| test -e pycuda-${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 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 | |
| ) | |
| ( | |
| # orig: https://github.com/openmm/openmm/archive/refs/tags/7.5.1.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/12fefb6ca030d1f4aace78ac1a8b94c3/openmm-7.5.1.tar.gz | |
| test -e openmm-7.5.1.tar.gz || wget -nv $BEEHIVE | |
| test -d openmm-7.5.1 || tar -xf openmm-7.5.1.tar.gz | |
| cd openmm-7.5.1 | |
| # replace hardcoded "/usr/local/cuda/bin/nvcc" in libOpenMMCUDA.so (crying four trouble dude?) | |
| # Otherwise OPENMM_CUDA_COMPILER needs to be used | |
| sed -i -e "/bin\/nvcc/ s,/usr/local/cuda/bin/nvcc,/$CUDADIR/bin/nvcc," \ | |
| platforms/cuda/src/CudaPlatform.cpp | |
| # apply 'DeepMind modification' to openmm, hopefully it will leave openmm usable :) | |
| sed -ne '/^#Epatch:openmmtopo/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose | |
| mkdir -p build | |
| cd build | |
| cmake \ | |
| -DCMAKE_INSTALL_PREFIX=$PREFIX \ | |
| -DCUDA_TOOLKIT_ROOT_DIR=$CUDADIR \ | |
| -DBUILD_TESTING=OFF \ | |
| .. | |
| make -j $NPROC | |
| make install | |
| # make PythonInstall # this one sucks! (ignoring all locations cleanly found by cmake before...) | |
| echo "# openmm library part done, now python-binding." | |
| cd python | |
| OPENMM_INCLUDE_PATH=$PREFIX/include OPENMM_LIB_PATH=$PREFIX/lib python3 setup.py build | |
| OPENMM_INCLUDE_PATH=$PREFIX/include OPENMM_LIB_PATH=$PREFIX/lib python3 setup.py install | |
| # place symlinks from plugins to lib, saving a LD_LIBRARY_PATH entry | |
| cd $PREFIX/lib | |
| for SO in plugins/*.so; do | |
| ln -sv $SO | |
| done | |
| ) | |
| ( | |
| # orig:https://github.com/openmm/pdbfixer/archive/refs/tags/v1.7.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/dd383722fcf5213537656f691f4c2053/pdbfixer-1.7.tar.gz | |
| test -e pdbfixer-1.7.tar.gz || wget -nv $BEEHIVE | |
| test -d pdbfixer-1.7 || tar -xf pdbfixer-1.7.tar.gz | |
| cd pdbfixer-1.7 | |
| python3 setup.py build | |
| python3 setup.py install | |
| ) | |
| ( | |
| # orig:https://github.com/brentp/bwa-meth/archive/refs/tags/v0.2.2.tar.gz # HD: Sven Klages 2021-09-02 | |
| BEEHIVE=https://beehive.molgen.mpg.de/85e77f8c2d832af13f31d5b612ab27eb/bwa-meth-0.2.2.tar.gz | |
| test -e bwa-meth-0.2.2.tar.gz || wget -nv $BEEHIVE | |
| test -d bwa-meth-0.2.2 || tar -xf bwa-meth-0.2.2.tar.gz | |
| cd bwa-meth-0.2.2 | |
| python3 setup.py build | |
| python3 setup.py install | |
| ) | |
| pip3 list > $PIPMETADIR/pip3list_ballpark | |
| # fi ######### DEBUG_TF | |
| # cd $BUILDDIR | |
| # finaly tensorflaw | |
| ( | |
| TFVERSION=2.5.0 | |
| NCCLSHORTVERSION=2.7 | |
| . ${PREFIX}/profile | |
| . /pkg/bazel-4.1.0-0/profile | |
| cd $BUILDDIR | |
| # https://github.com/tensorflow/tensorflow/archive/v2.5.0.tar.gz | |
| BEEHIVE=https://beehive.molgen.mpg.de/b152ebdc7f72c4d32f7a9e58aa41b80d/tensorflow-2.5.0.tar.gz | |
| test -e tensorflow-${TFVERSION}.tar.gz || wget -nv $BEEHIVE | |
| test -d tensorflow-${TFVERSION} || tar -xf tensorflow-${TFVERSION}.tar.gz | |
| cd tensorflow-${TFVERSION} | |
| # https://bugs.archlinux.org/task/65953 | |
| #vars for config | |
| export PYTHON_BIN_PATH=${PREFIX}/bin/python3 | |
| export USE_DEFAULT_PYTHON_LIB_PATH=1 | |
| export TF_NEED_JEMALLOC=1 | |
| export TF_NEED_KAFKA=0 | |
| export TF_NEED_OPENCL_SYCL=0 | |
| export TF_NEED_AWS=0 | |
| export TF_NEED_GCP=0 | |
| export TF_NEED_HDFS=0 | |
| export TF_NEED_S3=0 | |
| export TF_ENABLE_XLA=1 | |
| export TF_NEED_GDR=0 | |
| export TF_NEED_VERBS=0 | |
| export TF_NEED_OPENCL=0 | |
| export TF_NEED_MPI=0 | |
| export TF_NEED_TENSORRT=1 | |
| export TF_NEED_NGRAPH=0 | |
| export TF_NEED_IGNITE=0 | |
| export TF_NEED_ROCM=0 | |
| export TF_SET_ANDROID_WORKSPACE=0 | |
| export TF_DOWNLOAD_CLANG=0 | |
| export TF_NCCL_VERSION=${NCCLSHORTVERSION} | |
| export TF_IGNORE_MAX_BAZEL_VERSION=1 | |
| export NCCL_INSTALL_PATH=${CUDADIR} | |
| export GCC_HOST_COMPILER_PATH=/usr/bin/gcc | |
| export TF_CUDA_CLANG=0 | |
| export CLANG_CUDA_COMPILER_PATH=/usr/bin/clang | |
| export TF_CUDA_PATHS=${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 | |
| ./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 | |
| # inhibit downgrading of packages installed | |
| sed -ne '/^#Epatch:tfdep/ s/^#Epatch:\S* // p' $ME | patch -p2 --verbose | |
| python3 setup.py build | |
| python3 setup.py install --prefix $PREFIX | |
| ) | |
| pip3 list > $PIPMETADIR/pip3list_after_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 | |
| # 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." | |
| exit | |
| ### PATCHES | |
| # the code to cope with '--disable-pip-version-check' is spread over the module, so | |
| # just quieten the enervating/misleading update reminder for at least 3 minors ... | |
| #Epatch:pip *** a/pip/_internal/self_outdated_check.py Mon May 16 13:16:30 2022 | |
| #Epatch:pip --- b/pip/_internal/self_outdated_check.py Mon May 16 15:57:31 2022 | |
| #Epatch:pip *************** | |
| #Epatch:pip *** 206,211 **** | |
| #Epatch:pip --- 206,212 ---- | |
| #Epatch:pip local_version_is_older = ( | |
| #Epatch:pip local_version < remote_version | |
| #Epatch:pip and local_version.base_version != remote_version.base_version | |
| #Epatch:pip + and ( local_version.release[0] < remote_version.release[0] or local_version.release[1] < remote_version.release[1] - 3 ) | |
| #Epatch:pip ) | |
| #Epatch:pip if local_version_is_older: | |
| #Epatch:pip return UpgradePrompt(old=str(local_version), new=remote_version_str) | |
| # BTW: numpy is installed ... | |
| #Epatch:tfdep --- a/tensorflow-pip/setup.py.orig 2021-07-29 21:21:33.000000000 +0200 | |
| #Epatch:tfdep +++ b/tensorflow-pip/setup.py 2021-08-05 18:14:26.011647329 +0200 | |
| #Epatch:tfdep @@ -77,6 +77,2 @@ | |
| #Epatch:tfdep REQUIRED_PACKAGES = [ | |
| #Epatch:tfdep - # NOTE: As numpy has releases that break semver guarantees and several other | |
| #Epatch:tfdep - # deps depend on numpy without an upper bound, we must install numpy before | |
| #Epatch:tfdep - # everything else. | |
| #Epatch:tfdep - 'numpy ~= 1.19.2', | |
| #Epatch:tfdep # Install other dependencies | |
| # This is found in the docker image preparation for AlphaFold. | |
| # I'm not completely happy patching existing libraries ... | |
| #Epatch:openmmtopo --- a/wrappers/python/simtk/openmm/app/topology.py.orig 2021-04-07 22:09:01.000000000 +0200 | |
| #Epatch:openmmtopo +++ b/wrappers/python/simtk/openmm/app/topology.py 2021-08-05 16:49:10.191954117 +0200 | |
| #Epatch:openmmtopo @@ -355,2 +355,11 @@ | |
| #Epatch:openmmtopo return 'SG' in names and 'HG' not in names | |
| #Epatch:openmmtopo + # This function is used to prevent multiple di-sulfide bonds from being | |
| #Epatch:openmmtopo + # assigned to a given atom. This is a DeepMind modification. | |
| #Epatch:openmmtopo + def isDisulfideBonded(atom): | |
| #Epatch:openmmtopo + for b in self._bonds: | |
| #Epatch:openmmtopo + if (atom in b and b[0].name == 'SG' and | |
| #Epatch:openmmtopo + b[1].name == 'SG'): | |
| #Epatch:openmmtopo + return True | |
| #Epatch:openmmtopo + | |
| #Epatch:openmmtopo + return False | |
| #Epatch:openmmtopo | |
| #Epatch:openmmtopo @@ -361,2 +370,3 @@ | |
| #Epatch:openmmtopo pos1 = positions[sg1.index] | |
| #Epatch:openmmtopo + candidate_distance, candidate_atom = 0.3*nanometers, None | |
| #Epatch:openmmtopo for j in range(i): | |
| #Epatch:openmmtopo @@ -366,4 +376,10 @@ | |
| #Epatch:openmmtopo distance = sqrt(delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2]) | |
| #Epatch:openmmtopo - if distance < 0.3*nanometers: | |
| #Epatch:openmmtopo - self.addBond(sg1, sg2) | |
| #Epatch:openmmtopo + if distance < candidate_distance and not isDisulfideBonded(sg2): | |
| #Epatch:openmmtopo + candidate_distance = distance | |
| #Epatch:openmmtopo + candidate_atom = sg2 | |
| #Epatch:openmmtopo + # Assign bond to closest pair. | |
| #Epatch:openmmtopo + if candidate_atom: | |
| #Epatch:openmmtopo + self.addBond(sg1, candidate_atom) | |
| #Epatch:openmmtopo + | |
| #Epatch:openmmtopo + | |