MCMC algorithm -- understanding some paremeters

[Arman777]

Recently I have shared a question about a program called SimpleMC and how to run it.

Running a Github File on VS code for windows 10- File system problem ( | Physics Forums

I am trying to understand an MCMC program. I manage to run it, but I am trying to understand the meaning of the some parameters in the analysis.

The code is something like this

[mcmc]
;Nsamples
nsamp   = 50000

;Burn-in
skip    = 300

;temperature at which to sample
temp    = 2

; Gelman-Rubin for convergence
GRstop  = 0.01

;every number of steps check the GR-criteria
checkGR = 500

;1 if single cpu , otherwise is giving by the nproc-> mpi -np #
chainno = 0

This is for the metropolis-hastings algorithm. How my results depend on these parameters or what these parameters mean ?
I understood the nsamp and skip, I also kind of know what GRstop and checkGR means but I have no idea what temp and chainno means.

 

[jedishrfu]

Perhaps you can find the meaning behind the parameters by looking at where they are referenced in the source code you have.

The current programming paradigm is to skip documentation for the most part unless its going to be used by a lot of people. Instead they will embed comments that give you a hint of what they are used for.

 

[pbuk]

temp is the temperature at which to sample and if chainno is 1 then it will use 1 cpu, or you can set it to a different number.

 

[Arman777]

Perhaps you can find the meaning behind the parameters by looking at where they are referenced in the source code you have.

The current programming paradigm is to skip documentation for the most part unless its going to be used by a lot of people. Instead they will embed comments that give you a hint of what they are used for.

I tried but not luck. I have find this MrBayes (sourceforge.net)

 

[Arman777]

temp is the temperature at which to sample and if chainno is 1 then it will use 1 cpu, or you can set it to a different number.

I guess I have 2 cores but I am setting chains = 4 and temp = 0.2 it seems to be working.