Revision 5f4b66b247128720c6e7e8e9abfcecae4b518e41 authored by Miriam Cabero on 24 July 2017, 11:22:45 UTC, committed by Collin Capano on 24 July 2017, 11:22:45 UTC
* Fix Travis issues (hopefully) * Rebase with master (for spherical harmonics) and fix documentation typos * Change ringdown approximants' names * Adapt pycbc_ringinj to new approximants and names * Fix typos and remove unnecessary lines * Adapt generator ringdown classes to new approximants * Forgotten name-change in generator class * Missing inclination
1 parent 0a8adfc
docker_build_dist.sh
#!/bin/bash
set -e
for i in $*; do
case $i in
--pycbc-container=*) PYCBC_CONTAINER="`echo $i|sed 's/^--pycbc-container=//'`";;
--pull-request=*) TRAVIS_PULL_REQUEST="`echo $i|sed 's/^--pull-request=//'`";;
--commit=*) TRAVIS_COMMIT="`echo $i|sed 's/^--commit=//'`";;
--secure=*) TRAVIS_SECURE_ENV_VARS="`echo $i|sed 's/^--secure=//'`";;
--tag=*) TRAVIS_TAG="`echo $i|sed 's/^--tag=//'`";;
*) echo -e "unknown option '$i', valid are:\n$usage">&2; exit 1;;
esac
done
# determine the pycbc git branch and origin
if test x$TRAVIS_PULL_REQUEST = "xfalse" ; then
PYCBC_CODE="--pycbc-commit=${TRAVIS_COMMIT}"
else
PYCBC_CODE="--pycbc-fetch-ref=refs/pull/${TRAVIS_PULL_REQUEST}/merge"
fi
# set the lalsuite checkout to use
LALSUITE_HASH="539c8700af92eb6dd00e0e91b9dbaf5bae51f004"
if [ "x$TRAVIS_TAG" == "x" ] ; then
TRAVIS_TAG="master"
RSYNC_OPTIONS="--delete"
else
RSYNC_OPTIONS=""
fi
echo -e "\\n>> [`date`] Inside container ${PYCBC_CONTAINER}"
echo -e "\\n>> [`date`] Release tag is ${TRAVIS_TAG}"
echo -e "\\n>> [`date`] Using PyCBC code ${PYCBC_CODE}"
echo -e "\\n>> [`date`] Using lalsuite hash ${LALSUITE_HASH}"
echo -e "\\n>> [`date`] Travis pull request is ${TRAVIS_PULL_REQUEST}"
echo -e "\\n>> [`date`] Travis commit is ${TRAVIS_COMMIT}"
echo -e "\\n>> [`date`] Travis secure env is ${TRAVIS_SECURE_ENV_VARS}"
echo -e "\\n>> [`date`] Travis tag is ${TRAVIS_TAG}"
if [ "x${TRAVIS_SECURE_ENV_VARS}" == "xtrue" ] ; then
mkdir -p ~/.ssh
cp /pycbc/.ssh/* ~/.ssh
chmod 600 ~/.ssh/id_rsa
fi
if [ "x${PYCBC_CONTAINER}" == "xpycbc_inspiral_bundle" ] ; then
echo -e "\\n>> [`date`] Building pycbc_inspiral bundle for CentOS 6"
# create working dir for build script
BUILD=/pycbc/build
mkdir -p ${BUILD}
export PYTHONUSERBASE=${BUILD}/.local
export XDG_CACHE_HOME=${BUILD}/.cache
# get library to build optimized pycbc_inspiral bundle
wget_opts="-c --passive-ftp --no-check-certificate --tries=5 --timeout=30 --no-verbose"
primary_url="https://git.ligo.org/ligo-cbc/pycbc-software/raw/"
secondary_url="https://www.atlas.aei.uni-hannover.de/~dbrown"
pushd /pycbc
for p in "cea5bd67440f6c3195c555a388def3cc6d695a5c/x86_64/composer_xe_2015.0.090/composer_xe_2015.0.090.tar.gz" "2d7e4a4f2f1503db5b93d70907fa24ad54bffbcb/travis/testbank_TF2v4ROM.hdf" ; do
set +e
test -r `basename $p` || wget $wget_opts ${primary_url}/${p}
set -e
test -r `basename $p` || wget $wget_opts ${secondary_url}/${p}
done
popd
# run the einstein at home build and test script
echo -e "\\n>> [`date`] Running pycbc_build_eah.sh"
pushd ${BUILD}
/pycbc/tools/einsteinathome/pycbc_build_eah.sh --lalsuite-commit=${LALSUITE_HASH} ${PYCBC_CODE} --clean-pycbc --silent-build --download-url=https://git.ligo.org/ligo-cbc/pycbc-software/raw/710a51f4770cbba77f61dfb798472bebe6c43d38/travis --with-extra-approximant='SPAtmplt:mtotal<4' --with-extra-approximant='SEOBNRv4_ROM:else' --with-extra-approximant=--use-compressed-waveforms --with-extra-libs=file:///pycbc/composer_xe_2015.0.090.tar.gz --processing-scheme=mkl --with-extra-bank=/pycbc/testbank_TF2v4ROM.hdf
if [ "x${TRAVIS_SECURE_ENV_VARS}" == "xtrue" ] ; then
echo -e "\\n>> [`date`] Deploying pycbc_inspiral bundle"
BUNDLE_DEST=/home/pycbc/ouser.ligo/ligo/deploy/sw/pycbc/x86_64_rhel_6/bundle/${TRAVIS_TAG}
echo -e "\\n>> [`date`] Deploying pycbc_inspiral bundle to sugwg-condor.phy.syr.edu"
ssh pycbc@sugwg-condor.phy.syr.edu "mkdir -p ${BUNDLE_DEST}"
scp ${BUILD}/pycbc-build/environment/dist/pycbc_inspiral_osg* pycbc@sugwg-condor.phy.syr.edu:${BUNDLE_DEST}/pycbc_inspiral
if [ "x${TRAVIS_TAG}" != "xmaster" ] ; then
PYCBC_INSPIRAL_SUFFIX="_osg_${TRAVIS_TAG}"
BUNDLE_DEST=/home/login/ouser.ligo/ligo/deploy/sw/pycbc/x86_64_rhel_6/bundle/${TRAVIS_TAG}
echo -e "\\n>> [`date`] Deploying pycbc_inspiral${PYCBC_INSPIRAL_SUFFIX} to CVMFS"
ssh ouser.ligo@oasis-login.opensciencegrid.org "mkdir -p ${BUNDLE_DEST}"
scp ${BUILD}/pycbc-build/environment/dist/pycbc_inspiral${PYCBC_INSPIRAL_SUFFIX} ouser.ligo@oasis-login.opensciencegrid.org:${BUNDLE_DEST}/pycbc_inspiral
ssh ouser.ligo@oasis-login.opensciencegrid.org osg-oasis-update
fi
echo -e "\\n>> [`date`] pycbc_inspiral deployment complete"
fi
popd
fi
if [ "x${PYCBC_CONTAINER}" == "xpycbc_rhel_virtualenv" ] || [ "x${PYCBC_CONTAINER}" == "xpycbc_debian_virtualenv" ] ; then
if [ "x${PYCBC_CONTAINER}" == "xpycbc_rhel_virtualenv" ] ; then
echo -e "\\n>> [`date`] Building pycbc virtual environment for CentOS 7"
ENV_OS="x86_64_rhel_7"
elif [ "x${PYCBC_CONTAINER}" == "xpycbc_debian_virtualenv" ] ; then
echo -e "\\n>> [`date`] Building pycbc virtual environment for Debian"
ENV_OS="x86_64_deb_8"
apt-get -y install python-pip
apt-get -y install curl
echo "deb http://software.ligo.org/gridtools/debian jessie main" > /etc/apt/sources.list.d/gridtools.list
echo "deb http://software.ligo.org/lscsoft/debian jessie contrib" > /etc/apt/sources.list.d/lscsoft.list
apt-get update
apt-get --assume-yes --allow-unauthenticated install lscsoft-archive-keyring
apt-get update
curl -s -o pegasus-gpg.txt https://download.pegasus.isi.edu/pegasus/gpg.txt
apt-key add pegasus-gpg.txt
echo 'deb http://download.pegasus.isi.edu/wms/download/debian jessie main' > /etc/apt/sources.list.d/pegasus.list
apt-get update
apt-get -y install pegasus
apt-get -y install ligo-proxy-utils
apt-get -y install ecp-cookie-init
apt-get -y install uuid-runtime
else
echo -e "\\n>> [`date`] Unknown operating system for virtual environment build"
exit 1
fi
CVMFS_PATH=/cvmfs/oasis.opensciencegrid.org/ligo/sw/pycbc/${ENV_OS}/virtualenv
mkdir -p ${CVMFS_PATH}
VENV_PATH=${CVMFS_PATH}/pycbc-${TRAVIS_TAG}
pip install virtualenv
virtualenv ${VENV_PATH}
echo 'export PYTHONUSERBASE=${VIRTUAL_ENV}/.local' >> ${VENV_PATH}/bin/activate
echo "export XDG_CACHE_HOME=\${HOME}/cvmfs-pycbc-${TRAVIS_TAG}/.cache" >> ${VENV_PATH}/bin/activate
source ${VENV_PATH}/bin/activate
mkdir -p ${VIRTUAL_ENV}/.local
echo -e "[easy_install]\\nzip_ok = false\\n" > ~/.pydistutils.cfg
echo -e "[easy_install]\\nzip_ok = false\\n" > ${VIRTUAL_ENV}/.local/.pydistutils.cfg
echo -e "\\n>> [`date`] Upgrading pip and setuptools"
pip install --upgrade pip
pip install six packaging appdirs
pip install --upgrade setuptools
echo -e "\\n>> [`date`] Installing base python packages required to build lalsuite"
pip install "numpy>=1.6.4" "h5py>=2.5" unittest2 python-cjson Cython decorator
echo -e "\\n>> [`date`] Installing scipy"
pip install "scipy>=0.13.0" &>/dev/null
echo -e "\\n>> [`date`] Installing M2Crypto"
SWIG_FEATURES="-cpperraswarn -includeall -I/usr/include/openssl" pip install M2Crypto
echo -e "\\n>> [`date`] Installing LAL"
mkdir -p ${VIRTUAL_ENV}/src
cd ${VIRTUAL_ENV}/src
git clone https://github.com/lscsoft/lalsuite.git
cd ${VIRTUAL_ENV}/src/lalsuite
git checkout ${LALSUITE_HASH}
./00boot
./configure --prefix=${VIRTUAL_ENV}/opt/lalsuite --enable-swig-python --disable-lalstochastic --disable-lalxml --disable-lalinference --disable-laldetchar --disable-lalapps 2>&1 | grep -v checking
make -j 2 2>&1 | grep Entering
make install 2>&1 | grep Entering
echo 'source ${VIRTUAL_ENV}/opt/lalsuite/etc/lalsuite-user-env.sh' >> ${VIRTUAL_ENV}/bin/activate
deactivate
echo -e "\\n>> [`date`] Installing LALApps"
source ${VENV_PATH}/bin/activate
cd $VIRTUAL_ENV/src/lalsuite/lalapps
if [ "x${PYCBC_CONTAINER}" == "xpycbc_rhel_virtualenv" ] ; then
LIBS="-lhdf5_hl -lhdf5 -ldl -lz" ./configure --prefix=${VIRTUAL_ENV}/opt/lalsuite --enable-static-binaries --disable-lalinference --disable-lalburst --disable-lalpulsar --disable-lalstochastic 2>&1 | grep -v checking
elif [ "x${PYCBC_CONTAINER}" == "xpycbc_debian_virtualenv" ] ; then
LIBS="-L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_hl -lhdf5 -ldl -lz" ./configure --prefix=${VIRTUAL_ENV}/opt/lalsuite --enable-static-binaries --disable-lalinference --disable-lalburst --disable-lalpulsar --disable-lalstochastic 2>&1 | grep -v checking
fi
cd $VIRTUAL_ENV/src/lalsuite/lalapps/src/lalapps
make -j 2 2>&1 | grep Entering
cd $VIRTUAL_ENV/src/lalsuite/lalapps/src/inspiral
make lalapps_inspinj
cp lalapps_inspinj $VIRTUAL_ENV/bin
cd $VIRTUAL_ENV/src/lalsuite/lalapps/src/ring
make lalapps_coh_PTF_inspiral
cp lalapps_coh_PTF_inspiral $VIRTUAL_ENV/bin
echo -e "\\n>> [`date`] Installing Pegasus and DQSegDB"
pip install http://download.pegasus.isi.edu/pegasus/4.7.4/pegasus-python-source-4.7.4.tar.gz
pip install dqsegdb
echo -e "\\n>> [`date`] Install matplotlib 1.5.3"
pip install 'matplotlib==1.5.3'
echo -e "\\n>> [`date`] Installing PyCBC and dependencies"
cd /pycbc
pip install -r requirements.txt
python setup.py install
echo -e "\\n>> [`date`] Installing PyCBC PyLAL 1.0.2"
pip install "pycbc-pylal==1.0.2"
echo -e "\\n>> [`date`] Installing modules needed to build documentation"
pip install "Sphinx>=1.5.0"
pip install sphinx-rtd-theme
pip install git+https://github.com/ligo-cbc/sphinxcontrib-programoutput.git#egg=sphinxcontrib-programoutput
echo -e "\\n>> [`date`] Installing ipython and jupyter"
pip install ipython
pip install jupyter
cat << EOF >> $VIRTUAL_ENV/bin/activate
# if a suitable MKL exists, set it up
if [ -f /opt/intel/composer_xe_2015/mkl/bin/mklvars.sh ] ; then
# location on syracuse cluster
. /opt/intel/composer_xe_2015/mkl/bin/mklvars.sh intel64
elif [ -f /opt/intel/2015/composer_xe_2015/mkl/bin/mklvars.sh ] ; then
# location on atlas cluster
. /opt/intel/2015/composer_xe_2015/mkl/bin/mklvars.sh intel64
elif [ -f /ldcg/intel/2017u0/compilers_and_libraries_2017.0.098/linux/mkl/bin/mklvars.sh ] ; then
# location on cit cluster
. /ldcg/intel/2017u0/compilers_and_libraries_2017.0.098/linux/mkl/bin/mklvars.sh intel64
fi
# Use the revison 11 ROM data from CVMFS
export LAL_DATA_PATH=/cvmfs/oasis.opensciencegrid.org/ligo/sw/pycbc/lalsuite-extra/11/share/lalsimulation
EOF
deactivate
if [ "x${TRAVIS_SECURE_ENV_VARS}" == "xtrue" ] ; then
echo -e "\\n>> [`date`] Running test_coinc_search_workflow.sh"
mkdir -p /pycbc/workflow-test
pushd /pycbc/workflow-test
/pycbc/tools/test_coinc_search_workflow.sh ${VENV_PATH} ${TRAVIS_TAG}
popd
fi
if [ "x${TRAVIS_SECURE_ENV_VARS}" == "xtrue" ] ; then
echo -e "\\n>> [`date`] Setting virtual environment permissions for deployment"
find ${VENV_PATH} -type d -exec chmod go+rx {} \;
chmod -R go+r ${VENV_PATH}
echo -e "\\n>> [`date`] Deploying virtual environment ${VENV_PATH}"
echo -e "\\n>> [`date`] Deploying virtual environment to sugwg-condor.phy.syr.edu"
ssh pycbc@sugwg-condor.phy.syr.edu "mkdir -p /home/pycbc/ouser.ligo/ligo/deploy/sw/pycbc/${ENV_OS}/virtualenv/pycbc-${TRAVIS_TAG}"
rsync --rsh=ssh $RSYNC_OPTIONS -qraz ${VENV_PATH}/ pycbc@sugwg-condor.phy.syr.edu:/home/pycbc/ouser.ligo/ligo/deploy/sw/pycbc/${ENV_OS}/virtualenv/pycbc-${TRAVIS_TAG}/
if [ "x${TRAVIS_TAG}" != "xmaster" ] ; then
echo -e "\\n>> [`date`] Deploying release ${TRAVIS_TAG} to CVMFS"
# remove lalsuite source and deploy on cvmfs
rm -rf ${VENV_PATH}/src/lalsuite
ssh ouser.ligo@oasis-login.opensciencegrid.org "mkdir -p /home/login/ouser.ligo/ligo/deploy/sw/pycbc/${ENV_OS}/virtualenv/pycbc-${TRAVIS_TAG}"
rsync --rsh=ssh $RSYNC_OPTIONS -qraz ${VENV_PATH}/ ouser.ligo@oasis-login.opensciencegrid.org:/home/login/ouser.ligo/ligo/deploy/sw/pycbc/${ENV_OS}/virtualenv/pycbc-${TRAVIS_TAG}/
ssh ouser.ligo@oasis-login.opensciencegrid.org osg-oasis-update
fi
echo -e "\\n>> [`date`] virtualenv deployment complete"
fi
fi
echo -e "\\n>> [`date`] Docker script exiting"
exit 0
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