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#!/bin/bash
set -e -x
export MANYLINUX=1
BUILD_PREFIX="/usr/local"
OPENBLAS_VERS="0.2.18"
OPENBLAS_TAR="/io/python/openblas_${OPENBLAS_VERS}.tgz"
OPENBLAS_PATH="/usr/local/lib/libopenblasp-r${OPENBLAS_VERS}.so"
PACKAGE_NAME='scrappie'
function build_openblas {
# this takes a long time so record success in openblas-built
if [ -e "openblas-built" ]; then return; fi
if [ -d "OpenBLAS" ]; then
(cd OpenBLAS && git clean -fxd && git reset --hard)
else
git clone https://github.com/xianyi/OpenBLAS
fi
(cd OpenBLAS \
&& git checkout "v${OPENBLAS_VERSION}" \
&& make DYNAMIC_ARCH=1 USE_OPENMP=0 NUM_THREADS=64 TARGET=NEHALEM > /dev/null)
touch openblas-built
}
function install_openblas {
(cd OpenBLAS && make PREFIX=$BUILD_PREFIX install)
# copy license to a sensible place
license_path="/usr/share/doc/openblas"
mkdir -p ${license_path}
cp OpenBLAS/LICENSE ${license_path}
tar zcf ${OPENBLAS_TAR} /usr/local/lib /usr/local/include ${license_path}
}
cd /io
# OpenBLAS possibilities:
# i) check /usr/local/lib for openblas -> nothing to do
# ii) look for a tar (containing compiled blas) -> unpack
# iii) build from scratch
if [ -e ${OPENBLAS_PATH} ]; then
echo "Found OpenBLAS at ${OPENBLAS_PATH}"
elif [ -e ${OPENBLAS_TAR} ]; then
echo "Unpacking OpenBLAS tar ${OPENBLAS_TAR}"
tar xzf ${OPENBLAS_TAR} -C /
else
echo "Building OpenBLAS"
build_openblas
install_openblas
fi
cd /io/python
# Compile wheels
for minor in 4 5 6; do
PYBIN="/opt/python/cp3${minor}-cp3${minor}m/bin"
"${PYBIN}/pip" wheel . -w wheelhouse/
done
# Bundle external shared libraries into the wheels
for whl in "wheelhouse/${PACKAGE_NAME}"*.whl; do
auditwheel repair "${whl}" -w wheelhouse/
rm "${whl}"
done
# Install packages and "test"
for minor in 4 5 6; do
PYBIN="/opt/python/cp3${minor}-cp3${minor}m/bin"
"${PYBIN}/pip" install "${PACKAGE_NAME}" --no-index -f wheelhouse
"${PYBIN}/python" -c "from scrappy import *; import numpy as np; print(basecall_raw(np.random.normal(10,4,1000)))"
done
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