nbody: add "nodes or sockets" experiment
This commit is contained in:
Antoni Navarro
parent
48a61dc292
commit
58294d4467
@ -9,6 +9,7 @@
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{
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{
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nbody = rec {
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nbody = rec {
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granularity = callPackage ./nbody/granularity-mpi.nix { };
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granularity = callPackage ./nbody/granularity-mpi.nix { };
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nodesorsockets = callPackage ./nbody/nodes-or-sockets-mpi.nix { };
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};
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};
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saiph = {
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saiph = {
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72
garlic/exp/nbody/nodes-or-sockets-mpi.nix
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72
garlic/exp/nbody/nodes-or-sockets-mpi.nix
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@ -0,0 +1,72 @@
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{
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stdenv
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, stdexp
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, bsc
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, targetMachine
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, stages
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, garlicTools
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, numactl
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}:
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with stdenv.lib;
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with garlicTools;
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let
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# Initial variable configuration
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varConf = with bsc; {
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blocksize = [ 256 512 1024 ];
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gitBranch = [ "garlic/tampi+send+oss+task" ];
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attachToSocket = [ true false ];
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numactl = [ true false ];
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};
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# Generate the complete configuration for each unit
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genConf = c: targetMachine.config // rec {
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hw = targetMachine.config.hw;
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particles = 4 * 4096 * hw.cpusPerSocket;
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timesteps = 10;
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blocksize = c.blocksize;
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gitBranch = c.gitBranch;
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socketAtt = c.attachToSocket;
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useNumact = c.numactl;
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expName = "nbody-granularity";
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attachName = if (socketAtt) then "PerSocket" else "PerNode";
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numaName = if (useNumact) then "True" else "False";
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unitName = expName +
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"-${toString gitBranch}" +
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"-bs${toString blocksize}" +
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"-ranks${toString attachName}" +
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"-useNuma${toString numaName}";
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loops = 30;
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qos = "debug";
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ntasksPerNode = if (socketAtt) then 2 else 1;
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nodes = 4;
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time = "02:00:00";
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cpusPerTask = if (socketAtt) then hw.cpusPerSocket else 2*hw.cpusPerSocket;
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jobName = unitName;
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};
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# Compute the array of configurations
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configs = stdexp.buildConfigs {
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inherit varConf genConf;
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};
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exec = {nextStage, conf, ...}: stages.exec ({
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inherit nextStage;
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argv = [ "-t" conf.timesteps "-p" conf.particles ];
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} // optionalAttrs (conf.useNumact) {
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program = "${numactl}/bin/numactl --interleave=all ${stageProgram nextStage}";
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});
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program = {nextStage, conf, ...}: with conf; bsc.garlic.apps.nbody.override {
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inherit (conf) blocksize gitBranch;
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};
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pipeline = stdexp.stdPipeline ++ [ exec program ];
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in
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stdexp.genExperiment { inherit configs pipeline; }
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@ -31,6 +31,7 @@ in
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{
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{
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nbody = with exp.nbody; {
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nbody = with exp.nbody; {
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granularity = stdPlot ./nbody/granularity.R [ granularity ];
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granularity = stdPlot ./nbody/granularity.R [ granularity ];
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nodesorsockets = stdPlot ./nbody/nodes-or-sockets.R [ nodesorsockets ];
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};
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};
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hpcg = with exp.hpcg; {
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hpcg = with exp.hpcg; {
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168
garlic/fig/nbody/nodes-or-sockets.R
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168
garlic/fig/nbody/nodes-or-sockets.R
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@ -0,0 +1,168 @@
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library(ggplot2)
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library(dplyr, warn.conflicts = FALSE)
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library(scales)
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library(jsonlite)
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library(viridis, warn.conflicts = FALSE)
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# Load the arguments (argv)
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args = commandArgs(trailingOnly=TRUE)
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if (length(args)>0) { input_file = args[1] } else { input_file = "input" }
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dfNuma = jsonlite::stream_in(file(input_file), verbose=FALSE) %>%
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jsonlite::flatten() %>%
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select(config.blocksize, config.gitBranch, config.socketAtt, config.useNumact, unit, time) %>%
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rename(blocksize=config.blocksize, branch=config.gitBranch, attachment=config.socketAtt, usenuma=config.useNumact) %>%
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mutate(blocksize = as.factor(blocksize)) %>%
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mutate(branch = as.factor(branch)) %>%
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mutate(attachment = as.factor(attachment)) %>%
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mutate(usenuma = as.factor(usenuma)) %>%
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mutate(unit = as.factor(unit)) %>%
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group_by(unit) %>%
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mutate(median.time = median(time)) %>%
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mutate(normalized.time = time / median.time - 1) %>%
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mutate(log.median.time = log(median.time)) %>%
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filter(usenuma == TRUE) %>%
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ungroup()
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dfNonuma = jsonlite::stream_in(file(input_file), verbose=FALSE) %>%
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jsonlite::flatten() %>%
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select(config.blocksize, config.gitBranch, config.socketAtt, config.useNumact, unit, time) %>%
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rename(blocksize=config.blocksize, branch=config.gitBranch, attachment=config.socketAtt, usenuma=config.useNumact) %>%
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mutate(blocksize = as.factor(blocksize)) %>%
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mutate(branch = as.factor(branch)) %>%
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mutate(attachment = as.factor(attachment)) %>%
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mutate(usenuma = as.factor(usenuma)) %>%
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mutate(unit = as.factor(unit)) %>%
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group_by(unit) %>%
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mutate(median.time = median(time)) %>%
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mutate(normalized.time = time / median.time - 1) %>%
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mutate(log.median.time = log(median.time)) %>%
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filter(usenuma == FALSE) %>%
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ungroup()
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dpi = 300
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h = 5
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w = 8
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# ---------------------------------------------------------------------
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p = ggplot(dfNuma, aes(x=blocksize, y=median.time, color=attachment)) +
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geom_point() +
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geom_line(aes(group=attachment)) +
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theme_bw() +
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labs(x="Blocksize", y="Median time (s)", title="NBody Granularity (tampi+send+oss+task | numactl ON | 4 Nodes): Median Time",
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subtitle=input_file, color="Rank Attachment") +
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theme(plot.subtitle=element_text(size=5)) +
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theme(legend.position="bottom") +
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scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
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ggsave("median-numactl.time.png", plot=p, width=w, height=h, dpi=dpi)
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ggsave("median-numactl.time.pdf", plot=p, width=w, height=h, dpi=dpi)
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p = ggplot(dfNonuma, aes(x=blocksize, y=median.time, color=attachment)) +
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geom_point() +
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geom_line(aes(group=attachment)) +
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theme_bw() +
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labs(x="Blocksize", y="Median time (s)", title="NBody Granularity (tampi+send+oss+task | numactl OFF | 4 Nodes): Median Time",
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subtitle=input_file, color="Rank Attachment") +
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theme(plot.subtitle=element_text(size=5)) +
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theme(legend.position="bottom") +
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scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
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ggsave("median.time.png", plot=p, width=w, height=h, dpi=dpi)
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ggsave("median.time.pdf", plot=p, width=w, height=h, dpi=dpi)
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# ---------------------------------------------------------------------
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p = ggplot(dfNuma, aes(x=blocksize, y=normalized.time, color=attachment)) +
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geom_boxplot() +
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geom_hline(yintercept=c(-0.01, 0.01), linetype="dashed", color="red") +
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facet_wrap(~ attachment) +
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theme_bw() +
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labs(x="Blocksize", y="Normalized Time", title="NBody Granularity (tampi+send+oss+task | numactl ON | 4 Nodes): Normalized Time",
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subtitle=input_file, color="Rank Attachment") +
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theme(plot.subtitle=element_text(size=5)) +
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theme(legend.position="bottom") +
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scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
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ggsave("normalized-numactl.time.png", plot=p, width=w, height=h, dpi=dpi)
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ggsave("normalized-numactl.time.pdf", plot=p, width=w, height=h, dpi=dpi)
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p = ggplot(dfNonuma, aes(x=blocksize, y=normalized.time, color=attachment)) +
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geom_boxplot() +
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geom_hline(yintercept=c(-0.01, 0.01), linetype="dashed", color="red") +
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facet_wrap(~ attachment) +
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theme_bw() +
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labs(x="Blocksize", y="Normalized Time", title="NBody Granularity (tampi+send+oss+task | 4 Nodes): Normalized Time",
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subtitle=input_file, color="Rank Attachment") +
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theme(plot.subtitle=element_text(size=5)) +
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theme(legend.position="bottom") +
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scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
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ggsave("normalized.time.png", plot=p, width=w, height=h, dpi=dpi)
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ggsave("normalized.time.pdf", plot=p, width=w, height=h, dpi=dpi)
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# ---------------------------------------------------------------------
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p = ggplot(dfNuma, aes(x=blocksize, y=time, color=attachment)) +
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geom_point(shape=21, size=3) +
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theme_bw() +
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labs(x="Blocksize", y="Time (s)", title="NBody Granularity (tampi+send+oss+task | numactl ON | 4 Nodes): Time",
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subtitle=input_file, color="Rank Attachment") +
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theme(plot.subtitle=element_text(size=5)) +
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theme(legend.position="bottom") +
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scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
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ggsave("time-numactl.png", plot=p, width=w, height=h, dpi=dpi)
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ggsave("time-numactl.pdf", plot=p, width=w, height=h, dpi=dpi)
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p = ggplot(dfNonuma, aes(x=blocksize, y=time, color=attachment)) +
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geom_point(shape=21, size=3) +
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theme_bw() +
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labs(x="Blocksize", y="Time (s)", title="NBody Granularity (tampi+send+oss+task | 4 Nodes): Time",
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subtitle=input_file, color="Rank Attachment") +
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theme(plot.subtitle=element_text(size=5)) +
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theme(legend.position="bottom") +
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scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
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ggsave("time.png", plot=p, width=w, height=h, dpi=dpi)
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ggsave("time.pdf", plot=p, width=w, height=h, dpi=dpi)
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# ---------------------------------------------------------------------
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p = ggplot(dfNuma, aes(x=blocksize, y=attachment, fill=median.time)) +
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geom_raster() +
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scale_fill_viridis(option="plasma") +
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coord_fixed() +
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theme_bw() +
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labs(x="Blocksize", y="Attachment", title="NBody Granularity (tampi+send+oss+task | numactl ON | 4 Nodes): Time",
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subtitle=input_file, color = "Rank Attachment") +
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theme(plot.subtitle=element_text(size=5)) +
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theme(legend.position="bottom") +
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scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
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ggsave("time-numactl.heatmap.png", plot=p, width=w, height=h, dpi=dpi)
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ggsave("time-numactl.heatmap.pdf", plot=p, width=w, height=h, dpi=dpi)
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p = ggplot(dfNonuma, aes(x=blocksize, y=attachment, fill=median.time)) +
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geom_raster() +
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scale_fill_viridis(option="plasma") +
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coord_fixed() +
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theme_bw() +
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labs(x="Blocksize", y="Attachment", title="NBody Granularity (tampi+send+oss+task | 4 Nodes): Time",
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subtitle=input_file, color = "Rank Attachment") +
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theme(plot.subtitle=element_text(size=5)) +
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theme(legend.position="bottom") +
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scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
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ggsave("time.heatmap.png", plot=p, width=w, height=h, dpi=dpi)
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ggsave("time.heatmap.pdf", plot=p, width=w, height=h, dpi=dpi)
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