Pulsar Reference - Software Installation

Mac - OSX El Capitan

**Please note: This page is under development and may be incomplete**

[Last updated 02/03/2016]

This guide takes you through the necessary steps required to install software for pulsar data analysis on a Mac running OSX El Capitan. Please note that for installation to be successful, the software should be installed in the order described on this page.

Define some environmental variables

Add the following lines to your .bash_profile file (if it doesn't exist, create it) e.g:

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

# OSTYPE
export OSTYPE=linux

# 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

# PRESTO
export PRESTO=$ASTROSOFT/presto

# DYLD_LIBRARY_PATH
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$ASTROSOFT/lib:$PRESTO/lib

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

# PYTHONPATH
export PYTHONPATH=$PRESTO/lib/python:/usr/local/lib/python2.7/site-packages:/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages:$ASTROSOFT/lib/python2.7/site-packages

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

source ~/.bash_profile
echo $ASTROSOFT

Install some dependencies

XCode

Install the latest version of XCode, XCode command line tools and gfortran from the App store.

Homebrew

Follow the installation instructions on http://mxcl.github.io/homebrew/. Homebrew is installed to /usr/local by default.

After the installation, run

brew doctor

brew install gcc

glib

brew install glib

fftw

brew install fftw --with-fortran --with-mpi --with-openmp

cfitsio

brew install cfitsio

autoconf

brew install autoconf

automake

brew install automake

libtool

brew install libtool

brew install git

python

brew install python

swig (for psrchive python interface)

brew install swig

libpng12

brew install homebrew/versions/libpng12

cmake

brew install cmake

brew install gsl

pkg-config

brew install pkg-config

numpy

pip install numpy

scipy

pip install scipy

Build

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 pgp lot-{version} directory.

Copy pgplot-{version}/drivers.list to the pgp lot_build directory.

cd pgplot_build

Edit drivers.list as required to enable the a ppropriate drivers, then start the build:

../pgplot-{version}/makemake ../pgplot-{version} bsd

Edit the makefile with the following:

a) Set the fortran compiler to gfortran (line 25), add '-fPIC' to FFLAGC and CFLAGC, remove '-lipc' from LIBS, and add the path to libpng12/include to XINCL e.g:

FCOMPL=gfortran
FFLAGC=-O2 -fPIC
CFLAGC=-fPIC -DPG_PPU -O2 -I.
LIBS=-L/usr/X11R6/lib -lX11 -lm
XINCL=-I/usr/local/Cellar/libpng12/1.2.54/include/ -I/usr/X11R6/include

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 e.g:

pndriv.o : /usr/local/Cellar/libpng12/1.2.54/include/png.h /usr/local/Cellar/libpng12/1.2.54/include/pngconf.h /usr/include/zlib.h /usr/include/zconf.h

Save the file and compile it:

make
make clean
make cpg

Try the PGPLOT demo:

./pgdemo1

TEMPO

cd tempo
./prepare
./configure F77=gfortran --prefix=$ASTROSOFT
make
make install
make clean

TEMPO2

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

PSRCHIVE

cd psrchive
./bootstrap
./configure F77=gfortran --prefix=$ASTROSOFT --enable-shared --with-cfitsio-dir=$ASTROSOFT --with-fftw3-dir=$ASTROSOFT CFLAGS=-fPIC FFLAGS=-fPIC LDFLAGS=-L/usr/local/lib LIBS="-lgsl -lgslcblas"
make
make install
make clean

SIGPROC

cd ../sigproc-{version}
./configure

Click enter to install to default path

Edit makefile.darwin with the following:

a) Ensure the PGPLOT libraries in the LPGPLOT line are in the following order, and add -lpng to enable png output from PGPLOT:

-lcpgplot -lpgplot -lpng

c) Add the following line defining the fortran compiler:

FC = gfortran -ffixed-line-length-none

d) Uncomment LFITS and LFFTW and edit paths e.g:

LFITS = -L$ASTROSOFT/lib/ -lcfitsio
LFFTW = -L$ASTROSOFT/lib -lfftw3 -lfftw3f

Remove the backslash and quote from dosearch.f (line 265):

Change from:

write(llog,*) 'DB\'s slow-but-simple harmonic summing routine'

to:

write(llog,*) 'DBs slow-but-simple harmonic summing routine'

Save the file and compile it:

make
make quickplot

MULTINEST

cd MultiNest/build/
cmake -DCMAKE_INSTALL_PREFIX=$ASTROSOFT ..
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/local/Cellar/gcc/5.3.0/lib/gcc/5" LIBS=-lgomp CC=/usr/local/Cellar/gcc/5.3.0/bin/gcc-5
make
make install
make clean

DSPSR

cd dspsr

Create a file named 'backends.list' and add 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

./bootstrap
./configure --prefix=$ASTROSOFT --with-cfitsio-dir=$ASTROSOFT F77=gfortran CFLAGS=-fPIC FFLAGS=-fPIC LDFLAGS="-L$PGPLOT_DIR -L$ASTROSOFT/lib -L/usr/local/Cellar/gcc/5.3.0/lib/gcc/5"
make
make install
make clean

TEMPONEST

cd TempoNest
./autogen.sh
./configure CXXFLAGS=-I$ASTROSOFT/include LDFLAGS="-L$ASTROSOFT/lib -L/usr/local/Cellar/gcc/5.3.0/lib/gcc/5"
make && make install

PRESTO v2 (latest version)

cd presto/src

Edit Makefile as follows:

a) Define paths to libs and compiler e.g:

X11LINK = -L/usr/X11/lib -lX11
PNGLINK = -L/usr/local/Cellar/libpng12/1.2.54/lib -lpng12
CC = /usr/local/Cellar/gcc/5.3.0/bin/gcc-5

b) Add -lm flag to CFLAGS

CFLAGS = -I$(PRESTO)/include $(GLIBINC) $(CFITSIOINC) $(PGPLOTINC) $(FFTINC) \
        -DUSEFFTW -DUSEMMAP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 \
        -g -O3 -ffast-math -Wall -W -fPIC -lm

Continue the build:

make makewisdom
make prep
make

Common installation problems

PGPLOT ERROR:

...
../pgplot/drivers/pndriv.c:225:21: error: incomplete definition of type 'struct png_struct_def'
  if (setjmp(png_ptr->jmpbuf)) { /* not really sure what I'm doing here... */
             ~~~~~~~^
/usr/local/Cellar/libpng/1.6.21/include/png.h:444:16: note: forward declaration of 'struct png_struct_def'
typedef struct png_struct_def png_struct;
...

FIX: install libpng12 with brew and define paths in makefile

PSRCHIVE ERROR:

...
In file included from ../../local_include/Pulsar/WaveletSmooth.h:13:
../../local_include/Pulsar/WaveletTransform.h:14:10: fatal error: 'gsl/gsl_wavelet.h' file not found
...

FIX: install gsl with brew

SIGPROC ERROR (MK's version):

...
In file included from typeof_inputdata.c:29:
./mjk_cmd.h:1:10: fatal error: 'omp.h' file not found
...

FIX: install latest gcc with brew, and add path to CC variable in configure