create_std_pir_params is slow about pirouette HOT 12 CLOSED

There is something that escapes my comprehension, I will explain.

The goal of this function is to create pir_params and NOT to run a pir_run.
This means that there is no true_phylogeny, as pir_run requires a true_phylogeny as well as pir_params, but as INDEPENDENT inputs.
This means that the number max_n_tries should make no difference, because its meaning is to try n times to replicate the same numbers of mutations in the twin_alignment.
But to produce a twin alignment you need a twin_phylogeny as well as a true_alignment which, in turn, requires a true_phylogeny, which we CANNOT have because we are not yet running pir_run.

TL;DR
pirouette is not running, we are just building pir_params.
The time grows as max_n_tries increases but there should be no tries going on because there is no phylogeny, only pir_params. Yet something is running max_n_tries times. I suspect is a test and it should not do it so many times.
I will investigate further.

from pirouette.

The problem is in check_pir_params

from pirouette.

And also in check_twinning_params

from pirouette.

Digging in -> check_sim_twal_fun

from pirouette.

I switched to a simpler test phylogeny and a different root sequence (of higher entropy) in check_sim_twal_fun.
Now it seems to go faster but there is one thing that must be kept in mind: this test depends on random variables, as the twin alignment is randomly generated. I thought of adding a set.seed, but we do not want to impose a specific pseudorandomness when checking variables, so I preferred to simplify the test.

from pirouette.

I merged your Pull Request, well done 👍

What is the result of the code profile? I know, these are hard to interpret 👨‍🔬

from pirouette.

I will take over from here 👍

from pirouette.

Running:

library(pirouette)
filename <- tempfile()
utils::Rprof(filename)
create_std_pir_paramses(n = 1)
utils::Rprof(NULL)
print(utils::summaryRprof(filename))

Results in

$by.self
                                                               total.pct
"pirouette::check_experiments"                                     91.64
"pirouette::check_experiments_candidates_have_same_mcmcs"          74.29
"check_mcmc_values"                                                58.45
"beautier::check_treelog"                                          24.02
"check_treelog_values"                                             23.58
"check_screenlog_values"                                           23.40
"check_tracelog_values"                                            22.95
"is_in_range"                                                      12.54
"are_equal_treelogs"                                               11.21

$by.total
                                                               total.time total.pct self.time
"create_std_pir_paramses"                                           22.48    100.00      0.00
"pirouette::check_experiments"                                      20.60     91.64      0.02
"pirouette::check_pir_params_data_types"                            17.96     79.89      0.00
"pirouette::check_pir_params"                                       17.96     79.89      0.00
"pirouette::check_experiments_candidates_have_same_mcmcs"           16.70     74.29      0.02
"beautier::are_equal_mcmcs"                                         16.62     73.93      0.00
"create_std_pir_params"                                             14.88     66.19      0.00
"beautier::check_mcmc"                                              13.16     58.54      0.00
"check_mcmc_values"                                                 13.14     58.45      0.04

$sample.interval
[1] 0.02

$sampling.time
[1] 22.48

Number 1 time waster: check_experiments_candidates_have_same_mcmcs

• Full profile here: profile.txt

from pirouette.

I couldn't speed up check_experiments_candidates_have_same_mcmcs easily [*], I think beautier::check_mcmc is the sweet spot.

• [*] I thought replacing experiment_1 by experiments[[i]] would reduce long copies, but that was a misconception

from pirouette.

Created a repo to let Travis check: https://github.com/richelbilderbeek/pirouette_profile

from pirouette.

A repo to let Travis check beautier's speed: https://github.com/richelbilderbeek/beautier_profile

from pirouette.

It's fine as it is 👍

from pirouette.