Add dataset attrset in garlic

Modify nbody to evenly distribute blocks per cpu

garlic/exp/nbody/tampi.nix

@@ -8,7 +8,7 @@
 
 # Leave the first CPU per socket unused?
 , freeCpu ? false
-, particles ? 1024 * 32
+, particles ? 4096 * 24
 }:
 
 with stdenv.lib;
@@ -16,8 +16,7 @@ with stdenv.lib;
 let
   # Initial variable configuration
   varConf = with bsc; {
-    # We need at least cpusPerNode blocks
+    nblocks = [ 12 24 48 96 192 384 768 ];
-    nblocks = [ 4 8 16 32 64 128 256 512 ];
   };
 
   machineConfig = targetMachine.config;

garlic/fig/nbody/freeCpu.R

@@ -6,29 +6,34 @@ library(jsonlite)
 args=commandArgs(trailingOnly=TRUE)
 
 # Read the timetable from args[1]
-input_file = "timetable.json.gz"
+input_file = "input.json"
 if (length(args)>0) { input_file = args[1] }
 
 # Load the dataset in NDJSON format
 dataset = jsonlite::stream_in(file(input_file)) %>%
 	jsonlite::flatten()
 
-# We only need the cpu bind, blocksize and time
+particles = unique(dataset$config.particles)
-df = select(dataset, config.freeCpu, config.blocksize, time) %>%
+
-	rename(blocksize=config.blocksize, freeCpu=config.freeCpu)
+# We only need the cpu bind, nblocks and time
+df = select(dataset, config.freeCpu, config.nblocks, config.hw.cpusPerSocket, time) %>%
+	rename(nblocks=config.nblocks,
+		freeCpu=config.freeCpu,
+		cpusPerSocket=config.hw.cpusPerSocket)
+
+df = df %>% mutate(blocksPerCpu = nblocks / cpusPerSocket)
 
-# Use the blocksize as factor
-df$blocksize = as.factor(df$blocksize)
 df$freeCpu = as.factor(df$freeCpu)
+df$nblocks = as.factor(df$nblocks)
+df$blocksPerCpuFactor = as.factor(df$blocksPerCpu)
 
 # Split by malloc variant
-D=df %>% group_by(freeCpu, blocksize) %>%
+D=df %>% group_by(freeCpu, nblocks) %>%
 	mutate(tnorm = time / median(time) - 1)
 
-bs_unique = unique(df$blocksize)
+bs_unique = unique(df$nblocks)
 nbs=length(bs_unique)
 
-
 print(D)
 
 ppi=300
@@ -39,12 +44,12 @@ png("box.png", width=w*ppi, height=h*ppi, res=ppi)
 #
 #
 #
-# Create the plot with the normalized time vs blocksize
+# Create the plot with the normalized time vs nblocks
-p = ggplot(data=D, aes(x=blocksize, y=tnorm)) +
+p = ggplot(data=D, aes(x=blocksPerCpuFactor, y=tnorm)) +
 
 	# Labels
-	labs(x="Block size", y="Normalized time",
+	labs(x="Blocks/CPU", y="Normalized time",
-              title="Nbody normalized time",
+              title=sprintf("Nbody normalized time. Particles=%d", particles), 
               subtitle=input_file) +
 
 	# Center the title
@@ -85,14 +90,15 @@ dev.off()
 #
 png("scatter.png", width=w*ppi, height=h*ppi, res=ppi)
 #
-## Create the plot with the normalized time vs blocksize
+## Create the plot with the normalized time vs nblocks
-p = ggplot(D, aes(x=blocksize, y=time, color=freeCpu)) +
+p = ggplot(D, aes(x=blocksPerCpuFactor, y=time, color=freeCpu)) +
 
-	labs(x="Block size", y="Time (s)",
+	labs(x="Blocks/CPU", y="Time (s)",
-              title="Nbody granularity",
+              title=sprintf("Nbody granularity. Particles=%d", particles), 
               subtitle=input_file) +
 	theme_bw() +
 	theme(plot.subtitle=element_text(size=8)) +
+	theme(legend.position = c(0.5, 0.88)) +
 
 	geom_point(shape=21, size=3) +
 	#scale_x_continuous(trans=log2_trans()) +

garlic/fig/nbody/jemalloc.R

@@ -6,30 +6,36 @@ library(jsonlite)
 args=commandArgs(trailingOnly=TRUE)
 
 # Read the timetable from args[1]
-input_file = "timetable.json.gz"
+input_file = "input.json"
 if (length(args)>0) { input_file = args[1] }
 
 # Load the dataset in NDJSON format
 dataset = jsonlite::stream_in(file(input_file)) %>%
 	jsonlite::flatten()
 
-# We only need the cpu bind, blocksize and time
+particles = unique(dataset$config.particles)
-df = select(dataset, config.enableJemalloc, config.blocksize, time) %>%
+
-	rename(blocksize=config.blocksize,
+# We only need the cpu bind, nblocks and time
-	       jemalloc=config.enableJemalloc)
+df = select(dataset, config.enableJemalloc, config.nblocks, config.hw.cpusPerSocket, time) %>%
+	rename(nblocks=config.nblocks,
+		jemalloc=config.enableJemalloc,
+		cpusPerSocket=config.hw.cpusPerSocket)
+
+df = df %>% mutate(blocksPerCpu = nblocks / cpusPerSocket)
 
-# Use the blocksize as factor
-df$blocksize = as.factor(df$blocksize)
 df$jemalloc = as.factor(df$jemalloc)
+df$nblocks = as.factor(df$nblocks)
+df$blocksPerCpuFactor = as.factor(df$blocksPerCpu)
 
 # Split by malloc variant
-D=df %>% group_by(jemalloc, blocksize) %>%
+D=df %>% group_by(jemalloc, nblocks) %>%
 	mutate(tnorm = time / median(time) - 1)
+	# Add another column: blocksPerCpu (we assume one task per socket, using
+	# all CPUs)
 
-bs_unique = unique(df$blocksize)
+bs_unique = unique(df$nblocks)
 nbs=length(bs_unique)
 
-
 print(D)
 
 ppi=300
@@ -40,12 +46,12 @@ png("box.png", width=w*ppi, height=h*ppi, res=ppi)
 #
 #
 #
-# Create the plot with the normalized time vs blocksize
+# Create the plot with the normalized time vs nblocks
-p = ggplot(data=D, aes(x=blocksize, y=tnorm)) +
+p = ggplot(data=D, aes(x=nblocks, y=tnorm)) +
 
 	# Labels
-	labs(x="Block size", y="Normalized time",
+	labs(x="Num blocks", y="Normalized time",
-              title="Nbody normalized time",
+              title=sprintf("Nbody normalized time. Particles=%d", particles), 
               subtitle=input_file) +
 
 	# Center the title
@@ -62,8 +68,7 @@ p = ggplot(data=D, aes(x=blocksize, y=tnorm)) +
 	geom_boxplot(aes(fill=jemalloc)) +
 
 #	# Use log2 scale in x
-#	scale_x_continuous(trans=log2_trans(),
+#	scale_x_continuous(trans=log2_trans()) +
-#			   breaks=bs_unique) +
 #
 	scale_y_continuous(breaks = scales::pretty_breaks(n = 10)) +
 
@@ -86,17 +91,18 @@ dev.off()
 #
 png("scatter.png", width=w*ppi, height=h*ppi, res=ppi)
 #
-## Create the plot with the normalized time vs blocksize
+## Create the plot with the normalized time vs nblocks
-p = ggplot(D, aes(x=blocksize, y=time, color=jemalloc)) +
+p = ggplot(D, aes(x=blocksPerCpu, y=time, color=jemalloc)) +
 
-	labs(x="Block size", y="Time (s)",
+	labs(x="Blocks/CPU", y="Time (s)",
-              title="Nbody granularity",
+              title=sprintf("Nbody granularity. Particles=%d", particles), 
               subtitle=input_file) +
 	theme_bw() +
 	theme(plot.subtitle=element_text(size=8)) +
+	theme(legend.position = c(0.5, 0.88)) +
 
 	geom_point(shape=21, size=3) +
-	#scale_x_continuous(trans=log2_trans()) +
+	scale_x_continuous(trans=log2_trans()) +
 	scale_y_continuous(trans=log2_trans())
 
 # Render the plot

garlic/pp/timetable.nix

@@ -20,8 +20,7 @@ stdenv.mkDerivation {
         conf=garlic_config.json
         for run in $(ls -d [0-9]* | sort -n); do
           time=$(awk '/^time /{print $2}' $run/stdout.log)
-          jq -cn "{ exp:\"$exp\", unit:\"$unit\", config:inputs, time:$time}" \
+          jq -cn "{ exp:\"$exp\", unit:\"$unit\", config:inputs, time:$time, run:$run }" $conf >> $out
-            $conf >> $out
         done
       done
     done

overlay.nix

@@ -284,7 +284,7 @@ let
           tampi = callPackage ./garlic/exp/nbody/tampi.nix { };
 
           # Experiment variants
-          medium = tampi.override { particles = 64 * 1024; };
+          medium = tampi.override { particles = 24 * 4096; };
           baseline = medium;
           freeCpu = baseline.override { freeCpu = true; };
           jemalloc = baseline.override { enableJemalloc = true; };
@@ -329,23 +329,31 @@ let
         timetableFromTrebuchet = tre: timetable (resultFromTrebuchet tre);
         mergeDatasets = callPackage ./garlic/pp/merge.nix { };
 
-        # Takes a list of experiments and returns a file that contains the
+        # Takes a list of experiments and returns a file that contains
         # all timetable results from the experiments.
         merge = exps: mergeDatasets (map timetableFromTrebuchet exps);
       };
 
+      # Datasets used in the figures
+      ds = with self.bsc.garlic; {
+        nbody = {
+          jemalloc = with exp.nbody; pp.merge [ baseline jemalloc ];
+          freeCpu = with exp.nbody; pp.merge [ baseline freeCpu ];
+        };
+      };
+
       # Figures generated from the experiments
       fig = with self.bsc.garlic; {
         nbody = {
 
           jemalloc = pp.rPlot {
             script = ./garlic/fig/nbody/jemalloc.R;
-            dataset = with exp.nbody; pp.merge [ baseline jemalloc ];
+            dataset = ds.nbody.jemalloc;
           };
 
           freeCpu = pp.rPlot {
             script = ./garlic/fig/nbody/freeCpu.R;
-            dataset = with exp.nbody; pp.merge [ baseline freeCpu ];
+            dataset = ds.nbody.freeCpu;
           };
 
         };
@@ -359,5 +367,5 @@ in
 
     # Aliases
     garlic = bsc.garlic;
-    inherit (bsc.garlic) exp fig apps;
+    inherit (bsc.garlic) exp fig apps ds;
   }