Software Installation for Pulsar Data Analysis

Research

Publish Date: 2019-01-18

1. Ubuntu Linux (64-bit)

This guide takes you through the necessary steps required to install software for pulsar data analysis on a machine running Ubuntu Linux. These notes are based on installation onto a fresh install of Ubuntu 14.04 LTS on a 64-bit machine. Please note that for installation to be successful, the software should be installed in the order described on this page.

2. Installation

2.1 Define some environmental variables

# Path to the pulsar software installation directory e.g:
export ASTROSOFT=/home/{user}/pulsar_software

# OSTYPE
export OSTYPE=linux

# BOOST
export BOOST_ROOT=$ASTROSOFT/boost_1_68_0
export BOOST_LIB=$BOOST_ROOT/stage/lib

# PSRCAT
export PSRCAT_RUNDIR=$ASTROSOFT/psrcat_tar
export PSRCAT_FILE=$ASTROSOFT/psrcat_tar/psrcat.db

# Tempo
export TEMPO=$ASTROSOFT/tempo

# Tempo2
export TEMPO2=$ASTROSOFT/tempo2/T2runtime

# PGPLOT
export PGPLOT_DIR=$ASTROSOFT/pgplot_build
export PGPLOT_DEV=/xwindow
export PGPLOT_FONT=$ASTROSOFT/pgplot_build/grfont.dat

# PRESTO
export PRESTO=$ASTROSOFT/presto

# MULTINEST
export MULTINEST_DIR=$ASTROSOFT/TempoNest/MultiNest

# LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/usr/lib:/usr/lib/x86_64-linux-gnu:$PGPLOT_DIR:$ASTROSOFT/lib:$PRESTO/lib:$PRESTO/lib64:$MULTINEST_DIR

# PATH
# Some Presto executables match sigproc executables so keep separate -
# all other executables are found in $ASTROSOFT/bin
export PATH=$PATH:$ASTROSOFT/bin:$PRESTO/bin:$PGPLOT_DIR

# PYTHON PATH eg.
export PYTHONPATH=$PRESTO/lib/python:$PRESTO/lib64/python:/usr/lib/python2.7/site-packages/:/usr/lib64/python2.7/site-packages:$ASTROSOFT/lib/python2.7/site-packages

Then reload your .bashrc file and check changes are taken up:

$ source ~/.bashrc
$ echo $ASTROSOFT

2.2 Install some dependencies

sudo apt-get install ftp wget csh build-essential gfortran  cvs autoconf automake libtool m4 git gsl-bin libgsl-dev flex bison fort77 libglib2.0-dev gnuplot gnuplot-x11 python-dev python-numpy python-scipy python-matplotlib ipython python-sympy python-nose swig libltdl-dev libltdl7 dkms htop screen xterm emacs gpicview xpdf cmake default-jre default-jdk libblas3 liblapack3 libblas-dev liblapack-dev libxext-dev libx11-dev libopenmpi-dev openmpi-bin libhdf5-openmpi-dev mpich libmpich-dev libhdf5-mpich-dev

2.3 Build

ZLIB

cd zlib-1.2.11/
./configure --prefix=$ASTROSOFT
make
make install

CURL

cd curl-7.61.1/
./configure --prefix=$ASTROSOFT --with-ssh --with-zlib
make
make install

GIT

cd git-2.19.0/
./configure --prefix=$ASTROSOFT CFLAGS=-I$ASTROSOFT/include LDFLAGS=-L$ASTROSOFT/lib
make
make install

LAPACK

cd lapack-release/
make PREFIX=$ASTROSOFT

BOOST

cd boost_1_68_0/
./bootstrap.sh --prefix=$ASTROSOFT
./b2

PRF2FITS

cd prf2fits/
make cfgen prf2fits
cp {prf2fits,cfgen} $ASTROSOFT/bin

FFTW

cd fftw-{version}

a) single precision (for Ps

./configure --prefix=$ASTROSOFT --enable-float --enable-threads --enable-shared --enable-single CFLAGS=-fPIC FFLAGS=-fPIC
make
make check
make install
make clean

b) double precision (for Tempo2)

./configure --prefix=$ASTROSOFT CFLAGS=-fPIC FFLAGS=-fPIC
make
make check
make install
make clean

CFITISO

cd cfitsio
./configure --prefix=$ASTROSOFT CFLAGS=-fPIC FFLAGS=-fPIC
make shared
make install
make clean

PSRCAT

cd psrcat_tar
source makeit

Copy psrcat executable to $ASTROSOFT/bin:

cp psrcat $ASTROSOFT/bin

PGPLOT

Create an empty directory (pgplot_build) alongside the pgplot-{version} directory.
Copy pgplot-{version}/drivers.list to the pgplot_build directory.

cd pgplot_build

Edit drivers.list as required to enable the appropriate drivers(suggest to uncomment the following lines:),

#GIDRIV 1
#GIDRIV 2
#PNDRIV 1 
#PNDRIV 2 
#PSDRIV 1
#PSDRIV 2
#PSDRIV 3
#PSDRIV 4
#X2DRIV 0
#XWDRIV 1
#XWDRIV 2

then start the build:

../pgplot/makemake ../pgplot linux g77_gcc_aout

Edit the makefile with the following:

a) Set the fortran compiler to gfortran, and append FFLAGC and CFLAGC with -fPIC e.g:

FCOMPL=gfortran
FFLAGC=-fPIC -Wall -O
CFLAGC=-fPIC -DPG_PPU -O2 -I.

b) Check paths to png.h, pngconf.h, zlib.h, zconf.h, and change line 882

pndriv.o : ./png.h ./pngconf.h ./zlib.h ./zconf.h

to eg:

pndriv.o : /usr/include/libpng12/png.h /usr/include/libpng12/pngconf.h /usr/include/zlib.h /usr/src/linux-headers-4.18.0-15/incluede/linux/zconf.h

Save the file and compile it:

make
make clean
make cpg
ld -shared -o libcpgplot.so --whole-archive libcpgplot.a

Try the PGPLOT demo:

./pgdemo1

Press enter at the prompt.

TEMPO

cd tempo
./prepare
./configure F77=gfortran --prefix=$ASTROSOFT CFLAGS=-fPIC FFLAGS=-fPIC
make
make install

TEMPO2

cd tempo2
./bootstrap
./configure F77=gfortran --prefix=$ASTROSOFT --with-cfitsio-dir=$ASTROSOFT --with-fftw3-dir=$ASTROSOFT CFLAGS=-fPIC FFLAGS=-fPIC CXXFLAGS="-I$ASTROSOFT/include -I$PGPLOT_DIR" LDFLAGS=-L$PGPLOT_DIR
make && make install
make plugins && make plugins-install
make unsupported
make clean

PSRCHIVE (with python interface)

cd psrchive
./bootstrap
./configure F77=gfortran --prefix=$ASTROSOFT --with-cfitsio-dir=$ASTROSOFT --with-fftw3-dir=$ASTROSOFT --enable-shared CFLAGS=-fPIC FFLAGS=-fPIC CXXFLAGS="-I$INC -I$PGPLOT_DIR" LDFLAGS=-L$PGPLOT_DIR
make
make install
make clean

SIGPROC (Mike Keith’s version)

cd sigproc
./bootstrap
./configure --prefix=$ASTROSOFT --with-cfitsio-dir=$ASTROSOFT --with-fftw-dir=$ASTROSOFT F77=gfortran CFLAGS=-fPIC FFLAGS=-fPIC CPPFLAGS=-I$ASTROSOFT/include LDFLAGS="-L$ASTROSOFT/lib -L$PGPLOT_DIR -L/usr/lib/x86_64-linux-gnu" LIBS="-lX11 -ltempo2pred -lpng"
make
make install
make clean

DSPSR

To select the backend support to be compiled, create a text file named ‘backends.list’ containing e.g:

apsr asp bcpm bpsr caspsr cpsr2 cpsr dummy fits gmrt guppi kat lbadr64 lbadr lump lwa mark4 mark5 maxim mwa pdev pmdaq s2 sigproc spda1k spigot vdif

Continue the build:

./bootstrap
./configure --prefix=$ASTROSOFT --with-cfitsio-dir=$ASTROSOFT F77=gfortran CFLAGS=-fPIC FFLAGS=-fPIC LDFLAGS=-L$PGPLOT_DIR
make
make install
make clean

TEMPONEST

cd TempoNest

# build MultiNest
cd MultiNest/
mv Makefile MakefileMPI
cp MakefileNoMPI Makefile
make
make libnest3.so

cd ../
./autogen.sh
./configure CXXFLAGS=-I$ASTROSOFT/include LDFLAGS=-L$ASTROSOFT/lib
make && make install

PRESTO v2 (latest version)

cd presto/src

Edit Makefile as follows:

a) Define paths to fftw and cfitsio includes and libs

FFTINC = -I$(ASTROSOFT)/include
FFTLINK = -L$(ASTROSOFT)/lib -lfftw3f
CFITSIOINC = -I$(ASTROSOFT)/include
CFITSIOLINK = -L$(ASTROSOFT)/lib -lcfitsio

b) Add ‘-lm’ flag to CFLAGS

c) Add ‘-g -fPIC’ to FFLAGS

Continue the build:

make makewisdom
make prep
make
make clean

Now for the python:

cd $PRESTO/python

Edit library and include paths in setup.py and setup_ppgplot.py e.g.:

setup.py
---
extra_compile_args = ["-DUSEFFTW -fPIC"]
include_dirs = ["/home/{user}/pulsar_software/include"]
ppgplot_libraries = ["cpgplot", "pgplot", "X11", "png", "m", "gfortran"]
ppgplot_library_dirs = ["/home/{user}/pulsar_software/pgplot_build"]
presto_libraries = ["presto", "fftw3f", "m"]
presto_library_dirs = ["/home/{user}/pulsar_software/lib","/home/{user}/pulsar_software/presto/lib"]
---
setup_ppgplot.py
---
extra_compile_args = ["-fPIC"]
ppgplot_libraries = ["cpgplot", "pgplot", "X11", "png", "m", "g2c", "gfortran"]
ppgplot_library_dirs = ["/home/{user}/pulsar_software/pgplot_build"]
---

Continue the build:

make
make clean

Packages Download

# zlib
curl -L "https://zlib.net/zlib-1.2.11.tar.gz" -o zlib-1.2.11..tar.gz
# git
curl -L "https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.9.4.tar.gz" -o git-2.9.4.tar.gz
# boost
curl -L "https://dl.bintray.com/boostorg/release/1.68.0/source/boost_1_68_0.tar.gz" -o boost_1_68_0.tar.gz
# curl
curl -L "https://curl.haxx.se/download/curl-7.61.1.tar.gz" -o curl-7.61.1.tar.gz
# calceph
curl -L "https://www.imcce.fr/content/medias/recherche/equipes/asd/calceph/calceph-3.1.0.tar.gz" -o calceph-3.1.0.tar.gz
# lapack
git clone https://github.com/Reference-LAPACK/lapack-release.git
# psr2fits
git clone https://github.com/shiningsurya/prf2fits.git
# cfitsio
curl -L "http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio3450.tar.gz" -o cfitsio3450.tar.gz 
# psrcat
curl -L "http://www.atnf.csiro.au/research/pulsar/psrcat/downloads/psrcat_pkg.tar.gz" -o psrcat_pkg.tar.gz
# fftw
curl -L "http://www.fftw.org/fftw-3.3.8.tar.gz" -o fftw-3.3.8.tar.gz
# pgplot
curl -L "ftp://ftp.astro.caltech.edu/pub/pgplot/pgplot5.2.tar.gz" -o pgplot5.2.tar.gz
# psrchive
git clone git://git.code.sf.net/p/psrchive/code psrchive
# tempo
git clone git://git.code.sf.net/p/tempo/tempo
# tempo2
git clone https://bitbucket.org/psrsoft/tempo2.git
# presto
git clone git://github.com/scottransom/presto.git
# dspsr
git clone git://git.code.sf.net/p/dspsr/code dspsr
# tempoNest
git clone https://github.com/LindleyLentati/TempoNest.git
# Mike Keith's version of sigproc which handles PSRFITS format files:
git clone https://github.com/SixByNine/sigproc.git

Jun Wang

http://www.drjun.wang/2019/01/18/20190118-pulsar-software/

All articles in this blog are used except for special statements CC BY 4.0 reprint policy. If reproduced, please indicate source Jun Wang !

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Software Installation for Pulsar Data Analysis

1. Ubuntu Linux (64-bit)

2. Installation

2.1 Define some environmental variables

2.2 Install some dependencies

2.3 Build

ZLIB

CURL

GIT

LAPACK

BOOST

PRF2FITS

FFTW

CFITISO

PSRCAT

PGPLOT

TEMPO

TEMPO2

PSRCHIVE (with python interface)

SIGPROC (Mike Keith’s version)

DSPSR

TEMPONEST

PRESTO v2 (latest version)

Packages Download

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