Transcript General view for installing tempo2

Tempo2 software installation
George Hobbs
August 2015
ASTRONOMY AND SPACE SCIENCE
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.369..655H
-
TEMPO2 paper 2 “TEMPO2, a new pulsar timing package - II. The timing model
and precision estimates” 2006MNRAS.372.1549E
-
TEMPO2 paper 3 “TEMPO2: a new pulsar timing package - III. Gravitational
wave simulation” 2009MNRAS.394.1945H
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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.
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General view for installing tempo2
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General view for installing tempo2
Don’t do it!
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General view for installing tempo2
Don’t do it!
Use pre-installed versions on e.g., the Virtual Machines instead!
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If you really want to do it! Download
1. Currently being moved from Sourceforge/CVS to Bitbucket/Git
2. git clone https://bitbucket.org/mkeith/tempo2.git
3. (update your version:
git pull origin)
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If you really want to do it! Installation
1. brew install automake
2. brew install libtool
3. brew install autoconf
Specific to a
Mac. Different for
linux.
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
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If you really want to do it! Installation
Will not compile
plugins that require
GSL
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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
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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
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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
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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
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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!
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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
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A few commands to try to test the installation
> tempo2
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A few commands to try to test the installation
> tempo2 –v
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A few commands to try to test the installation
> tempo2 –h
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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
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Output plugins
1. Change the default text
output from tempo2
2. tempo2 –f data1.par
data1.tim
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Output plugins: general
> tempo2 -output general -s "F0 = {F0_v} +/- {F0_e}\n" -f
data1.par data1.tim
F0 = 245.42611974713 +/- 6.8386838388727e-11
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Output plugins: general2
> tempo2 -output general2 -s ”{sat} {bat} {pre}
{shapiro}\n" -f data1.par data1.tim
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Output plugins: publish
> tempo2 -output publish
-f data1.par data1.tim
produces table.tex
> latex table.tex
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Graphical interfaces: plk
1. Can completely change how tempo2 presents its results using
graphical interfaces
2. tempo2 –gr plk –f data1.par data1.tim
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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)
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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
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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
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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
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plk setup
> tempo2 –gr plk –f 1857.par 1857.tim
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plk setup
tempo2 –gr plk –f 1857.par 1857.tim -publish
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plk setup
> cd $TEMPO2/plugin_data
# Set up for the defaults used by the plk plotting package
#
aspect 0.8
fontsize 1.0
Colour and
fonttype 1
font
linewidth 1
menu 3
freq -1 500 1 16
freq 500 1000 2 16
freq 1000 1700 3 16
freq 1700 2500 6 16
freq 2500 1000000 5 16
background black
line white
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Finding some tempo2 usage instructions
http://adsabs.harvard.edu/abs/2012arXiv1205.6273H
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The tempo2 email list
1. Please join the tempo2 email list. Ask questions, answer
questions, have discussions …
2. Join at: http://lists.pulsarastronomy.net/mailman/listinfo
3. Send emails to [email protected]
4. (Note that emails are being sent to a lot of people!)
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Current usage of tempo2: recent papers
1. Testing Theories of Gravitation Using 21-Year Timing of Pulsar Binary J1713+0747
2. 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 J1717-4054
9. Optical phase coherent timing of the Crab nebula pulsar with Iqueye at the ESO New
Technology Telescope
10. …
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Current usage of tempo2: recent papers
1. Testing Theories of Gravitation Using 21-Year Timing of Pulsar Binary J1713+0747
2. 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 J1717-4054
9. Optical phase coherent timing of the Crab nebula pulsar with Iqueye at the ESO New
Technology Telescope
10. …
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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!
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Thank you
CSIRO Astronomy and Space
Science
George Hobbs
Research Scientist
t +61 2 9372 4652
E [email protected]
w
www.atnf.csiro.au/people/g
hobbs
CSIRO
ASTRONOMY AND SPACE SCIENCE