diff --git a/garlic/exp/creams/size.nix b/garlic/exp/creams/size.nix new file mode 100644 index 0000000..c9911b0 --- /dev/null +++ b/garlic/exp/creams/size.nix @@ -0,0 +1,130 @@ +{ + stdenv +, stdexp +, bsc +, targetMachine +, stages +, garlicTools +, enableExtended ? false +}: + +with stdenv.lib; +with garlicTools; + +let + # Initial variable configuration + varConf = { + + #nodes = range2 1 16; + nodes = [ 16 ]; + sizeFactor = range2 1 32; + granul = [ 16 ] ++ optionals (enableExtended) [ 8 32 ]; + + # Max. number of iterations + iterations = [ 20 ] ++ optionals (enableExtended) [ 10 ]; + + gitBranch = [ + "garlic/tampi+isend+oss+task" + "garlic/mpi+send+omp+fork" + #"garlic/mpi+send+omp+task" + #"garlic/mpi+send+seq" + ] ++ optionals (enableExtended) [ + "garlic/mpi+send+oss+task" + "garlic/mpi+isend+omp+task" + "garlic/mpi+isend+oss+task" + ]; + }; + + # We use these auxiliary functions to assign different configurations + # depending on the git branch. + getGranul = branch: oldGranul: + if (branch == "garlic/mpi+send+seq") + then 999999 else oldGranul; + + getCpusPerTask = branch: hw: + if (branch == "garlic/mpi+send+seq") + then 1 else hw.cpusPerSocket; + + getNtasksPerNode = branch: hw: + if (branch == "garlic/mpi+send+seq") + then hw.cpusPerNode else hw.socketsPerNode; + + # Generate the complete configuration for each unit + genConf = c: targetMachine.config // rec { + + expName = "creams-size"; + unitName = "${expName}" + + "-granul.${toString granul}" + + "-sf.${toString sizeFactor}"; + + inherit (targetMachine.config) hw; + + # Options for creams + inherit (c) iterations gitBranch nodes sizeFactor; + granul = getGranul gitBranch c.granul; + nprocz = ntasksPerNode * nodes; + baseSizePerCpu = 4; + baseSize = baseSizePerCpu * cpusPerTask * ntasksPerNode * nodes; + + nz = baseSize * sizeFactor; + + # Repeat the execution of each unit 10 times + loops = 10; + + # Resources + qos = "debug"; + time = "02:00:00"; + ntasksPerNode = getNtasksPerNode gitBranch hw; + cpusPerTask = getCpusPerTask gitBranch hw; + jobName = unitName; + }; + + # Compute the array of configurations + configs = unique (stdexp.buildConfigs { + inherit varConf genConf; + }); + + # Custom srun stage to copy the creams input dataset + customSrun = {nextStage, conf, ...}: + let + input = bsc.garlic.apps.creamsInput.override { + inherit (conf) gitBranch granul nprocz nz; + }; + in + stdexp.stdStages.srun { + inherit nextStage conf; + # Now we add some commands to execute before calling srun. These will + # only run in one rank (the first in the list of allocated nodes) + preSrun = '' + cp -r ${input}/SodTubeBenchmark/* . + chmod +w -R . + sed -i '/maximum number of iterations/s/50/${toString conf.iterations}/' input.dat + rm -f nanos6.toml + ''; + }; + + exec = {nextStage, conf, ...}: stages.exec { + inherit nextStage; + env = '' + export NANOS6_CONFIG_OVERRIDE="version.dependencies=regions" + ''; + + # Remove restarts as is not needed and is huge + post = '' + rm -rf restarts || true + ''; + }; + + # Creams program + creams = {nextStage, conf, ...}: bsc.apps.creams.override { + inherit (conf) gitBranch; + }; + + pipeline = stdexp.stdPipelineOverride { + # Replace the stdandard srun stage with our own + overrides = { srun = customSrun; }; + } ++ [ exec creams ]; + +in + + stdexp.genExperiment { inherit configs pipeline; } diff --git a/garlic/exp/index.nix b/garlic/exp/index.nix index d467881..f531d34 100644 --- a/garlic/exp/index.nix +++ b/garlic/exp/index.nix @@ -21,6 +21,7 @@ creams = rec { ss = callPackage ./creams/ss.nix { }; granularity = callPackage ./creams/granularity.nix { }; + size = callPackage ./creams/size.nix { }; # These experiments are the extended versions of the previous # ones. We split them so we can keep a reasonable execution time diff --git a/garlic/fig/creams/size.R b/garlic/fig/creams/size.R new file mode 100644 index 0000000..21e3335 --- /dev/null +++ b/garlic/fig/creams/size.R @@ -0,0 +1,96 @@ +library(ggplot2) +library(dplyr, warn.conflicts = FALSE) +library(scales) +library(jsonlite) +library(viridis, warn.conflicts = FALSE) +library(stringr) + +args = commandArgs(trailingOnly=TRUE) + +# Set the input dataset if given in argv[1], or use "input" as default +if (length(args)>0) { input_file = args[1] } else { input_file = "input" } +if (length(args)>1) { output = args[2] } else { output = "?" } + +df = jsonlite::stream_in(file(input_file), verbose=FALSE) %>% + + jsonlite::flatten() %>% + + select(unit, + config.nodes, + config.gitBranch, + config.granul, + config.iterations, + config.sizeFactor, + config.nz, + time, + total_time) %>% + + rename(nodes=config.nodes, + gitBranch=config.gitBranch, + granul=config.granul, + sizeFactor=config.sizeFactor, + nz=config.nz, + iterations=config.iterations) %>% + + # Remove the "garlic/" prefix from the gitBranch + mutate(branch = str_replace(gitBranch, "garlic/", "")) %>% + + # Computations before converting to factor + mutate(time.nodes = time * nodes) %>% + mutate(time.elem = time / sizeFactor) %>% + mutate(time.nodes.iter = time.nodes / iterations) %>% + + # Convert to factors + mutate(unit = as.factor(unit)) %>% + mutate(nodes = as.factor(nodes)) %>% + mutate(gitBranch = as.factor(gitBranch)) %>% + mutate(granul = as.factor(granul)) %>% + mutate(iterations = as.factor(iterations)) %>% + mutate(sizeFactor = as.factor(sizeFactor)) %>% + mutate(nz = as.factor(nz)) %>% + mutate(unit = as.factor(unit)) %>% + + # Compute median times + group_by(unit) %>% + mutate(median.time = median(time)) %>% + mutate(median.time.nodes = median(time.nodes)) %>% + mutate(normalized.time = time / median.time - 1) %>% + mutate(log.median.time = log(median.time)) %>% + mutate(median.time.nodes.iter = median(time.nodes.iter)) %>% + ungroup() + +dpi = 300 +h = 3 +w = 6 + +# --------------------------------------------------------------------- + +#p = ggplot(df, aes(x=sizeFactor, y=normalized.time, fill=granul, color=iterations)) + +# geom_boxplot() + +# geom_hline(yintercept=c(-0.01, 0.01), linetype="dashed", color="red") + +# theme_bw() + +# facet_wrap(branch ~ .) + +# labs(x="nodes", y="Normalized time", +# title="Creams strong scaling: normalized time", +# subtitle=output) + +# theme(plot.subtitle=element_text(size=8)) +# +#ggsave("normalized.time.png", plot=p, width=w, height=h, dpi=dpi) +#ggsave("normalized.time.pdf", plot=p, width=w, height=h, dpi=dpi) + +# --------------------------------------------------------------------- + +p = ggplot(df, aes(x=sizeFactor, y=time.elem, color=branch)) + + geom_point(shape=21, size=3) + +# geom_line(aes(y=median.time, group=gitBranch)) + + theme_bw() + +# facet_wrap(branch ~ .) + + labs(x="Size factor k (nz=k*3072)", y="Time / k (s)", + #title="Creams size: time per object", + subtitle=output) + + theme(plot.subtitle=element_text(size=8, family="mono"), + legend.position="bottom") + +ggsave("time.png", plot=p, width=w, height=h, dpi=dpi) +ggsave("time.pdf", plot=p, width=w, height=h, dpi=dpi) + diff --git a/garlic/fig/index.nix b/garlic/fig/index.nix index 6f6ff4b..a54ed9f 100644 --- a/garlic/fig/index.nix +++ b/garlic/fig/index.nix @@ -56,6 +56,7 @@ in creams = with exp.creams; { ss = stdPlot ./creams/ss.R [ ss ]; granularity = stdPlot ./creams/granularity.R [ granularity ]; + size = stdPlot ./creams/size.R [ size ]; # Extended version (we could use another R script for those plots big.ss = stdPlot ./creams/ss.R [ big.ss ];