## Workstation in CUHK

# AC: [USERNAME]; PW: [PASSWORD]
$ ssh [USERNAME]@137.189.40.204
$ [PASSWORD]


ldappasswd -x -S xu4y34jxu3 -W -D 'cn=ling-wei.luo,cn=lvk,dc=cuhk-gw,dc=org'

## One has to install the following packages.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
libframe
metato
xml2
fftw3
gsl
hdf5 (zlib, sztp)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


## Add new command into .bashrc file

$ vim .bashrc
===============================================================
#-------------------- New command --------------------#
LOCAL_SRC=${HOME}/src # Location to store source codes locally. Change if necessary.
LOCAL_PREFIX=${HOME} # Location to install libraries locally. Change if necessary.

export LD_LIBRARY_PATH="${LOCAL_PREFIX}/lib:${LD_LIBRARY_PATH}"
export C_INCLUDE_PATH="${LOCAL_PREFIX}/include:${C_INCLUDE_PATH}"
export CPLUS_INCLUDE_PATH="${LOCAL_PREFIX}/include:${CPLUS_INCLUDE_PATH}"
export LIBRARY_PATH="${LOCAL_PREFIX}/lib:${LIBRARY_PATH}"
export PKG_CONFIG_PATH="${LOCAL_PREFIX}/lib/pkgconfig:${PKG_CONFIG_PATH}"
export PATH="${LOCAL_PREFIX}/bin:${PATH}"
===============================================================

# Reload the .bashrc file.
$ source .bashrc 

$ mkdir $LOCAL_SRC
$ ll
$ cd src
$ src

----------
## Install fftw3

$ mkdir fftw3
$ cd fftw3
$ wget http://www.fftw.org/fftw-3.3.8.tar.gz
$ tar -xzvf fftw-3.3.8.tar.gz
$ rm -r fftw-3.3.8.tar.gz 
$ cd fftw-3.3.8/
$ ./configure --prefix=${LOCAL_PREFIX} --enable-shared --enable-static --enable-threads
$ make
$ make install
$ make clean
$ ./configure --prefix=${LOCAL_PREFIX} --enable-float --enable-shared --enable-static --enable-threads
$ make 
$ make install
$ make clean

----------
## Install gsl

$ cd $LOCAL_SRC
$ mkdir gsl
$ cd gsl
$ wget http://ftp.yzu.edu.tw/gnu/gsl/gsl-2.5.tar.gz
$ tar -xzvf gsl-2.5.tar.gz
$ rm -r gsl-2.5.tar.gz
$ cd gsl-2.5
$ ./configure --prefix=${LOCAL_PREFIX}
$ make
$ make install
$ make clean

----------
## Install zlib

$ cd $LOCAL_SRC
$ mkdir zlib
$ cd zlib
$ wget https://zlib.net/zlib-1.2.11.tar.gz
$ tar -xzvf zlib-1.2.11.tar.gz
$ rm -r zlib-1.2.11.tar.gz
$ cd zlib-1.2.11
$ ./configure --prefix=${LOCAL_PREFIX}
$ make
$ make install
$ make clean

----------
## Install szip

$ cd ${LOCAL_SRC}
$ mkdir szip
$ cd szip
$ wget https://support.hdfgroup.org/ftp/lib-external/szip/2.1.1/src/szip-2.1.1.tar.gz
$ tar -xzvf szip-2.1.1.tar.gz
$ rm -r szip-2.1.1.tar.gz
$ cd szip-2.1.1
$ ./configure --prefix=${LOCAL_PREFIX}
$ make
$ make install
$ make clean

----------
## Install hdf5

$ cd $LOCAL_SRC
$ mkdir hdf5
$ cd hdf5
$ wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.4/src/hdf5-1.10.4.tar.gz
$ tar -xzvf hdf5-1.10.4.tar.gz
$ rm -r hdf5-1.10.4.tar.gz
$ cd hdf5-1.10.4

# 1) If zlib is ignore to install.
$ ./configure --prefix=${LOCAL_PREFIX} --enable-shared --enable-static --enable-hl 

# 2) If zlib is installed.
$ ./configure --prefix=${LOCAL_PREFIX} --with-zlib=${LOCAL_PREFIX} --with-szlib=${LOCAL_PREFIX} --enable-shared --enable-static --enable-hl
$ make
$ make install
$ make clean

----------
## Install libframe

# Because one needs the autoconf package without root, remember to login LIGO-VM first
$ ssh LIGO-VM
$ [PASSWORD]
$ cd $LOCAL_SRC
$ mkdir libframe
$ cd libframe
$ wget http://lappweb.in2p3.fr/virgo/FrameL/libframe-8.33.tar.gz
$ tar -xzvf libframe-8.33.tar.gz
$ ls
$ rm -r libframe-8.33.tar.gz
$ cd v8r33
# Go to the diretory again
$ cd src/libframe/v8r33/
$ autoreconf
$ ./configure --prefix=${LOCAL_PREFIX}
$ make
$ make install
$ make clean

----------
## Install metaio

$ cd ${LOCAL_SRC}
$ git clone https://git.ligo.org/lscsoft/metaio.git
$ cd metaio
$ git checkout branch-8.4.x
$ ./00boot
$ ./configure --prefix=${LOCAL_PREFIX} --without-matlab
$ make
$ make install
$ make clean

----------
## Create a directory for the python packages because of no permission

$ mkdir -p $LOCAL_PREFIX/lib/python2.7/site-packages

----------
## Install xml2 ---> It is necessary if one need to use pycbc.

$ cd $LOCAL_SRC
$ mkdir xml2
$ cd xml2
$ wget ftp://xmlsoft.org/libxml2/libxml2-2.9.9-rc2.tar.gz
$ tar -xzvf libxml2-2.9.9-rc2.tar.gz
$ rm -r libxml2-2.9.9-rc2.tar.gz
$ cd libxml2-2.9.9
$ ./configure --prefix=${LOCAL_PREFIX}
$ make
$ make install
$ make clean


----------
## Install lalsuite

$ cd $LOCAL_SRC
$ git clone https://github.com/lscsoft/lalsuite.git
$ cd lalsuite
$ git checkout lalinference_o2
$ git checkout
$ ./00boot
$ ./configure --prefix=${LOCAL_PREFIX}
$ make
$ make install
$ make clean

----------
## Check generated files

lalapps-user-env.csh       lalmetaio-user-env.sh
lalapps-user-env.sh        lalpulsar-user-env.csh
lalburst-user-env.csh      lalpulsar-user-env.sh
lalburst-user-env.sh       lalsimulation-user-env.csh
laldetchar-user-env.csh    lalsimulation-user-env.sh
laldetchar-user-env.sh     lalstochastic-user-env.csh
lalframe-user-env.csh      lalstochastic-user-env.sh
lalframe-user-env.sh       lalsuiterc
lalinference-user-env.csh  lal-user-env.csh
lalinference-user-env.sh   lal-user-env.sh
lalinspiral-user-env.csh   lalxml-user-env.csh
lalinspiral-user-env.sh    lalxml-user-env.sh
lalmetaio-user-env.csh

# ``lalsuiterc'' is the top-level LALSuite runtime.
----------
## Options of bash file

## Option 1
## Follow the instruciton, add the following lines to ~/.profile for Bourne shells (e.g. bash):
$ vim ~/.profile
===============================================================
. ${LOCAL_PREFIX}/etc/lalsuiterc
===============================================================
$ source ~/.profile

## Option 2 
## , or to ~/.login for C shells (e.g. tcsh):
$ vim ~/.login
===============================================================
source ${LOCAL_PREFIX}/etc/lalsuiterc
===============================================================
$ source ~/.login

## Option 3
$ vim ~/.bashrc
## Add the following line to .bashrc
===============================================================
source ${LOCAL_PREFIX}/etc/lalsuiterc
===============================================================
$ source ~/.bashrc



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

## source lalsuite

$ cd /home/ling-wei.luo/etc
$ . lalsimulation-user-env.sh
$ . lalinference-user-env.sh
$ . lalinspiral-user-env.sh

$ mkdir /home/ling-wei.luo/2019_NTHU_visit/example1
$ cd /home/ling-wei.luo/2019_NTHU_visit/example1


## Simulation
# Be aware that the first blank is `tab' rather than `space'.
$ vim makefile
===============================================================
all: IMRPhenomPv2.hdf5

IMR_injection.xml:
	lalapps_inspinj  --output IMR_injection.xml  --seed 0  --f-lower 40  --gps-start-time 966384015  --gps-end-time 966470415  --t-distr uniform  --time-step 3600  --time-interval 20  --i-distr uniform  --l-distr random  --d-distr uniform  --min-distance 200000 --max-distance 200000 --m-distr fixMasses --fixed-mass1 15.0 --fixed-mass2 15.0 --disable-spin --amp-order -1 --waveform  IMRPhenomPv2threePointFivePN  --taper-injection start


IMRPhenomPv2.hdf5:IMR_injection.xml
	lalinference_nest --progress --L1-timeslide 0 --L1-flow 40 --approx IMRPhenomPv2threePointfivePN --nlive 16 --srate 8192 --seglen 4 --L1-channel L1:DCS-CALIB_STRAIN_C02 --H1-channel H1:DCS-CALIB_STRAIN_C02 --fix-distance 200 --trigtime 966387623 --dt 0.1 --maxmcmc 16 --deltalogl 5 --L1-cache LALSimAdLIGO --ifo L1 --H1-cache LALSimAdLIGO --ifo H1 --randomseed 108107666 --amporder 0 --psdstart 966384026 --psdlength 128 --outfile IMRPhenomPv2.hdf5 --disable-spin --dataseed 8000 --inj $^ --event 1 --pinparams [mass1,mass2,time,distance,declination,rightascension,polarisation,phase,costheta_jn]
===============================================================

# injection -> simulation
# lalapps_inspinj -> to load an injection table
# "	"lalapps_inspinj -> TAB+lalapps_inspinj
# --amp-order -1 -> post-Newtonian (PN) approx. for all stage of the injection
# -1 -> the most accurate choice 
# 1 PN order -> 1/2 = 0.5th PN order
# ...
# 8 PN order -> 8/2 = 4th PN order (However we do not have 4th PN order now!)
# detail can be found in the file /lalsuite/lalsimulation/src/LALSimInspiralTaylorEt.c
# 

## For test GR
$ mkdir /home/ling-wei.luo/2019_NTHU_visit/testgr
$ cd /home/ling-wei.luo/2019_NTHU_visit/testgr
$ vim makefile
===============================================================
all: IMRPhenomPv2.hdf5

IMR_injection.xml:
	lalapps_inspinj  --output IMR_injection.xml  --seed 0  --f-lower 40  --gps-start-time 966384015  --gps-end-time 966470415  --t-distr uniform  --time-step 3600  --time-interval 20  --i-distr uniform  --l-distr random  --d-distr uniform  --min-distance 200000 --max-distance 200000 --m-distr fixMasses --fixed-mass1 15.0 --fixed-mass2 15.0 --disable-spin --amp-order -1 --waveform  IMRPhenomPv2threePointFivePN  --taper-injection start


IMRPhenomPv2.hdf5:IMR_injection.xml
	lalinference_nest --progress --L1-timeslide 0 --L1-flow 40 --approx IMRPhenomPv2threePointfivePN --nlive 16 --srate 8192 --seglen 4 --L1-channel L1:DCS-CALIB_STRAIN_C02 --H1-channel H1:DCS-CALIB_STRAIN_C02 --fix-distance 200 --trigtime 966387623 --dt 0.1 --maxmcmc 16 --deltalogl 5 --L1-cache LALSimAdLIGO --ifo L1 --H1-cache LALSimAdLIGO --ifo H1 --randomseed 108107666 --amporder 0 --psdstart 966384026 --psdlength 128 --outfile IMRPhenomPv2.hdf5 --disable-spin --dataseed 8000 --inj $^ --event 1 --pinparams [mass1,mass2,time,distance,declination,rightascension,polarisation,phase,costheta_jn] --grtest-parameters dchi2
===============================================================

# details of dchi2 can be found in the file /lalsuite/lalinference/src/LALInferenceInitCBC.c

# Remember to put --Resume when you work on the cluster!!!
# Zratio -> log(Zratio) -> it should not be too low!