Tempo2 software installation ASTRONOMY AND SPACE SCIENCE George Hobbs August 2015

History of tempo2 ~2005 myself, Russell Edwards and Dick Manchester decided to update tempo1: - from Fortran->C (C++) -From ~100ns timing precision -> ~1ns timing precision -To use TCB instead of TDB -To be more versatile and have better graphical interfaces -To be able to process many pulsars simultaneously -TEMPO2 paper 1 “TEMPO2, a new pulsar-timing package - I. An overview” 2006MNRAS H -TEMPO2 paper 2 “TEMPO2, a new pulsar timing package - II. The timing model and precision estimates” 2006MNRAS E -TEMPO2 paper 3 “TEMPO2: a new pulsar timing package - III. Gravitational wave simulation” 2009MNRAS H Presentation title | Presenter name | Page 2

History of TEMPO2 1.Work with Bill Coles (UCSD) and Mike Keith (Manchester) has led to significantly improved fitting algorithms 2.Rutger van Haasteren etc. developed gravitational wave software 3.Lindley Lentati developed Bayesian-based methods (tempoNest) 4.Many plug-in interfaces written for different projects. Presentation title | Presenter name | Page 3

General view for installing tempo2 Presentation title | Presenter name | Page 4

General view for installing tempo2 Don’t do it! Presentation title | Presenter name | Page 5

General view for installing tempo2 Don’t do it! Presentation title | Presenter name | Page 6 Use pre-installed versions on e.g., the Virtual Machines instead!

If you really want to do it! Download 1.Currently being moved from Sourceforge/CVS to Bitbucket/Git 2.git clone 3.(update your version: git pull origin) Presentation title | Presenter name | Page 7

If you really want to do it! Installation 1.brew install automake 2.brew install libtool 3.brew install autoconf 4.brew install gcc (for gcc and gfortran) 5../bootstrap 6.export set TEMPO2=/Users/hob044/software/bitbucket/tempo2/T2rundir/ (directory containing T2runtime) 7../configure CXXFLAGS=-I/Users/hob044/software/pgplot Presentation title | Presenter name | Page 8 Specific to a Mac. Different for linux.

If you really want to do it! Installation Presentation title | Presenter name | Page 9 Will not compile plugins that require GSL

If you really want to do it! Installation > make clean > make > make plugins > make install > make plugins-install (can also try: > make complete-install) Open ~/.bashrc Add: TEMPO2=/Users/hob044/software/bitbucket/tempo2/T2rundir/; export TEMPO2 PATH=$PATH:/Users/hob044/software/bitbucket/tempo2/T2rundir/bin/; export PATH Restart your terminal Presentation title | Presenter name | Page 10

Most common problems 1.Forgetting to set $TEMPO2 2.Having different versions of “g++” and “gfortran” try g++ -v and gfortran –v (make sure that they are the same) 3.Installing pgplot 4.Forgetting to type make install 5.Forgetting to type make clean to re-compile after changes have been made Presentation title | Presenter name | Page 11

Use of VM 1.tempo2 is installed on both virtual machines that you were given 2.See /software/tempo2 3.Test it by typing: tempo2 -h Presentation title | Presenter name | Page 12

The software structure of tempo2 1.tempo2.C – main code to run tempo2 2.tempo2.h – header file that contains information such as maximum number of observations, pulsars etc. 3.*.C – lots of files for carrying out the basic algorithms 4./plugin/*_plug.C – various plugin packages 5.$TEMPO2/clock – clock correction files $TEMPO2/ephemeris – solar system ephemerides $TEMPO2/observatory – files about the observatory $TEMPO2/earth – Earth orientation files Presentation title | Presenter name | Page 13

What is necessary and what is not? 1.Look in /plugin/plugin_lists/*.plugins 2.vanilla.plugins – do not need much to install them 3.pgplot.plugins – plugins that require pgplot 4.pgplot_fftw.plugins – plugins that require pgplot and fftw 5.cfitsio.plugins – plugins that require the cfitsio library 6.… 7.You can decide if you need these libraries or not! Presentation title | Presenter name | Page 14

Creating your own plugin 1.If you can program in C or C++ then it is easy to create your own plugin 2.See /plugin/grTemplate_plug.C 3.Change that to your plugin 4.Add your plugin into /plugin/plugin_lists 5../bootstrap 6../configure 7.make clean 8.make install 9.make plugins-install Presentation title | Presenter name | Page 15

A few commands to try to test the installation > tempo2 Presentation title | Presenter name | Page 16

A few commands to try to test the installation > tempo2 –v Presentation title | Presenter name | Page 17

A few commands to try to test the installation > tempo2 –h Presentation title | Presenter name | Page 18

A few useful command line arguments 1.-npsr XX -- allocate memory for specified number of pulsars 2.-nobs XX – allocate this number of observations for each pulsar 3.-nofit – turn off all the fitting 4.-fit RAJ –fit DECJ – turn on fitting for RAJ and DECJ Example: tempo2 –gr plk –f psr.par psr.tim –npsr 1 –nobs 1000 –nofit –fit f0 –fit f1 Presentation title | Presenter name | Page 19

Output plugins 1.Change the default text output from tempo2 2.tempo2 –f data1.par data1.tim Presentation title | Presenter name | Page 20

Output plugins: general > tempo2 -output general -s "F0 = {F0_v} +/- {F0_e}\n" -f data1.par data1.tim F0 = / e-11 Presentation title | Presenter name | Page 21

Output plugins: general2 > tempo2 -output general2 -s ”{sat} {bat} {pre} {shapiro}\n" -f data1.par data1.tim Presentation title | Presenter name | Page 22

Output plugins: publish > tempo2 -output publish -f data1.par data1.tim produces table.tex > latex table.tex Presentation title | Presenter name | Page 23

Graphical interfaces: plk 1.Can completely change how tempo2 presents its results using graphical interfaces 2.tempo2 –gr plk –f data1.par data1.tim Presentation title | Presenter name | Page 24

Graphical interfaces: plotMany tempo2 –gr plotMany -g plot.ps/cps -centremjd -1 –plotus –f psr1.par psr1.tim –f psr2.par psr2.tim –f psr3.par psr3.tim … (use tempo2 –gr plotMany –h for help) Presentation title | Presenter name | Page 25

Other important plugins 1.-output matrix – shows the covariance matrix of the fitted parameters 2.-gr fermi – used for processing Fermi data 3.-gr compareDsets – provides a method to compare different datasets 4.-gr efacEquad – provides method to improve ToA uncertainties 5.-gr cholSpectra – uses Cholesky fitting routines to obtain a power spectrum of the timing residuals 6.-gr spectralModel – allows the user to get a red noise spectrum of the residuals 7.-gr glitch – plugin to search for glitch events 8.-gr interpolate – plugin to interpolate/extrapolate timing residuals 9.-gr temponest – use Bayesian methodology Presentation title | Presenter name | Page 26

Select files 1.Sometimes you wish to remove some particular observations 2.Can use command line arguments or select files (can also use select plugins for really complex systems). Use “flags” on ToA lines to define observations of interest. 3.tempo2 –gr plk –f data.par data.tim –pass “-rcvr mb h-oh” 4.tempo2 –gr plk –f data.par data.tim –filter “-rcvr mb h-oh” 5.tempo2 –gr plk –f data.par data.tim –select select.dat Presentation title | Presenter name | Page 27

Example select file LOGIC -bad_config = 1 REJECT LOGIC -nocal = 1 REJECT LOGIC -pdfb4_reset_bug = 1 REJECT LOGIC -pks_clk_prob = 1 REJECT LOGIC -length < 90 REJECT LOGIC -snr < 10 REJECT PROCESS -fe DRAO REJECT Presentation title | Presenter name | Page 28

plk setup > tempo2 –gr plk –f 1857.par 1857.tim Presentation title | Presenter name | Page 29

plk setup tempo2 –gr plk –f 1857.par 1857.tim -publish Presentation title | Presenter name | Page 30

plk setup > cd $TEMPO2/plugin_data # Set up for the defaults used by the plk plotting package # aspect 0.8 fontsize 1.0 fonttype 1 linewidth 1 menu 3 freq freq freq freq freq background black line white Presentation title | Presenter name | Page 31 Colour and font

Finding some tempo2 usage instructions Presentation title | Presenter name | Page 32

The tempo2 list 1.Please join the tempo2 list. Ask questions, answer questions, have discussions … 2.Join at: 3.Send s to 4.(Note that s are being sent to a lot of people!) Presentation title | Presenter name | Page 33

Current usage of tempo2: recent papers 1.Testing Theories of Gravitation Using 21-Year Timing of Pulsar Binary J Modeling the evolution and distribution of the frequency's second derivative and the braking index of pulsar spin 3.Limits on Anisotropy in the Nanohertz Stochastic Gravitational Wave Background 4.Parkes radio searches of Fermi gamma-ray sources and millisecond pulsar discoveries 5.Deep NuSTAR and Swift Monitoring Observations of the Magnetar 1E 1841–045 6.A Bayesian method for pulsar template generation 7.Detection of VHE Bridge emission from the Crab pulsar with the MAGIC Telescopes 8.The three discrete nulling time-scales of PSR J Optical phase coherent timing of the Crab nebula pulsar with Iqueye at the ESO New Technology Telescope 10.… Presentation title | Presenter name | Page 34

Current usage of tempo2: recent papers 1.Testing Theories of Gravitation Using 21-Year Timing of Pulsar Binary J Modeling the evolution and distribution of the frequency's second derivative and the braking index of pulsar spin 3.Limits on Anisotropy in the Nanohertz Stochastic Gravitational Wave Background 4.Parkes radio searches of Fermi gamma-ray sources and millisecond pulsar discoveries 5.Deep NuSTAR and Swift Monitoring Observations of the Magnetar 1E 1841–045 6.A Bayesian method for pulsar template generation 7.Detection of VHE Bridge emission from the Crab pulsar with the MAGIC Telescopes 8.The three discrete nulling time-scales of PSR J Optical phase coherent timing of the Crab nebula pulsar with Iqueye at the ESO New Technology Telescope 10.… Presentation title | Presenter name | Page 35

The future of tempo2 1.The original tempo software package is still being used (and being developed) 2.A new package PINT is being produced by North American group. Based on python. 3.Need multiple timing packages to confirm any detection such as gravitational waves 4.Tempo2 is currently the most advanced timing software package and will remain so for a long time 5.Likely that the Bayesian methodology in tempo2 will develop significantly over the next few years 6.Likely that it will be used for unexpected uses! 7.Please use it and please help develop it! Presentation title | Presenter name | Page 36

Thank you CSIRO Astronomy and Space Science George Hobbs Research Scientist t w hobbs CSIRO ASTRONOMY AND SPACE SCIENCE