Merge pull request #613 from etmc/profile_all

in the hmc_mk2 profiler, optionally include all timings

profiling/hmc_mk2/README.md

@@ -3,19 +3,22 @@ We use tmLQCD hierarchical timer and R to produce profiles of the HMC.
 To collect time informations from the file `example_log.out` type
 
 ```
-    Rscript make_profile.R example_log.out output_basename
+    Rscript make_profile.R example_log.out output_basename [1]
 ```
 
 The `make_profile.R` file will first collect the data and then render the file `profile.Rmd`, producing the pdf `output_basename.pdf`, where the name of the output file is set by passing something for `output_basename`.
+The last argument is optional and controls whether all timings are included in per-monomial plots and tables or timings below 5% of the total time spent in that particular step (heatbath, derivative, acceptance) for a particular monomial are grouped under the "other" category.
 
-Alternatively, the script can also be sourced from an interactive session:
+Alternatively, the script can also be sourced from an interactive session where the variables `infile` and `outbase` must be defined.
 
 ```
 > infile <- "example_log.out"
 > outbase <- "output_basename"
 > source("make_profile.R")
 ```
 
+The treshold for whether all timings should be shown on a per-monomial basis is set via the `other_threshold` variable and defaults to `0.05`.
+
 The R packages `dplyr, data.tree, stringr` and `microseq` are required for data extraction and the R packages `ggplot2, knitr, treemap, hadron` and `kableExtra` are required to render the Rmarkdown document.
 
 The raw and summary data are stored in `profile.RData` which includes the `data.tree` structure `t_tree` which nicely shows the call stack.

profiling/hmc_mk2/make_profile.R

@@ -9,6 +9,7 @@ require(hadron)
 require(kableExtra) 
 require(ggrepel)
 
+
 # wrapper around base::gregexpr which makes it operate like microseq::gregexpr
 extract_gregexpr <- function(pattern, text, ignore.case = FALSE, perl = FALSE, fixed = FALSE, useBytes = FALSE){
   lst <- base::gregexpr(pattern, text, ignore.case, perl, fixed, useBytes)
@@ -40,16 +41,23 @@ extract_type <- function(str){
 if(!interactive()){
   args <- commandArgs(trailingOnly=TRUE)
   if( length(args) < 2 ){
-    stop("usage: Rscript make_profile.R <logfile> <output_basename>")
+    stop("usage: Rscript make_profile.R <logfile> <output_basename> [include_all]")
   }
   infile <<- args[1]
   outbase <<- args[2]
+  if( length(args) == 3 ){
+    other_threshold <<- 0.0
+  }
 } else {
   if( !exists("infile") | !exists("outbase") ){
     stop("When not running interactively, the variables 'infile' (path to log file) and 'outbase' (basename for ouput files) must be defined!")
   }
 }
 
+if( !exists("other_threshold") ){
+  other_threshold <<- 0.05
+}
+
 stopifnot(file.exists(infile))
 
 # extract the different monomial names from the log file
@@ -120,7 +128,7 @@ t_tree <- data.tree::as.Node(sum_data)
 # and logical unit
 sum_data_per_mon <- dplyr::filter(sum_data, nchar(monomial) > 0) %>%
                     dplyr::group_by(monomial, type, level) %>%
-                    dplyr::mutate(name = ifelse(time < 0.05 * sum(time),
+                    dplyr::mutate(name = ifelse(time < other_threshold * sum(time),
                                                 'other', name)) %>%
                     dplyr::group_by(monomial, type, level, name) %>%
                     dplyr::summarise(time = sum(time),

profiling/hmc_mk2/profile.Rmd

@@ -116,7 +116,7 @@ cat("\\par\n")
 cat(knitr::kable(dplyr::select(hb_acc_der_data, monomial, type, time, prop, invocations, unit_time),
                  format = 'latex',
                  booktabs = TRUE,
-                 digits = 1,
+                 digits = 3,
                  linesep = "") %>%
     kableExtra::kable_styling(latex_options = "striped")
 )
@@ -156,7 +156,7 @@ if(!all(is.na(quda_data))){
   cat(knitr::kable(plot_data,
                    format = 'latex',
                    booktabs = TRUE,
-                   digits = 1,
+                   digits = 2,
                    caption = sprintf("Time spent in different QUDA regions. Compare to total time of %.1f seconds.",
                                      total_time)) %>%
       kableExtra::kable_styling(latex_options = "striped")
@@ -197,7 +197,7 @@ for( mon in total_per_mon$monomial ){
     cat(knitr::kable(dplyr::select(type_data, level, name, time, prop, invocations, unit_time),
                      format = 'latex',
                      booktabs = TRUE,
-                     digits = 1,
+                     digits = 3,
                      linesep = "",
                      caption = sprintf("%s %s", mon, tp) ) %>%
           kable_styling(latex_options = "HOLD_position") %>%