Getting Started

Third-party Package Dependence

• MPICH — an MPI implementation library, available at http://www-unix.mcs.anl.gov/mpi/mpich

• GSL — the GNU Scientific Library, downloaded at http://www.gnu.org/software/gsl

• CDNest — Diffusive nested sampling, downloaded at https://github.com/LiyrAstroph/CDNest

Note

In Linux systems, there are package managers that can install the above libraries conveniently (except for CDNest). For example, DNF package managers in Fedora distribution. If so, use them. In such a case, the libraries usually are installed in standard environment path. Otherwise, if any of the above libraries is not installed in standard locations on your system, the Makefile provided with the code may need slight adjustments.

Compiling

Edit the configurations in Makefile to be consistent with your system if necessary. Then compile the package with the command

make

This creates an executable file trains.

Running

To run the package in a parallel computer/cluster, use the following command:

mpiexec -n np ./trains param/param

where np is the number of cores and param is the parameter file (see Parameter File), which specifies configurations for trains.

An exemplary pulsar timing residuals dataset is provided in the subdirectory data/, including:

pulsar_catalog.txt            # location and timing uncertainties of pulsars
sim_ptr.txt                   # timing residuals of pulsars

One can try to run the above command to test trains with the provided dataset. See Data Format for the information of data format.

Command-line Options

trains also adimits several command-line options:

-h or --help
    print help information.
-p or --post_proc
    only do posterior processing.
-r or --restart
    restart from the backup.
-t or --temperature or --temp
    specify tempering temperature in posterior processing, e.g., ``-t 2``, ``--temperature 2``, or ``--temp 2``.
-s or --seed
    set a seed for the random number generator, e.g., ``-s 100`` or ``--seed 100``
-c or --recalc_info
    only do posterior processing, but recalculate the posterior sample information.
-e or --exam_prior
    examine the priors.
-v or --version
    print version.
-n or --para_name
    print parameter name.

For example, if one wants to redo posterior processing with a different temperature, say 10 (the default is 1), one may use the command

./trains src/param -pt10

MCMC Sampling

The output Markov chain is stored in data/posterior_sample_pt.txt.

The parameter names and prior ranges are stored in data/para_names_pt.txt. The last column of those files indicates the prior type of the parameter with 1 means Gaussian and 2 means uniform.

One need to tune the corresponding option files OPTIONSPT, which specify configurations for nested sampling.