In venelin/POUMM: The Phylogenetic Ornstein-Uhlenbeck Mixed Model

library(ggplot2)
library(scales)
library(data.table)
knitr::opts_chunk$set(echo = TRUE)

system('rsync -cv -r --progress ~/Documents/Bio/Projects/POUMM_1.3.0.tar.gz vmitov@euler:~/')

system('rsync -cv -r --progress ~/Documents/Bio/Projects/diversitree_0.9-9.tar.gz vmitov@euler:~/')

system('rsync -cv -r --progress ~/Documents/Bio/Projects/poummBayesianValidation/DATA/Microbenchmark/microbenchmark.R vmitov@euler:~/POUMM2/src/microbenchmark.R ')

system('rsync -cv -r --progress ~/Documents/Bio/Projects/POUMM/benchmark/runMicrobenchmark.sh vmitov@euler:~/POUMM2/src/')

system('rsync -cv -r --progress vmitov@euler:~/POUMM2/src/Results_icpc-omp-*.RData ~/Documents/Bio/Projects/poummBayesianValidation/DATA/Microbenchmark/')

system('rsync -cv -r --progress vmitov@euler:~/POUMM2/src/TreesAndValues.RData
 ~/Documents/Bio/Projects/poummBayesianValidation/DATA/Microbenchmark/')

# read RData files
timeTable <- NULL
valueTable <- NULL

for(compiler in c("icpc-omp-for", "icpc-omp-simd", "icpc-omp-for-simd")) {
  for(tryNo in 1:10) {
    for(nCores in c(1, 2, 4, 6, 8, 10)) {
      dataFile <- paste0("Results_", compiler, "_", nCores, "_cores_", tryNo, ".RData")

      if(file.exists(dataFile)) {
        load(dataFile)
        if(is.null(values[['tryNo']])) {
          values[, tryNo:=1]
        } 
        if(is.null(times[['tryNo']])) {
          times[, tryNo:=1]
        }
        valueTable <- rbind(valueTable, values)
        timeTable <- rbind(timeTable, times)
      }
    }
  }
}

setkey(timeTable, compilerInfo, cpuInfo, nCores, treeType, N, expr)

timeTable <- timeTable[expr != "gc"]

# average the times over the four trees for each N
# we remove the implementation "POUMM (C++/Arrays+SIMD)" 
# since it only uses the default vectorization (not omp-simd)
timeTable <- 
  timeTable[
    cpuInfo=="model name\t: Intel(R) Xeon(R) CPU E5-2697 v2 @ 2.70GHz", 
            list(time_ms_per_try = mean(mean)),
            by=list(cpuInfo, nCores, compilerInfo, expr, N, tryNo)]

# pick the mins over the tries
timeTable <- 
  timeTable[, list(time_ms = min(time_ms_per_try)),
            by=list(cpuInfo, nCores, compilerInfo, expr, N)]


# take best single-core time as reference for omp-for-simd
timeTable <- merge(
  timeTable,
  timeTable[expr == "POUMM: C++, omp" & 
              compilerInfo == "icpc-omp-for-simd" & nCores == 1, 
            list(ref_time_omp_for_simd = time_ms), keyby = N],
  by = "N")

#take best single-core time as reference for omp-for
timeTable <- merge(
  timeTable,
  timeTable[expr == "POUMM: C++, omp" &
              compilerInfo == "icpc-omp-for" & nCores == 1,
            list(ref_time_omp_for = time_ms), keyby = N],
  by = "N")

timeTable[, rel_speedup_omp_for_simd:=ref_time_omp_for_simd/time_ms]
timeTable[, rel_speedup_omp_for:=ref_time_omp_for/time_ms]


timeTable[, compiler:='Intel v16.0.0']
timeTable[, omp_for:= ((compilerInfo %in% c("icpc-omp-for", "icpc-omp-for-simd")) &
                          expr == "POUMM: C++, omp")]
timeTable[, omp_simd:= (compilerInfo != "icpc-omp-for" &
                          expr == "POUMM: C++, omp")]

timeTable[, Implementation:=expr]
timeTable[compilerInfo == "icpc-omp-simd" & expr == "POUMM: C++, omp", 
          Implementation := paste0(Implementation, "-simd")]
timeTable[compilerInfo == "icpc-omp-for" & expr == "POUMM: C++, omp", 
          Implementation := paste0(Implementation, "-for")]
timeTable[compilerInfo == "icpc-omp-for-simd" & expr == "POUMM: C++, omp", 
          Implementation := paste0(Implementation, "-for-simd")]

timeTable[, Implementation := 
            paste0(Implementation,' on ', 
                   nCores, ifelse(nCores == 1," core"," cores"))]

timeTable <- timeTable[N %in% 10^(5:2)]

save(timeTable, file='timeTable.RData')

venelin/POUMM documentation built on Oct. 25, 2020, 12:07 a.m.