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pkg-scripts/python-3.10.12-0.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-$COOKIE.sh
#TESTING=1
#SKIPTENSORFLOW=1
# ---------------------------------------------------------------- Preamble
#set -x
PKG=python
VERSION=3.10.12
BUILD=0
PYTHONVER=${VERSION%.*}
CUDADIR=/pkg/cuda-11.8.0-0
PREFIX=/pkg/$PKG-$VERSION-$BUILD
if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$PKG-$VERSION-$BUILD ; fi
PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
# set -xe
set -e
umask 022
BUILD_TMPDIR=/scratch/local2/$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_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 $*
}
# ---------------------------------------- Build Python & support libraries
(
# orig: https://www.python.org/ftp/python/3.10.10/Python-3.10.10.tar.xz
BEEHIVE="https://beehive.molgen.mpg.de/49b0342476b984e106d308c25d657f12/Python-3.10.12.tar.xz"
test -e Python-$VERSION.tar.xz || wget -nv $BEEHIVE
test -d Python-$VERSION || tar -xf Python-$VERSION.tar.xz
cd Python-$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' $ME | patch -p1 --verbose
)
)
install setuptools==65.3.0 # see numba below
piplist; track START
# build various pythonbindings 'by hand', because pip installs do not deliver
# header files and the like.
# BTW: builds need meson
install meson
(
DBUS_PYTHON_VERSION=1.3.2
#PyPi
# https://files.pythonhosted.org/packages/c1/d3/6be85a9c772d6ebba0cc3ab37390dd6620006dcced758667e0217fb13307/dbus-python-1.3.2.tar.gz
BEEHIVE=https://beehive.molgen.mpg.de/33be8a4a766e1c7c9a377b8f934ce21a/dbus-python-1.3.2.tar.gz
test -e dbus-python-$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 $NPROC
make install
)
# ------------------------------------------------ build tool fuer Thomas
(
set -x
GYP_VERSION=20230301_c6d8b9f7
# orig: https://mirror.netcologne.de/slackware/slackware64-current/source/d/gyp/
BEEHIVE=https://beehive.molgen.mpg.de/ba0357be23ca55555714261afccc7aab/gyp-20230301_c6d8b9f7.tar.xz
test -e gyp-${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:gyp1/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose
sed -ne '/^#Epatch:gyp2/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose
python3 setup.py build
python3 setup.py install --prefix $PREFIX
)
piplist; track gyp
(
PYCAIRO_VERSION=1.23.0
#PyPi
# https://files.pythonhosted.org/packages/69/ca/9e9fa2e8be0876a9bbf046a1be7ee33e61d4fdfbd1fd25c76c1bdfddf8c4/pycairo-1.23.0.tar.gz
BEEHIVE=https://beehive.molgen.mpg.de/7a3729d21659098e1b9a411b62e88966/pycairo-1.23.0.tar.gz
test -e pycairo-$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
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=5.15.9
#PyPi
# 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 $NPROC
make install
)
piplist; track qt-support-riverbankcomputing
# -------------------------------------------------------- Install packages
# Install the psychotic diva first
install numpy==1.23.4
install Cython~=0.29 #last stable release, version 3 ganz frisch unlogische versionierung
# libxml2-python from pypi isn't up to date, cause lxml seems to be the favored binding
# do this early, not that some dependency tries it on its own.
# (btw. libxslt-python isn't ported to python3)
(
LIBXML2_VERSION=2.9.12
# orig: http://xmlsoft.org/sources/libxml2-${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-$LIBXML2_VERSION/python
python3 setup.py build
python3 setup.py install
)
piplist; track legacy-libxml2
# 'numba' the cuda enabled numpy
(
NUMBA_VERSION=0.56.3
# orig: https://files.pythonhosted.org/packages/a3/95/7df08647e773a2417e24de8fea9087606b37074f63830a3f2dbabd97f01b/numba-0.56.3.tar.gz
BEEHIVE=https://beehive.molgen.mpg.de/ae0a008447f2f246523af143b1488e88/numba-0.56.3.tar.gz
test -e numba-$NUMBA_VERSION.tar.gz || wget -nv $BEEHIVE
test -d numba-$NUMBA_VERSION || tar -xf numba-$NUMBA_VERSION.tar.gz
cd numba-$NUMBA_VERSION
# numba assumes that libcudart.so and friends reside in 'CUDA_HOME/lib64'
sed -ne '/^#Epatch:numba1/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose
sed -ne '/^#Epatch:numba2/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose
install .
# useful to see if numba works
cp -p numba/misc/numba_sysinfo.py $PREFIX/bin
chmod 0755 $PREFIX/bin/numba_sysinfo.py
)
piplist; track numba
PACKAGES=$(sed -e s/#.*$// <<- __PKGLIST__
protobuf==3.19.4 # tensorflow likes to have an slightly older one [< 3.20], no conflicts with this
onnx==1.12.0 # newer onnx (dep helen) needs newer protobuf
Pillow<10.0.0 # pyimagej 1.4.1 downgrade to latest 9
keras==2.11.0 # tensorflow 2.11.1 requires keras<2.12,>=2.11.0
urllib3<2.0.0 # oauth brauch wird von tensorflow gebraucht
Sphinx==4.5.0 # hic2cool(0.8.3) moecht gern was aelteres
jedi<0.19.0 # spyder dwowngrade spyder 5.4.4
black[d] #onnx want but not install it
flask
ipython[all]
SciPy
pandas
SymPy
nose
statsmodels
pysam
seaborn
scikit-learn
Mako
pyimagej # Mikroscop
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
hvplot #ont/nextflow pipelines
pyarrow #ont/nextflow pipelines
umi-tools
recommonmark
fastcluster
pydot
pygraphviz
deeptools
HTSeq
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
plotly
pyOpenCL
docopt
distro
ply
threadpoolctl
HiCMatrix
pybedtools
gffutils
python-bioformats
jupyter
jupyterlab
jupyterlab-git # request Peter Arndt
igv_jupyterlab # Matthias Lienhard 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 Gemma Noviello
petab
tadtool # HD 26.01.21 Michael Robson
pyperf # Paul sep-20
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
spyder
spyder-kernels
# 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
scanpy
asciidoc
__PKGLIST__
)
for PKG in $PACKAGES; do
install $PKG
done
(
#install from git to get .so
pip3 install git+https://github.com/open2c/pairtools.git@v1.0.2
)
piplist; track 'pairtools'
(
TRITON_VERSION=2.0.0
#triton 2.0.0 hat cmake als install dep, ist in 2.1.0 gefixt
# orig: https://github.com/openai/triton/archive/refs/tags/v2.0.0.tar.gz
BEEHIVE=https://beehive.molgen.mpg.de/56b46016609039fac839f8297c88454c/triton-2.0.0.tar.gz
test -e triton-${TRITON_VERSION}.tar.gz || wget -nv $BEEHIVE
test -d triton-${TRITON_VERSION} || tar -xf triton-${TRITON_VERSION}.tar.gz
cd triton-${TRITON_VERSION}/python
sed -ne '/^#Epatch:triton/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose
pip install . --prefix=$PREFIX
piplist; track triton==${TRITON_VERSION}
)
# 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
# install helen after our torch, otherwise we might catch the default torch from pip ...
install helen # HD, a dependency from a request by helene
mkdir -vp $PREFIX/share/jupyter/lab/settings # try to defeat a silly error in jupyter labextension install
# --------------------------------------------------- Install misc packages
(
BOOST_VERSION=(1.80.0 1_80_0)
PKGCFLAGS="-O2 -fPIC"
# orig: https://boostorg.jfrog.io/artifactory/main/release/1.80.0/source/boost_1_80_0.tar.gz
BEEHIVE=https://beehive.molgen.mpg.de/077f074743ea7b0cb49c6ed43953ae95/boost_1_80_0.tar.gz
test -e boost_${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${PYTHONVER/./}
# orig: https://files.pythonhosted.org/packages/2d/1f/48a3a5b2c715345e7af1e09361100bd98c3d72b4025371692ab233f523d3/pycuda-2022.1.tar.gz # maybe those very long URLs compensate for other (shorter) things ...
BEEHIVE="https://beehive.molgen.mpg.de/2fad5a15db4153d825822eba7cb25f25/pycuda-2022.1.tar.gz"
test -e pycuda-${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 $PREFIX
)
(
IDR_VERSION=2.0.3
# orig: https://github.com/nboley/idr/archive/2.0.3/idr-2.0.3.tar.gz # HD: Tobias Zehnder, 18.3.21
BEEHIVE=https://beehive.molgen.mpg.de/1bec61b526bb1dcf92a5ab99c27852d0/idr-2.0.3.tar.gz
test -e idr-${IDR_VERSION}.tar.gz || wget -nv $BEEHIVE
test -d idr-${IDR_VERSION} || tar -xf idr-${IDR_VERSION}.tar.gz
cd idr-${IDR_VERSION}
python3 setup.py build
python3 setup.py install --prefix $PREFIX
)
(
STGIT_VERSSION=1.0
# orig: https://github.com/stacked-git/stgit/archive/v1.0/stgit-1.0.tar.gz # Paul mariux64/pkg-scripts/issues/152
BEEHIVE=https://beehive.molgen.mpg.de/b20ab5a197fc3a141f4b00c5859c0a3b/stgit-1.0.tar.gz
test -e stgit-${STGIT_VERSSION}.tar.gz || wget -nv $BEEHIVE
test -d stgit-${STGIT_VERSSION} || tar -xf stgit-${STGIT_VERSSION}.tar.gz
cd stgit-${STGIT_VERSSION}
python3 setup.py build
python3 setup.py install --prefix $PREFIX
)
(
METH_VERSION=0.2.5
# https://github.com/brentp/bwa-meth/archive/refs/tags/v0.2.5.tar.gz
BEEHIVE=https://beehive.molgen.mpg.de/33a4c416760dd67e77f17e07791527e2/bwa-meth-0.2.5.tar.gz
test -e bwa-meth-${METH_VERSION}.tar.gz || wget -nv $BEEHIVE
test -d bwa-meth-${METH_VERSION} || tar -xf bwa-meth-${METH_VERSION}.tar.gz
cd bwa-meth-${METH_VERSION}
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=2.11.1
NCCLSHORTVERSION=$(pkg-config nccl --modversion | grep -Po '\d+\.\d+')
. /pkg/bazel-5.4.1-0/profile
# orig: https://github.com/tensorflow/tensorflow/archive/refs/tags/v2.11.1.tar.gz
BEEHIVE=https://beehive.molgen.mpg.de/e1b60c6e074f8b4c83f184e2c298774f/tensorflow-2.11.1.tar.gz
test -e tensorflow-${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=${PREFIX}/bin/python3
export USE_DEFAULT_PYTHON_LIB_PATH=1
export TF_NEED_JEMALLOC=1
export TF_NEED_KAFKA=0
export TF_NEED_OPENCL_SYCL=0
export TF_NEED_AWS=0
export TF_NEED_GCP=0
export TF_NEED_HDFS=0
export TF_NEED_S3=0
export TF_ENABLE_XLA=1
export TF_NEED_GDR=0
export TF_NEED_VERBS=0
export TF_NEED_OPENCL=0
export TF_NEED_MPI=0
export TF_NEED_TENSORRT=0
export TF_NEED_NGRAPH=0
export TF_NEED_IGNITE=0
export TF_NEED_ROCM=0
export TF_SET_ANDROID_WORKSPACE=0
export TF_DOWNLOAD_CLANG=0
export TF_NCCL_VERSION=${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') # 11.5
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 {} +
echo "For Deeper checks:"
echo "cd ${BUILDDIR} ; git log --patch "
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:numba1 # Fix lib location, turn numba_sysinfo.py into a common diag tool
#Epatch:numba1 --- a/numba/cuda/cuda_paths.py 2022-10-14 09:57:25.616827200 +0200
#Epatch:numba1 +++ b/numba/cuda/cuda_paths.py 2022-10-20 11:20:15.106019523 +0200
#Epatch:numba1 @@ -68,3 +68,3 @@
#Epatch:numba1 else:
#Epatch:numba1 - return 'lib64'
#Epatch:numba1 + return 'lib'
#Epatch:numba2 --- a/numba/misc/numba_sysinfo.py 2022-10-14 09:57:25.628827000 +0200
#Epatch:numba2 +++ b/numba/misc/numba_sysinfo.py 2022-10-20 11:02:54.056767540 +0200
#Epatch:numba2 @@ -1 +1,2 @@
#Epatch:numba2 +#! /usr/bin/env python3
#Epatch:numba2 import json
#Epatch:numba2 @@ -367,3 +368,3 @@
#Epatch:numba2 with redirect_stdout(output):
#Epatch:numba2 - cudadrv.libs.test(sys.platform, print_paths=False)
#Epatch:numba2 + cudadrv.libs.test(sys.platform, print_paths=True)
#Epatch:numba2 sys_info[_cu_lib_test] = output.getvalue()
#Epatch:numba2 @@ -626,9 +627,2 @@
#Epatch:numba2 ("",),
#Epatch:numba2 - ("__Conda Information__",),
#Epatch:numba2 - (DisplayMap({k: v for k, v in info.items()
#Epatch:numba2 - if k.startswith('Conda')}) or ("Conda not available.",)),
#Epatch:numba2 - ("",),
#Epatch:numba2 - ("__Installed Packages__",),
#Epatch:numba2 - DisplaySeq(info.get(_inst_pkg, ("Couldn't retrieve packages info.",))),
#Epatch:numba2 - ("",),
#Epatch:numba2 ("__Error log__" if info.get(_errors, [])
#Epatch:gyp1 --- a/pylib/gyp/generator/cmake.py
#Epatch:gyp1 +++ b/pylib/gyp/generator/cmake.py
#Epatch:gyp1 @@ -41,7 +41,7 @@
#Epatch:gyp1 try:
#Epatch:gyp1 # maketrans moved to str in python3.
#Epatch:gyp1 + _maketrans = str.maketrans
#Epatch:gyp1 +except NameError:
#Epatch:gyp1 _maketrans = string.maketrans
#Epatch:gyp1 -except NameError:
#Epatch:gyp1 - _maketrans = str.maketrans
#Epatch:gyp1 generator_default_variables = {
#Epatch:gyp1 'EXECUTABLE_PREFIX': '',
#Epatch:gyp1 @@ -283,2 +283,2 @@
#Epatch:gyp1 if int(action.get('process_outputs_as_sources', False)):
#Epatch:gyp1 - extra_sources.extend(zip(cmake_outputs, outputs))
#Epatch:gyp1 + extra_sources.extend(list(zip(cmake_outputs, outputs)))
#Epatch:gyp1 @@ -988,6 +988,6 @@
#Epatch:gyp1 # XCode settings
#Epatch:gyp1 xcode_settings = config.get('xcode_settings', {})
#Epatch:gyp1 - for xcode_setting, xcode_value in xcode_settings.viewitems():
#Epatch:gyp1 + for xcode_setting, xcode_value in xcode_settings.items():
#Epatch:gyp1 SetTargetProperty(output, cmake_target_name,
#Epatch:gyp1 "XCODE_ATTRIBUTE_%s" % xcode_setting, xcode_value,
#Epatch:gyp1 '' if isinstance(xcode_value, str) else ' ')
#Epatch:gyp2 diff --git a/pylib/gyp/input.py b/pylib/gyp/input.py
#Epatch:gyp2 index 4c12891..2bea334 100644
#Epatch:gyp2 --- a/pylib/gyp/input.py
#Epatch:gyp2 +++ b/pylib/gyp/input.py
#Epatch:gyp2 @@ -1183,7 +1183,7 @@
#Epatch:gyp2 if variable_name in variables:
#Epatch:gyp2 # If the variable is already set, don't set it.
#Epatch:gyp2 continue
#Epatch:gyp2 - if the_dict_key is 'variables' and variable_name in the_dict:
#Epatch:gyp2 + if the_dict_key == 'variables' and variable_name in the_dict:
#Epatch:gyp2 # If the variable is set without a % in the_dict, and the_dict is a
#Epatch:gyp2 # variables dict (making |variables| a varaibles sub-dict of a
#Epatch:gyp2 # variables dict), use the_dict's definition.
#Epatch:triton diff --git a/setup.py b/setup.py
#Epatch:triton index 2ac3accd2..e7357be58 100644
#Epatch:triton --- a/setup.py
#Epatch:triton +++ b/setup.py
#Epatch:triton @@ -211,10 +211,7 @@ setup(
#Epatch:triton long_description="",
#Epatch:triton packages=["triton", "triton/_C", "triton/language", "triton/tools", "triton/impl", "triton/ops", "triton/runtime", "triton/ops/blocksparse"],
#Epatch:triton install_requires=[
#Epatch:triton - "cmake",
#Epatch:triton "filelock",
#Epatch:triton - "torch",
#Epatch:triton - "lit",
#Epatch:triton ],
#Epatch:triton package_data={"triton": ["third_party/**/*"]},
#Epatch:triton include_package_data=True,
#Epatch:triton @@ -233,6 +231,10 @@ setup(
#Epatch:triton ],
#Epatch:triton test_suite="tests",
#Epatch:triton extras_require={
#Epatch:triton + "build": [
#Epatch:triton + "cmake>=3.18",
#Epatch:triton + "lit",
#Epatch:triton + ],
#Epatch:triton "tests": [
#Epatch:triton "autopep8",
#Epatch:triton "flake8",
# -------------------------------------------------------- This is the end.