nbody: update granularity tests

garlic/exp/index.nix

@@ -9,6 +9,8 @@
 {
   nbody = rec {
     baseline = callPackage ./nbody/nblocks.nix { };
+    granularity = callPackage ./nbody/granularity-mpi.nix { };
+    scaling = callPackage ./nbody/scaling.nix { };
 
     # Experiment variants
     small = baseline.override {
@@ -25,10 +27,6 @@
       };
 
     };
-
-    scaling = callPackage ./nbody/scaling.nix {
-      particles = 12 * 4096;
-    };
   };
 
   saiph = {

garlic/exp/nbody/granularity-mpi.nix

@@ -4,48 +4,42 @@
 , bsc
 , targetMachine
 , stages
+, garlicTools
 }:
 
 with stdenv.lib;
+with garlicTools;
 
 let
   # Initial variable configuration
   varConf = with bsc; {
     blocksize = [ 128 256 512 1024 2048 4096 ];
+    gitBranch = [
+      "garlic/mpi+send+oss+task" 
+      "garlic/tampi+send+oss+task" 
+      "garlic/tampi+isend+oss+task"
+    ];
   };
 
-  machineConfig = targetMachine.config;
-
   # Generate the complete configuration for each unit
-  genConf = with bsc; c: targetMachine.config // rec {
+  genConf = c: targetMachine.config // rec {
-    expName = "nbody.test";
+    hw = targetMachine.config.hw;
-    unitName = "${expName}.nb-${toString nblocks}";
+    particles = 4096 * hw.cpusPerSocket;
-
-    inherit (machineConfig) hw;
-    # nbody options
-    particles = 1024 * 64;
     timesteps = 10;
-    inherit (c) blocksize;
+    blocksize = c.blocksize;
-    totalTasks = ntasksPerNode * nodes;
+    gitBranch = c.gitBranch;
-    particlesPerTask = particles / totalTasks;
-    cc = icc;
-    mpi = impi;
-    gitBranch = "garlic/mpi+send";
 
-    # Repeat the execution of each unit 30 times
+    expName = "nbody-granularity";
-    loops = 10;
+    unitName = expName + "-${toString gitBranch}" + "-bs${toString blocksize}";
 
-    # Resources
+    loops = 30;
-    qos = "debug";
+
-    ntasksPerNode = 48;
+    qos = "bsc_cs";
+    ntasksPerNode = 1;
     nodes = 1;
-    time = "02:00:00";
+    time = "04:00:00";
-    cpuBind = "sockets,verbose";
+    cpusPerTask = hw.cpusPerSocket;
-    jobName = "bs-${toString blocksize}-${gitBranch}-nbody";
+    jobName = unitName;
-
-    # Experiment revision: this allows a user to run again a experiment already
-    # executed
-    rev = 0;
   };
 
   # Compute the array of configurations
@@ -53,18 +47,13 @@ let
     inherit varConf genConf;
   };
 
-  exec = {nextStage, conf, ...}: with conf; stages.exec {
+  exec = {nextStage, conf, ...}: stages.exec {
     inherit nextStage;
-    argv = [ "-t" timesteps "-p" particles ];
+    argv = [ "-t" conf.timesteps "-p" conf.particles ];
   };
 
-  program = {nextStage, conf, ...}: with conf;
+  program = {nextStage, conf, ...}: with conf; bsc.garlic.apps.nbody.override {
-  # FIXME: This is becoming very slow:
+    inherit (conf) blocksize gitBranch;
-  #let
-  #  customPkgs = stdexp.replaceMpi conf.mpi;
-  #in
-  bsc.garlic.apps.nbody.override {
-    inherit cc blocksize mpi gitBranch;
   };
 
   pipeline = stdexp.stdPipeline ++ [ exec program ];

garlic/exp/nbody/granularity-oss.nix

@@ -4,36 +4,38 @@
 , bsc
 , targetMachine
 , stages
+, garlicTools
 }:
 
 with stdenv.lib;
+with garlicTools;
 
 let
+
   # Initial variable configuration
-  varConf = with bsc; {
+  varConf = {
     blocksize = [ 128 256 512 1024 2048 4096 ];
   };
 
   # Generate the complete configuration for each unit
-  genConf = with bsc; c: targetMachine.config // rec {
+  genConf = c: targetMachine.config // rec {
-    # nbody options
+    hw = targetMachine.config.hw;
-    particles = 1024 * 64;
+    particles = 4096 * hw.cpusPerSocket;
     timesteps = 10;
-    inherit (c) blocksize;
+    blocksize = c.blocksize;
-    cc = icc;
+    
-    mpi = impi;
     gitBranch = "garlic/oss+task";
+    expName = "nbody-granularity";
+    unitName = expName + "-bs${toString blocksize}";
 
-    # Repeat the execution of each unit 30 times
     loops = 30;
 
-    # Resources
     qos = "debug";
     ntasksPerNode = 1;
     nodes = 1;
     time = "02:00:00";
-    cpuBind = "sockets,verbose";
+    cpusPerTask = hw.cpusPerSocket;
-    jobName = "nbody-bs-${toString blocksize}-${gitBranch}";
+    jobName = unitName;
   };
 
   # Compute the array of configurations
@@ -41,18 +43,14 @@ let
     inherit varConf genConf;
   };
 
-  exec = {nextStage, conf, ...}: with conf; stages.exec {
+  exec = {nextStage, conf, ...}: stages.exec {
     inherit nextStage;
-    argv = [ "-t" timesteps "-p" particles ];
+    argv = [ "-t" conf.timesteps "-p" conf.particles ];
   };
 
-  program = {nextStage, conf, ...}: with conf;
+  program = {nextStage, conf, ...}: with conf; bsc.garlic.apps.nbody.override {
-  let
+    inherit (conf) blocksize gitBranch;
-    customPkgs = stdexp.replaceMpi conf.mpi;
+  };
-  in
-    customPkgs.apps.nbody.override {
-      inherit cc blocksize mpi gitBranch;
-    };
 
   pipeline = stdexp.stdPipeline ++ [ exec program ];
 

garlic/fig/index.nix

@@ -30,11 +30,12 @@ let
 in
 {
   nbody = with exp.nbody; {
-    baseline  = stdPlot ./nbody/baseline.R [ baseline ];
+    baseline    = stdPlot ./nbody/baseline.R    [ baseline ];
-    small     = stdPlot ./nbody/baseline.R [ small ];
+    small       = stdPlot ./nbody/baseline.R    [ small ];
-    jemalloc  = stdPlot ./nbody/jemalloc.R [ baseline jemalloc ];
+    jemalloc    = stdPlot ./nbody/jemalloc.R    [ baseline jemalloc ];
-    ctf       = stdPlot ./nbody/baseline.R [ ctf ];
+    ctf         = stdPlot ./nbody/baseline.R    [ ctf ];
-    scaling   = stdPlot ./nbody/baseline.R [ scaling ];
+    scaling     = stdPlot ./nbody/baseline.R    [ scaling ];
+    granularity = stdPlot ./nbody/granularity.R [ granularity ];
   };
 
   hpcg = with exp.hpcg; {

garlic/fig/nbody/granularity.R

@@ -0,0 +1,92 @@
+library(ggplot2)
+library(dplyr, warn.conflicts = FALSE)
+library(scales)
+library(jsonlite)
+library(viridis, warn.conflicts = FALSE)
+
+# Load the arguments (argv)
+args = commandArgs(trailingOnly=TRUE)
+if (length(args)>0) { input_file = args[1] } else { input_file = "input" }
+
+df = jsonlite::stream_in(file(input_file), verbose=FALSE) %>%
+  jsonlite::flatten() %>%
+  select(config.blocksize, config.gitBranch, unit, time) %>%
+  rename(blocksize=config.blocksize, branch=config.gitBranch) %>%
+
+  mutate(blocksize = as.factor(blocksize)) %>%
+  mutate(branch = as.factor(branch)) %>%
+  mutate(unit = as.factor(unit)) %>%
+
+  group_by(unit) %>%
+
+  mutate(median.time = median(time)) %>%
+  mutate(normalized.time = time / median.time - 1) %>%
+  mutate(log.median.time = log(median.time)) %>%
+
+  ungroup()
+
+dpi = 300
+h = 5
+w = 8
+
+# ---------------------------------------------------------------------
+
+p = ggplot(df, aes(x=blocksize, y=median.time, color=branch)) +
+  geom_point() +
+  geom_line(aes(group=branch)) +
+  theme_bw() +
+  labs(x="Blocksize", y="Median time (s)", title="NBody Granularity: Median Time", 
+    subtitle=input_file) + 
+  theme(plot.subtitle=element_text(size=5)) +
+  theme(legend.position="bottom") +
+  theme(legend.text = element_text(size=7))
+
+ggsave("median.time.png", plot=p, width=w, height=h, dpi=dpi)
+ggsave("median.time.pdf", plot=p, width=w, height=h, dpi=dpi)
+
+# ---------------------------------------------------------------------
+
+p = ggplot(df, aes(x=blocksize, y=normalized.time, color=branch)) +
+  geom_boxplot() +
+  geom_hline(yintercept=c(-0.01, 0.01), linetype="dashed", color="red") +
+  facet_wrap(~ branch) +
+  theme_bw() +
+  labs(x="Blocksize", y="Normalized Time", title="NBody Granularity: Normalized Time", 
+    subtitle=input_file) + 
+  theme(plot.subtitle=element_text(size=5)) +
+  theme(legend.position="bottom") +
+  theme(legend.text = element_text(size=7))
+
+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=blocksize, y=time, color=branch)) +
+  geom_point(shape=21, size=3) +
+  theme_bw() +
+  labs(x="Blocksize", y="Time (s)", title="NBody Granularity: Time", 
+    subtitle=input_file) + 
+  theme(plot.subtitle=element_text(size=5)) +
+  theme(legend.position="bottom") +
+  theme(legend.text = element_text(size=7))
+
+ggsave("time.png", plot=p, width=w, height=h, dpi=dpi)
+ggsave("time.pdf", plot=p, width=w, height=h, dpi=dpi)
+
+
+# ---------------------------------------------------------------------
+
+p = ggplot(df, aes(x=blocksize, y=branch, fill=median.time)) +
+  geom_raster() + 
+  scale_fill_viridis(option="plasma") +
+  coord_fixed() +
+  theme_bw() +
+  labs(x="Blocksize", y="Branch", title="NBody Granularity: Time", 
+    subtitle=input_file) + 
+  theme(plot.subtitle=element_text(size=5)) +
+  theme(legend.position="bottom") +
+  theme(legend.text = element_text(size=7))
+
+ggsave("time.heatmap.png", plot=p, width=w, height=h, dpi=dpi)
+ggsave("time.heatmap.pdf", plot=p, width=w, height=h, dpi=dpi)