Revision 94d00b8eef1242b10cecd053f21710a796c467b4 authored by spxiwh on 22 September 2016, 14:14:24 UTC, committed by Alex Nitz on 22 September 2016, 14:14:24 UTC
1 parent 64c1ed1
install_pycbc.sh
#!/bin/bash
# Copyright 2015 Amber Lenon, Steve Reyes, Duncan Brown, Larne Pekowsky, Soumi De.
# Exit if any command fails
set -e
# this makes sure everything is logged to a file
LOGPATH=${PWD}/install_pycbc_`date +%Y%m%d%H%M%S`.log
if [ "$1" != "noscript" ] ; then
# just in case the user is calling us via bash or sh
chmod +x $0
exec script -q -c "$0 noscript" ${LOGPATH}
exit 1;
fi
# Clear all environment variables except the ones we need
KEEP="+USER+HOME+UID+SSH_AUTH_SOCK+SSH_AGENT_PID+TMPDIR+tmpdir+"
set +e
for name in $(env | cut -d '=' -f 1); do
if [[ $KEEP != *${name}* ]] ; then
# Some variables can't be unset, that's OK
unset $name 2>/dev/null
fi
done
set -e
export PATH=/usr/bin:/bin:/usr/sbin:/sbin
export _CONDOR_DAGMAN_LOG_ON_NFS_IS_ERROR=FALSE
# Make sure there's nothing lingering from previous builds
if [[ -e ${HOME}/.local ]]
then
while true; do
echo "Existing .local directory found, this can interfere with the build process."
echo "Should I delete this directory (recommended)?"
echo
read -p "Enter yes or no: " DELETE_DOT_LOCAL
echo
if [[ $DELETE_DOT_LOCAL == "yes" ]] ; then
rm -rf ${HOME}/.local
echo ".local deleted"
break
elif [[ $DELETE_DOT_LOCAL == "no" ]] ; then
echo "Preserving .local"
break
else
echo "Please enter yes or no."
fi
done
fi
# Set up Python
while true; do
echo "Do you want to use the OSG build of Python 2.7?"
echo
echo "This is used for building bundled executables for use on OSG."
echo "If you are not sure, say no to use the standard system Python."
echo
read -p "Enter yes or no: " OSG_PYTHON
echo
if [[ $OSG_PYTHON == "yes" ]] ; then
if [ ! -e /cvmfs/oasis.opensciencegrid.org/osg/modules/lmod/current/init/bash ] ; then
echo "Error: Could not find script to set up OSG modules."
echo "Check that /cvmfs/oasis.opensciencegrid.org is mounted on this machine."
exit 1
fi
set +e
source /cvmfs/oasis.opensciencegrid.org/osg/modules/lmod/current/init/bash
set -e
module load python/2.7
break
elif [[ $OSG_PYTHON == "no" ]] ; then
break
else
echo "Please enter yes or no."
fi
done
py_path=`which python`
py_ver=`python --version 2>&1`
echo "Using Python from ${py_path} which is ${py_ver}"
echo
#Make a temporary directory and install pip into it
echo "--- installing pip and virtualenv into temporary directory ------"
echo
PY_VERSION=`python -c 'import sys; print "%d.%d" % (sys.version_info[0], sys.version_info[1])'`
OLD_PATH=$PATH
OLD_PYTHONPATH=$PYTHONPATH
PIP_DIR=`mktemp --tmpdir -d -t pip-XXXXXXXXXX`
PIP_PYTHONPATH=${PIP_DIR}/lib/python${PY_VERSION}/site-packages
mkdir -p ${PIP_PYTHONPATH}
export PATH=${PIP_DIR}/bin:${PATH}
export PYTHONPATH=${PIP_PYTHONPATH}:${PYTHONPATH}
easy_install --prefix=${PIP_DIR} https://pypi.python.org/packages/source/p/pip/pip-7.1.0.tar.gz#md5=d935ee9146074b1d3f26c5f0acfd120e
export PYTHONUSERBASE=`mktemp --tmpdir -d -t virtualenv-XXXXXXXXXX`
pip --no-cache install virtualenv --user --ignore-installed --upgrade
export PATH=${PYTHONUSERBASE}/bin:${PATH}
export PYTHONPATH=${PYTHONUSERBASE}/lib/python${PY_VERSION}/site-packages:${OLD_PYTHONPATH}
#Installing pyCBC
while true ; do
echo
echo "Are you installing a virtualenv to build bundled exectuables for distribution?"
read -p "Enter yes or no (if you are not sure, say no): " IS_BUNDLE_ENV
if [[ $IS_BUNDLE_ENV == "yes" ]] ; then
UNIQUE_ID=pycbc-`uuidgen`
NAME=${HOME}/${UNIQUE_ID}
break
elif [[ $IS_BUNDLE_ENV == "no" ]] ; then
while true; do
# Ask the user where they want pycbc installed
read -p "Enter the location where you want the virtual env created: " NAME
if [[ $NAME == ~* ]] ; then
if [[ ! "$NAME" =~ "/" ]] ; then
NAME=${HOME}
else
# chomp the ~
NAME=${NAME/##~}
# chomp anything else before the first slash to catch e.g. ~alenon/
NAME=${NAME#*\/}
# expand to the user's home directory
NAME=${HOME}/${NAME}
fi
fi
if [[ -z $NAME ]] ; then
echo "ERROR: you must specify a path for your virtual environment."
continue
fi
if [[ -d $NAME ]] ; then
echo "ERROR: the directory $NAME already exists."
echo "Do you want to remove the previous directory and overwrite the existing location?"
echo
read -p "Enter yes or no: " DEL_EXISTING_VIRTENV
echo
if [[ $DEL_EXISTING_VIRTENV == "yes" ]] ; then
echo "Deleting previous virtual environment directory with the same name"
rm -rf $NAME
break
elif [[ $DEL_EXISTING_VIRTENV == "no" ]] ; then
echo "You have to enter a new location for your virtual environment."
else
echo "Please enter yes or no."
fi
else
break
fi
done
break
else
echo "Please enter yes or no."
fi
done
#Virualenv check
echo
echo "You are installing PyCBC in $NAME."
echo
#Number of Processors for the installation
read -p "Enter the number of processors that you want to use for builds: " nproc
if [[ -z $nproc ]] ; then
nproc=1
fi
if [[ $nproc -lt 1 ]] ; then
echo "ERROR: invalid number of processors specified: $nproc"
continue
fi
if [[ $nproc -gt 24 ]] ; then
echo "ERROR: please do not use more than 24 CPUs for the build. You asked for $nproc"
continue
fi
echo "Using $nproc processors for parallel build."
echo
while true ; do
#Inputs for code
#LIGO.ORG username
read -p "Enter your LIGO.ORG username in (e.g. albert.einstein): " directory
#Valid ECP cookie to clone
set +e
while true; do
echo
echo "Enter your LIGO.ORG password to get a cookie to clone lalsuite."
ecp-cookie-init LIGO.ORG https://versions.ligo.org/git $directory
if [[ $? -eq 0 ]] ; then
break
fi
done
set -e
echo
#Lalsuite
echo "--- select lalsuite branch or tag -------------------------------"
echo
echo "Enter the name of the lalsuite branch or tag that you want to use."
echo
echo "A list of branches can be found at:"
echo " https://versions.ligo.org/cgit/lalsuite/refs/heads"
echo "A list of tags can be found at:"
echo " https://versions.ligo.org/cgit/lalsuite/refs/tags"
echo
read -rp "Enter a valid tag or branch name (e.g. master or lalsuite_o1_branch): " lalbranch
#github
echo "Would you like to install a released version of PyCBC or a development copy?"
echo "Please choose either"
echo " 1. Release version"
echo " 2. Development version"
echo
read -rp "Enter either 1 or 2: " dev_or_rel
#released version
if [[ $dev_or_rel -eq 1 ]] ; then
#Installing a released version of pyCBC
#Choose release version
echo "Please enter the name of a valid release tag. These can be found at"
echo " https://github.com/ligo-cbc/pycbc/releases"
read -rp "Enter the tag name (e.g. v1.1.5): " reltag
#development
elif [[ $dev_or_rel -eq 2 ]] ; then
#Fork pyCBC to your Github account
echo
echo To install a development version, you will need a GitHub account.
echo If you do not have a github account you will need to set one up.
echo
echo Once you have set up your GitHub account, follow the instruction at
echo
echo https://help.github.com/articles/fork-a-repo/
echo
echo to fork the respository
echo
echo https://github.com/ligo-cbc/pycbc
echo
echo into your own GitHub account. You will then need to enable ssh
echo keys on your GitHub account. You can follow these instructions:
echo
echo https://help.github.com/articles/generating-ssh-keys/
echo
read -rsp $'Once you have completed these steps, hit [Enter] to continue...\n' -n1 key
echo
#Create an ssh agent to connect to GitHub
echo "Do you already have an ssh agent running with the key connected to GitHub?"
while true ; do
read -p "Enter yes or no (if you are not sure, enter no): " ssh_key
if [[ $ssh_key == "yes" ]] ; then
created_socket=""
echo "Using $SSH_AUTH_SOCK"
break
elif [[ $ssh_key == "no" ]] ; then
created_socket="yes"
echo "Creating ssh agent to connect to GitHub:"
eval `ssh-agent`
echo "Please enter your ssh key passphrase."
ssh-add
break
else
echo "ERROR: please enter yes or no."
fi
done
#Input Username
read -rp "GitHub Username: " github
else
echo "You must enter 1 or 2."
fi
#MKL Optimized Code
echo "To run MKL optimized code, you need to enter the path and architecture"
echo "for the Intel optimized toolkit on your cluster. For example:"
echo "on sugar, enter"
echo " /opt/intel/bin/compilervars.sh intel64"
echo "on atlas, enter"
echo " /opt/intel/2015/bin/compilervars.sh intel64"
echo "on ldas-grid, enter"
echo " /opt/intel/composerxe/bin/compilervars.sh intel64"
echo "If you do not have these tools installed, just press return."
echo
read -p "Enter path and architecture for Intel compilervars.sh or press return: " intel_path
#ROM Data Path
LAL_DATA_PATH=""
if [[ $IS_BUNDLE_ENV == "yes" ]] ; then
check_rom="no"
else
check_rom="yes"
while true; do
echo
read -rp "Is the LAL Reduce Order Model (ROM) data installed on your cluster (Enter yes or no, if unsure type no)? " install_rom
if [[ ${install_rom} == "yes" ]] ; then
echo
echo "The install script will check that you have valid ROM data installed."
echo "Enter the path that contains the SEOBNRv2ROM*.dat files. This path probably"
echo "ends with lalsimulation/ if you installed the ROMS in the normal way."
echo
read -rp "Please enter the path to the ROM data: " rom_path
if [[ ${rom_path} == ~* ]] ; then
if [[ ! "${rom_path}" =~ "/" ]] ; then
rom_path=${HOME}
else
# chomp the ~
rom_path=${rom_path/##~}
# chomp anything else before the first slash to catch e.g. ~alenon/
rom_path=${rom_path#*\/}
# expand to the user's home directory
rom_path=${HOME}/${rom_path}
fi
fi
LAL_DATA_PATH="${rom_path}"
break
elif [[ ${install_rom} == "no" ]] ; then
echo
read -rp "Do you want to download the ROM data now (Enter yes or no): " rom_download
if [[ ${rom_download} == "no" ]] ; then
echo
echo "Warning: SEOBNRv2ROM waveforms will not work without the ROM data"
echo
check_rom="no"
break
elif [[ ${rom_download} == "yes" ]] ; then
echo
read -rp "Enter the path to store the ROM data: " rom_store
if [[ ${rom_store} == ~* ]] ; then
if [[ ! "${rom_store}" =~ "/" ]] ; then
rom_store=${HOME}
break
else
# chomp the ~
rom_store=${rom_store/##~}
# chomp anything else before the first slash to catch e.g. ~alenon/
rom_store=${rom_store#*\/}
# expand to the user's home directory
rom_store=${HOME}/${rom_store}
if [ ! -d ${rom_store} ] ; then
mkdir -p ${rom_store}
fi
LAL_DATA_PATH="${rom_store}/share/lalsimulation"
echo
break
fi
fi
else
continue
fi
else
continue
fi
done
fi
echo "------------Please check the inputs carefully-----------------"
echo
echo "LIGO.ORG username: " $directory
echo "Lalsuite Branch or Tag: " $lalbranch
echo "Development or released: " $dev_or_rel
echo " (1 is release, 2 is development)"
if [[ $dev_or_rel -eq 1 ]] ; then
echo "Released Tag: " $reltag
fi
if [[ $dev_or_rel -eq 2 ]] ; then
echo "Github Username: " $github
fi
echo "Path and architecture for Intel compilervars.sh:" $intel_path
if [[ ${check_rom} == "yes" ]] ; then
if [[ ${install_rom} == "yes" ]] ; then
echo "ROM data is located in ${LAL_DATA_PATH}"
fi
if [[ ${install_rom} == "no" ]] ; then
echo "ROM data will be installed in ${LAL_DATA_PATH}"
fi
else
echo "Not installing ROM data."
fi
echo
read -rp "Are these correct? (Enter yes or no) " questions
if [[ $questions == "yes" ]] ; then
break
elif [[ $questions == "no" ]] ; then
continue
else
echo "You must enter yes or no or ctrl-c to exit."
continue
fi
done
echo
#Create a Virtual Environment
echo "--- creating virtual environment --------------------------------"
VIRTENV_INSTALL_DIR=${PYTHONUSERBASE}
unset PYTHONUSERBASE
virtualenv $NAME
rm -rf ${VIRTENV_INSTALL_DIR}
rm -rf ${PIP_DIR}
echo
echo "--- setting up activate script ----------------------------------"
echo
mv $NAME/bin/activate $NAME/bin/activate.bak
if [[ $OSG_PYTHON == "yes" ]] ; then
cat >$NAME/bin/activate <<EOF
# Load OSG Python module
source /cvmfs/oasis.opensciencegrid.org/osg/modules/lmod/current/init/bash
module load python/2.7
EOF
else
touch $NAME/bin/activate
fi
echo "export XDG_CACHE_HOME=${NAME}/.cache" >> $NAME/bin/activate
echo "export PYTHONUSERBASE=${NAME}/.local" >> $NAME/bin/activate
if [[ ! -z "${intel_path}" ]] ; then
echo "source ${intel_path}" >> ${NAME}/bin/activate
fi
cat $NAME/bin/activate.bak >> $NAME/bin/activate
#Enter Virtual Environment
echo
echo "--- entering virtual environment --------------------------------"
echo
set +e
source $NAME/bin/activate
set -e
mkdir -p $VIRTUAL_ENV/src
#Set up the software for the virtual environment
echo "--- installing required packages --------------------------------"
#Install Pegasus WMS python libraries
pip install http://download.pegasus.isi.edu/pegasus/4.6.1/pegasus-python-source-4.6.1.tar.gz
if [[ $dev_or_rel -eq 1 ]] ; then
#Installing a released version of pyCBC
curl https://raw.githubusercontent.com/ligo-cbc/pycbc/${reltag}/requirements.txt > ${VIRTUAL_ENV}/requirements.txt
sed -i 's/https:\/\/github.com\/duncan-brown\/dqsegdb.git/git+https:\/\/github.com\/duncan-brown\/dqsegdb.git/g' ${VIRTUAL_ENV}/requirements.txt
sed -i '/MySQL-python\|psycopg2/d' ${VIRTUAL_ENV}/requirements.txt
perl -pi.bak -e 's/pegasus-wms==4.5.2/pegasus-wms==4.6.1/g' ${VIRTUAL_ENV}/requirements.txt
pylal_version=`grep pycbc-pylal ${VIRTUAL_ENV}/requirements.txt`
glue_version=`grep pycbc-glue ${VIRTUAL_ENV}/requirements.txt`
mv ${VIRTUAL_ENV}/requirements.txt ${VIRTUAL_ENV}/requirements.txt.bak
grep -v pycbc-pylal ${VIRTUAL_ENV}/requirements.txt.bak | grep -v pycbc-glue > ${VIRTUAL_ENV}/requirements.txt
set +e
HDF5_DIR=${VIRTUAL_ENV} pip install -r ${VIRTUAL_ENV}/requirements.txt
set -e
HDF5_DIR=${VIRTUAL_ENV} pip install -r ${VIRTUAL_ENV}/requirements.txt
else
# Upgrade pip to get rid of any warnings
pip install --upgrade pip
pip install "numpy>=1.6.4" unittest2 python-cjson Cython
pip install "nose>=1.0.0"
HDF5_DIR=${VIRTUAL_ENV} pip install h5py
pylal_version="pycbc-pylal"
glue_version="pycbc-glue"
fi
pip install git+http://github.com/ligo-cbc/pyinstaller.git@pycbc_install#egg=pyinstaller
#Authenticate with LIGO Data Grid services, install M2Crypto
SWIG_FEATURES="-cpperraswarn -includeall -I/usr/include/openssl" pip install M2Crypto
echo
echo
echo "--- cloning lalsuite repository -----------------------------------"
echo
#Valid ECP cookie to clone
#Tell git the location of the cookie
git config --global http.cookiefile /tmp/ecpcookie.u`id -u`
#Get Copy of LalSuite Repository
LALSUITE_BUILD_DIR=`mktemp --tmpdir -d -t lalsuite-XXXXXXXXXX`
echo " LALSUITE_BUILD_DIR= "
echo "${LALSUITE_BUILD_DIR}"
ln -sf ${LALSUITE_BUILD_DIR} $VIRTUAL_ENV/src/lalsuite
cd $VIRTUAL_ENV/src/lalsuite
git clone https://versions.ligo.org/git/lalsuite.git
#Obtaining source code and checking version
#Change to lalsuite directory
cd lalsuite
#Upgrade numpy
pip install --upgrade numpy
#Determine which version of the code you want to install
echo
git checkout $lalbranch
#Building and Installing into your Virtual Environment
#Use the master configure script to build and install all the components
echo
echo "--- building lalsuite -------------------------------------------"
echo
./00boot
./configure --prefix=${VIRTUAL_ENV}/opt/lalsuite --enable-swig-python --disable-lalstochastic --disable-lalxml --disable-lalinference --disable-laldetchar --disable-lalapps --with-hdf5=no
make -j $nproc
make install
#Add to virtualenv activate script
echo 'source ${VIRTUAL_ENV}/opt/lalsuite/etc/lalsuiterc' >> ${VIRTUAL_ENV}/bin/activate
source ${VIRTUAL_ENV}/opt/lalsuite/etc/lalsuiterc
#Build a static lalapps_inspinj and install it
cd $VIRTUAL_ENV/src/lalsuite/lalsuite/lalapps
LIBS=-lz ./configure --prefix=${VIRTUAL_ENV}/opt/lalsuite --enable-static-binaries --disable-lalinference --disable-lalburst --disable-lalpulsar --disable-lalstochastic
cd $VIRTUAL_ENV/src/lalsuite/lalsuite/lalapps/src/lalapps
make -j $nproc
cd $VIRTUAL_ENV/src/lalsuite/lalsuite/lalapps/src/inspiral
make lalapps_inspinj
cp lalapps_inspinj $VIRTUAL_ENV/bin
cd $VIRTUAL_ENV/src/lalsuite/lalsuite/lalapps/src/ring
make lalapps_coh_PTF_inspiral
cp lalapps_coh_PTF_inspiral $VIRTUAL_ENV/bin
#Check that lalsuite is installed
echo "LAL installed into $LAL_PREFIX"
#Installing pyCBC to Virtual Environment
echo
echo "--- installing dqsegdb ------------------------------------------"
echo
#Install dqsegb from Duncan's repository
pip install git+https://github.com/ligo-cbc/dqsegdb.git@pypi_release#egg=dqsegdb
#Install gracedb client tools
pip install ligo-gracedb
#Install pycbc and glue from non-cached versions to get the rpaths correct
if [[ $dev_or_rel -eq 1 ]] ; then
pip --no-cache install ${glue_version} ${pylal_version}
else
pip --no-cache install git+https://github.com/ligo-cbc/pycbc-glue.git
pip --no-cache install git+https://github.com/ligo-cbc/pycbc-pylal.git
fi
#ROM Data Download
if [[ ${install_rom} == "no" ]] ; then
if [[ ${rom_download} == "yes" ]] ; then
pushd ${VIRTUAL_ENV}/src
echo "--- Downloading ROM DATA ---------------------------------"
svn co -r 7 https://svn.ligo.caltech.edu/svn/lalsuite-extra/
pushd lalsuite-extra
./00boot
./configure --prefix=${rom_store}
make install
popd
popd
fi
fi
#ROM Data Validation
if [[ ${check_rom} == "yes" ]] ; then
echo "--- checking rom data -------------------------------------------"
rom_files=('SEOBNRv1ROM_DS_Amp_ciall.dat' 'SEOBNRv1ROM_DS_AmpPrefac_ci.dat' 'SEOBNRv1ROM_DS_Bamp_bin.dat' 'SEOBNRv1ROM_DS_Bphase_bin.dat' 'SEOBNRv1ROM_DS_Phase_ciall.dat' 'SEOBNRv1ROM_SS_Amp_ciall.dat' 'SEOBNRv1ROM_SS_AmpPrefac_ci.dat' 'SEOBNRv1ROM_SS_Bamp_bin.dat' 'SEOBNRv1ROM_SS_Bphase_bin.dat' 'SEOBNRv1ROM_SS_Phase_ciall.dat' 'SEOBNRv2ChirpTimeSS.dat' 'SEOBNRv2ROM_DS_HI_v1.0.hdf5' 'SEOBNRv2ROM_DS_sub1_Amp_ciall.dat' 'SEOBNRv2ROM_DS_sub1_AmpPrefac_ci.dat' 'SEOBNRv2ROM_DS_sub1_Bamp_bin.dat' 'SEOBNRv2ROM_DS_sub1_Bphase_bin.dat' 'SEOBNRv2ROM_DS_sub1_Phase_ciall.dat' 'SEOBNRv2ROM_DS_sub2_Amp_ciall.dat' 'SEOBNRv2ROM_DS_sub2_AmpPrefac_ci.dat' 'SEOBNRv2ROM_DS_sub2_Bamp_bin.dat' 'SEOBNRv2ROM_DS_sub2_Bphase_bin.dat' 'SEOBNRv2ROM_DS_sub2_Phase_ciall.dat' 'SEOBNRv2ROM_DS_sub3_Amp_ciall.dat' 'SEOBNRv2ROM_DS_sub3_AmpPrefac_ci.dat' 'SEOBNRv2ROM_DS_sub3_Bamp_bin.dat' 'SEOBNRv2ROM_DS_sub3_Bphase_bin.dat' 'SEOBNRv2ROM_DS_sub3_Phase_ciall.dat' 'SEOBNRv2ROM_SS_Amp_ciall.dat' 'SEOBNRv2ROM_SS_AmpPrefac_ci.dat' 'SEOBNRv2ROM_SS_Bamp_bin.dat' 'SEOBNRv2ROM_SS_Bphase_bin.dat' 'SEOBNRv2ROM_SS_Phase_ciall.dat')
rom_hash=('0cc069d487b72ab8ebf0df690c01d4ba' '9b4f4eacd9151a20acfb0a08e30ac49f' 'db884a753b6f0a7516af12915472cb15' '9faae84c8c9d376681baac029955c47a' '2261539962b88cd32f383c67ff6f1893' 'ecebe37ead05afa211b0a5619c4d1d1c' '97ab150b8e558d2cd9a0d0123584eec5' 'f8249222f0ac0b9878e0a96516633cff' 'fea200dc979f2dd50dfc84feb57a433d' 'b8651dde261001c0600e066a3aa9dadf' '7b7dbadacc3f565fb2c8e6971df2ab74' 'b22c167bd665c6de1debd05038251a72' 'f82ddc5dc0b6fdc75122e767bd5e78c8' '62afa5351d6b775ac33cb4d898f0016b' 'a6829fa05437cc0aad81e3f8dae839cc' '98ea14b01e729d15ff666caa25afaed6' 'b41f0f7fbaf8be1d1848de7ee702bc67' '20ee260c870109766a6f048e20c7e10f' '96c384617edd8375ceaa03f9b7456467' '67d4f206fe19104fbc98b923b37318bb' 'd0bf97b4e17b5c9a7cfd222aaaafd742' 'c2ea5d296fee01abe16c0dd9e5f71f04' '412953726ca4bc72a810b27b810831c7' '4d5378935a7fba5e96f671581bce99fb' '31f48cb651a60837a3e99ee050aa9bc2' '727d31f6dc678aba8539817c8d0ae930' 'd0e1601c7cf4bd727d03e6cf7d2f722b' 'e6c243f76609cada55612cfe53f82e41' '08186a21682d2e73cb00a3ef35aa5c9c' '1ef7953a977a1fb551f59585c5d63d7a' 'b5923860bf021e6a2a23d743e5724bee' '2947032d0ad7ffde9704e24bf9e676f5')
md5sum_hash=()
for rom_dat_file in "${rom_files[@]}" ; do
hash=$( echo -n 'test' | md5sum ${LAL_DATA_PATH}/${rom_dat_file} | cut -d' ' -f1)
md5sum_hash+=(${hash})
done
for((j=0;j<${#rom_files[@]};j++)) ; do
if [[ ${rom_hash[j]} == ${md5sum_hash[j]} ]] ; then
echo "ROM file ${rom_files[j]} is OK."
else
echo "Error: ROM checksum for ${rom_files[j]} is bad or file is missing."
exit 1
fi
done
echo "All files are in ${LAL_DATA_PATH}."
echo "export LAL_DATA_PATH=${LAL_DATA_PATH}" >> ${VIRTUAL_ENV}/bin/activate
fi
#Released or Development
echo
echo "--- downloading PyCBC -------------------------------------------"
echo
echo
while true ; do
if [[ $dev_or_rel -eq 1 ]] ; then
#Installing a released version of pyCBC
pip install -e git+https://github.com/ligo-cbc/pycbc@${reltag}#egg=pycbc --process-dependency-links
rm -f ${VIRTUAL_ENV}/src/pip-delete-this-directory.txt
# continue with install
break
elif [[ $dev_or_rel -eq 2 ]] ; then
#Fork pyCBC to your Github account
echo
#Install PyCBC source code from GitHub URL
pip install -e git+git@github.com:${github}/pycbc.git#egg=pycbc --process-dependency-links
#Prevent Pip from removing source directory
rm -f ${VIRTUAL_ENV}/src/pip-delete-this-directory.txt
#Connect the user to the main PyCBC repo and bring in the objects
cd ${VIRTUAL_ENV}/src/pycbc
git remote add upstream git@github.com:ligo-cbc/pycbc.git
git fetch upstream
#Continue with install
break
else
echo "You must enter 1 or 2."
fi
done
#Build static sbank
echo
echo "--- building static version of lalapps sbank tools --------------"
echo
LALAPPS_INSPIRAL_DIR=${VIRTUAL_ENV}/src/lalsuite/lalsuite/lalapps/src/inspiral
pushd ${LALAPPS_INSPIRAL_DIR}
mkdir -p ${LALAPPS_INSPIRAL_DIR}/site-packages/lalapps
touch ${LALAPPS_INSPIRAL_DIR}/site-packages/lalapps/__init__.py
cp -v ${LALAPPS_INSPIRAL_DIR}/inspiral.py ${LALAPPS_INSPIRAL_DIR}/site-packages/lalapps/
TMP_PYTHONPATH=${PYTHONPATH}
export PYTHONPATH=${LALAPPS_INSPIRAL_DIR}/site-packages:${PYTHONPATH}
export PYINSTALLER_CONFIG_DIR=`mktemp --tmpdir -d -t pyinstaller-XXXXXXXXXX`
for prog in lalapps_cbc_sbank_choose_mchirp_boundaries lalapps_cbc_sbank_merge_sims lalapps_cbc_sbank_pipe lalapps_cbc_sbank lalapps_cbc_sbank_sim
do
pyinstaller ${prog}.py \
--hidden-import scipy.linalg.cython_blas \
--hidden-import scipy.linalg.cython_lapack \
--hidden-import scipy.special._ufuncs_cxx \
--hidden-import scipy.integrate \
--strip \
--onefile
cp dist/${prog} $VIRTUAL_ENV/bin
done
popd
rm -rf ${PYINSTALLER_CONFIG_DIR}
unset PYINSTALLER_CONFIG_DIR
export PYTHONPATH=${TMP_PYTHONPATH}
if [[ $dev_or_rel -eq 2 ]] ; then
#Building and Installing Documentation
#Install Sphinx and the helper tools
echo
echo "--- downloading documentation tools -----------------------------"
echo
pip install "Sphinx>=1.3.1"
pip install sphinxcontrib-programoutput
pip install numpydoc
#patch the bug in numpydoc for python 2.6
cat <<EOF > ${VIRTUAL_ENV}/plot_directive.patch
--- lib/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py 2015-09-26 13:48:46.000000000 -0400
+++ lib/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py 2015-09-24 20:59:35.843029957 -0400
@@ -333,8 +333,13 @@
"""
Remove the coding comment, which six.exec_ doesn't like.
"""
- return re.sub(
+ try:
+ return re.sub(
"^#\s*-\*-\s*coding:\s*.*-\*-$", "", text, flags=re.MULTILINE)
+ except TypeError:
+ return re.sub(
+ "^#\s*-\*-\s*coding:\s*.*-\*-$", "", text, re.MULTILINE)
+
#------------------------------------------------------------------------------
# Template
EOF
set +e
patch -f -p0 ${VIRTUAL_ENV}/lib/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py < ${VIRTUAL_ENV}/plot_directive.patch
if [[ $? -eq 0 ]] ; then
echo "patched sphinxext/plot_directive.py successfully"
else
echo "patch to sphinxext/plot_directive.py failed"
echo "plots in documentation build may not work"
fi
rm ${VIRTUAL_ENV}/plot_directive.patch
set -e
fi
echo
if [[ ! -z "$create_agent" ]] ; then
echo "Terminating ssh agent $SSH_AGENT_PID"
kill -TERM $SSH_AGENT_PID
fi
echo
echo "=================================================================="
echo
echo "PyCBC has been installed in a virtual environment in the directory"
echo
echo " ${VIRTUAL_ENV}"
echo
echo "To use this virtual environment run the command"
echo
echo " source ${VIRTUAL_ENV}/bin/activate"
echo
if [[ $dev_or_rel -eq 2 ]] ; then
echo "A clone of your PyCBC repository has been placed in the directory"
echo
echo " ${VIRTUAL_ENV}/src/pycbc"
echo
echo "and connected to the ligo-cbc/pycbc repository as 'upstream.'"
echo
echo "You can use this repository to edit and make changes to the code."
echo "To install your updated code in your virtual environment, first"
echo "make sure you have run the activate script, then from the directory"
echo
echo " ${VIRTUAL_ENV}/src/pycbc"
echo
echo "run the command"
echo
echo " python setup.py install"
echo
fi
if [[ $IS_BUNDLE_ENV == "yes" ]] ; then
echo
echo "=================================================================="
echo
echo "Making bundled executables."
echo
echo "Virtual env directory is:"
echo " ${VIRTUAL_ENV}"
read -rp "Ready to continue? If yes hit [Enter] " ready
#Make the dag that makes the bundles
cd ${VIRTUAL_ENV}/src/pycbc/tools/static
mkdir dist
perl -pi.bak -e 's+log = /usr1/\${USER}/log/pyinstaller_build_1.log+log = \${PWD}/pyinstaller_build_1.log+g' build_dag.sh
bash build_dag.sh
sed -i.bak "2 a cd ${VIRTUAL_ENV}/src/pycbc/tools/static " build_one.sh
if [[ $OSG_PYTHON == "yes" ]] ; then
perl -pi.bak -e 's+universe = vanilla+universe = local+' build_one.sub
fi
SETUPTOOLS_VER=`python -c "import setuptools; print setuptools.__version__"`
if (( $(echo "$SETUPTOOLS_VER > 19.2" | bc -l) )) ; then
yes | pip uninstall setuptools
pip install setuptools==19.2
fi
#Run the dag that makes the bundles
condor_submit_dag build_static.dag
#Build the ligolw tools
export PYINSTALLER_CONFIG_DIR=`mktemp --tmpdir -d -t pyinstaller-XXXXXXXXXX`
pushd ${VIRTUAL_ENV}/bin
for prog in ligolw_add ligolw_combine_segments ligolw_segments_from_cats_dqsegdb ligolw_segment_query_dqsegdb
do pyinstaller ${prog} --strip --onefile --hidden-import M2Crypto --hidden-import cjson --hidden-import Cookie
done
popd
rm -rf ${PYINSTALLER_CONFIG_DIR}
unset PYINSTALLER_CONFIG_DIR
# Wait for the dag to finish
condor_wait -status -echo build_static.dag.dagman.log
# Check logs
condor_check_userlogs pyinstaller_build_1.log
grep "Normal termination (return value 0)" build_static.dag.dagman.log
# Create the pycbc_submit_dax "bundle" (inline tar with config files)
./bundle_pycbc_submit_dax.sh
#Copy the existing static files into the dist directory
cp -v ${VIRTUAL_ENV}/bin/lalapps_inspinj dist/
cp -v ${VIRTUAL_ENV}/bin/lalapps_coh_PTF_inspiral dist/
for prog in lalapps_cbc_sbank_choose_mchirp_boundaries lalapps_cbc_sbank_merge_sims lalapps_cbc_sbank_pipe lalapps_cbc_sbank lalapps_cbc_sbank_sim ligolw_add ligolw_combine_segments ligolw_segments_from_cats_dqsegdb ligolw_segment_query_dqsegdb
do cp -v ${VIRTUAL_ENV}/bin/$prog dist/
done
#Copy the completed build
cp -av dist/ ${VIRTUAL_ENV}/../${UNIQUE_ID}-dist
cd ${VIRTUAL_ENV}/..
rm $VIRTUAL_ENV/src/lalsuite
mv ${LALSUITE_BUILD_DIR} $VIRTUAL_ENV/src
pushd $VIRTUAL_ENV/src
ln -s `basename ${LALSUITE_BUILD_DIR}` lalsuite
popd
tar -zcvf ${VIRTUAL_ENV}/../${UNIQUE_ID}-dist/${UNIQUE_ID}.tar.gz ${VIRTUAL_ENV}
echo
echo "=================================================================="
echo
echo "Exiting and removing Virtual Environment"
VIRTUAL_ENV_PATH=${VIRTUAL_ENV}
deactivate
rm -rf ${VIRTUAL_ENV_PATH}
echo
echo
echo "Complete."
echo
echo "Bundles are in ${UNIQUE_ID}-dist"
echo "Environment saved in ${UNIQUE_ID}.tar.gz"
echo
echo "=================================================================="
else
#Leave the virtual environment and exit
deactivate
echo "PyCBC setup complete"
fi
echo
exit 0
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