nbody: update and simplify figures

garlic/fig/index.nix

@@ -31,8 +31,8 @@ in
 {
   nbody = with exp.nbody; {
     granularity = stdPlot ./nbody/granularity.R [ granularity ];
-    nodesorsockets = stdPlot ./nbody/nodes-or-sockets.R [ nodesorsockets ];
+    ss = stdPlot ./nbody/ss.R [ ss ];
-    scaling = stdPlot ./nbody/scaling.R [ scaling ];
+    numa = stdPlot ./nbody/numa.R [ numa ];
   };
 
   hpcg = with exp.hpcg; {

garlic/fig/nbody/granularity.R

@@ -10,10 +10,11 @@ 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) %>%
+  select(config.blocksize, config.gitBranch, config.particles, unit, time) %>%
-  rename(blocksize=config.blocksize, branch=config.gitBranch) %>%
+  rename(blocksize=config.blocksize, particles=config.particles, branch=config.gitBranch) %>%
 
   mutate(blocksize = as.factor(blocksize)) %>%
+  mutate(particles = as.factor(particles)) %>%
   mutate(branch = as.factor(branch)) %>%
   mutate(unit = as.factor(unit)) %>%
 
@@ -27,22 +28,7 @@ df = jsonlite::stream_in(file(input_file), verbose=FALSE) %>%
 
 dpi = 300
 h = 5
-w = 8
+w = 5
-
-# ---------------------------------------------------------------------
-
-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)
 
 # ---------------------------------------------------------------------
 
@@ -53,7 +39,7 @@ p = ggplot(df, aes(x=blocksize, y=normalized.time, color=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(plot.subtitle=element_text(size=8)) +
   theme(legend.position="bottom") +
   theme(legend.text = element_text(size=7))
 
@@ -62,31 +48,14 @@ ggsave("normalized.time.pdf", plot=p, width=w, height=h, dpi=dpi)
 
 # ---------------------------------------------------------------------
 
-p = ggplot(df, aes(x=blocksize, y=time, color=branch)) +
+p = ggplot(df, aes(x=blocksize, y=time)) +
-  geom_point(shape=21, size=3) +
+  geom_boxplot() +
   theme_bw() +
   labs(x="Blocksize", y="Time (s)", title="NBody Granularity: Time", 
     subtitle=input_file) + 
-  theme(plot.subtitle=element_text(size=5)) +
+  theme(plot.subtitle=element_text(size=8)) +
   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)

garlic/fig/nbody/nodes-or-sockets.R

@@ -1,168 +0,0 @@
-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" }
-
-dfNuma = jsonlite::stream_in(file(input_file), verbose=FALSE) %>%
-  jsonlite::flatten() %>%
-  select(config.blocksize, config.gitBranch, config.socketAtt, config.useNumact, unit, time) %>%
-  rename(blocksize=config.blocksize, branch=config.gitBranch, attachment=config.socketAtt, usenuma=config.useNumact) %>%
-
-  mutate(blocksize = as.factor(blocksize)) %>%
-  mutate(branch = as.factor(branch)) %>%
-  mutate(attachment = as.factor(attachment)) %>%
-  mutate(usenuma = as.factor(usenuma)) %>%
-  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)) %>%
-
-  filter(usenuma == TRUE) %>%
-
-  ungroup()
-
-dfNonuma = jsonlite::stream_in(file(input_file), verbose=FALSE) %>%
-  jsonlite::flatten() %>%
-  select(config.blocksize, config.gitBranch, config.socketAtt, config.useNumact, unit, time) %>%
-  rename(blocksize=config.blocksize, branch=config.gitBranch, attachment=config.socketAtt, usenuma=config.useNumact) %>%
-
-  mutate(blocksize = as.factor(blocksize)) %>%
-  mutate(branch = as.factor(branch)) %>%
-  mutate(attachment = as.factor(attachment)) %>%
-  mutate(usenuma = as.factor(usenuma)) %>%
-  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)) %>%
-
-  filter(usenuma == FALSE) %>%
-
-  ungroup()
-
-dpi = 300
-h = 5
-w = 8
-
-
-# ---------------------------------------------------------------------
-
-p = ggplot(dfNuma, aes(x=blocksize, y=median.time, color=attachment)) +
-  geom_point() +
-  geom_line(aes(group=attachment)) +
-  theme_bw() +
-  labs(x="Blocksize", y="Median time (s)", title="NBody Granularity (tampi+send+oss+task | numactl ON | 4 Nodes): Median Time", 
-    subtitle=input_file, color="Rank Attachment") + 
-  theme(plot.subtitle=element_text(size=5)) +
-  theme(legend.position="bottom") +
-  scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
-
-ggsave("median-numactl.time.png", plot=p, width=w, height=h, dpi=dpi)
-ggsave("median-numactl.time.pdf", plot=p, width=w, height=h, dpi=dpi)
-
-p = ggplot(dfNonuma, aes(x=blocksize, y=median.time, color=attachment)) +
-  geom_point() +
-  geom_line(aes(group=attachment)) +
-  theme_bw() +
-  labs(x="Blocksize", y="Median time (s)", title="NBody Granularity (tampi+send+oss+task | numactl OFF | 4 Nodes): Median Time", 
-    subtitle=input_file, color="Rank Attachment") + 
-  theme(plot.subtitle=element_text(size=5)) +
-  theme(legend.position="bottom") +
-  scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
-
-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(dfNuma, aes(x=blocksize, y=normalized.time, color=attachment)) +
-  geom_boxplot() +
-  geom_hline(yintercept=c(-0.01, 0.01), linetype="dashed", color="red") +
-  facet_wrap(~ attachment) +
-  theme_bw() +
-  labs(x="Blocksize", y="Normalized Time", title="NBody Granularity (tampi+send+oss+task | numactl ON | 4 Nodes): Normalized Time", 
-    subtitle=input_file, color="Rank Attachment") + 
-  theme(plot.subtitle=element_text(size=5)) +
-  theme(legend.position="bottom") +
-  scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
-
-ggsave("normalized-numactl.time.png", plot=p, width=w, height=h, dpi=dpi)
-ggsave("normalized-numactl.time.pdf", plot=p, width=w, height=h, dpi=dpi)
-
-p = ggplot(dfNonuma, aes(x=blocksize, y=normalized.time, color=attachment)) +
-  geom_boxplot() +
-  geom_hline(yintercept=c(-0.01, 0.01), linetype="dashed", color="red") +
-  facet_wrap(~ attachment) +
-  theme_bw() +
-  labs(x="Blocksize", y="Normalized Time", title="NBody Granularity (tampi+send+oss+task | 4 Nodes): Normalized Time", 
-    subtitle=input_file, color="Rank Attachment") + 
-  theme(plot.subtitle=element_text(size=5)) +
-  theme(legend.position="bottom") +
-  scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
-
-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(dfNuma, aes(x=blocksize, y=time, color=attachment)) +
-  geom_point(shape=21, size=3) +
-  theme_bw() +
-  labs(x="Blocksize", y="Time (s)", title="NBody Granularity (tampi+send+oss+task | numactl ON | 4 Nodes): Time", 
-    subtitle=input_file, color="Rank Attachment") + 
-  theme(plot.subtitle=element_text(size=5)) +
-  theme(legend.position="bottom") +
-  scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
-
-ggsave("time-numactl.png", plot=p, width=w, height=h, dpi=dpi)
-ggsave("time-numactl.pdf", plot=p, width=w, height=h, dpi=dpi)
-
-p = ggplot(dfNonuma, aes(x=blocksize, y=time, color=attachment)) +
-  geom_point(shape=21, size=3) +
-  theme_bw() +
-  labs(x="Blocksize", y="Time (s)", title="NBody Granularity (tampi+send+oss+task | 4 Nodes): Time", 
-    subtitle=input_file, color="Rank Attachment") + 
-  theme(plot.subtitle=element_text(size=5)) +
-  theme(legend.position="bottom") +
-  scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
-
-
-ggsave("time.png", plot=p, width=w, height=h, dpi=dpi)
-ggsave("time.pdf", plot=p, width=w, height=h, dpi=dpi)
-# ---------------------------------------------------------------------
-
-p = ggplot(dfNuma, aes(x=blocksize, y=attachment, fill=median.time)) +
-  geom_raster() + 
-  scale_fill_viridis(option="plasma") +
-  coord_fixed() +
-  theme_bw() +
-  labs(x="Blocksize", y="Attachment", title="NBody Granularity (tampi+send+oss+task | numactl ON | 4 Nodes): Time", 
-    subtitle=input_file, color = "Rank Attachment") + 
-  theme(plot.subtitle=element_text(size=5)) +
-  theme(legend.position="bottom") +
-  scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
-
-ggsave("time-numactl.heatmap.png", plot=p, width=w, height=h, dpi=dpi)
-ggsave("time-numactl.heatmap.pdf", plot=p, width=w, height=h, dpi=dpi)
-
-p = ggplot(dfNonuma, aes(x=blocksize, y=attachment, fill=median.time)) +
-  geom_raster() + 
-  scale_fill_viridis(option="plasma") +
-  coord_fixed() +
-  theme_bw() +
-  labs(x="Blocksize", y="Attachment", title="NBody Granularity (tampi+send+oss+task | 4 Nodes): Time", 
-    subtitle=input_file, color = "Rank Attachment") + 
-  theme(plot.subtitle=element_text(size=5)) +
-  theme(legend.position="bottom") +
-  scale_color_manual(labels = c("RanksPerNode", "RanksPerSocket"), values=c("blue", "red"))
-
-ggsave("time.heatmap.png", plot=p, width=w, height=h, dpi=dpi)
-ggsave("time.heatmap.pdf", plot=p, width=w, height=h, dpi=dpi)

garlic/fig/nbody/numa.R

@@ -0,0 +1,85 @@
+library(ggplot2)
+library(dplyr, warn.conflicts = FALSE)
+library(scales)
+library(jsonlite)
+library(viridis, warn.conflicts = FALSE)
+library(stringr)
+
+# 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(unit,
+    config.blocksize,
+    config.gitBranch,
+    config.attachToSocket,
+    config.interleaveMem,
+    config.nodes,
+    unit,
+    time) %>%
+
+  rename(blocksize=config.blocksize,
+    gitBranch=config.gitBranch,
+    nodes=config.nodes,
+    attachToSocket=config.attachToSocket,
+    interleaveMem=config.interleaveMem) %>%
+
+  # Remove the "garlic/" prefix from the gitBranch
+  mutate(branch = str_replace(gitBranch, "garlic/", "")) %>%
+
+  mutate(blocksize = as.factor(blocksize)) %>%
+  mutate(branch = as.factor(branch)) %>%
+  mutate(attachToSocket = as.factor(attachToSocket)) %>%
+  mutate(interleaveMem = as.factor(interleaveMem)) %>%
+  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()
+
+branch = unique(df$branch)
+nodes = unique(df$nodes)
+
+dpi = 300
+h = 5
+w = 8
+
+# ---------------------------------------------------------------------
+
+p = ggplot(df, aes(x=blocksize, y=normalized.time, color=interleaveMem)) +
+  geom_boxplot() +
+  geom_hline(yintercept=c(-0.01, 0.01), linetype="dashed", color="red") +
+  theme_bw() +
+  facet_wrap(~ attachToSocket, labeller=label_both) +
+  labs(x="Blocksize", y="Normalized time",
+    title=sprintf("NBody NUMA (%s | %d Nodes): Normalized time",
+      branch, nodes), 
+    subtitle=input_file) + 
+  theme(plot.subtitle=element_text(size=8)) +
+  theme(legend.position="bottom")
+
+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=interleaveMem)) +
+  geom_boxplot() +
+  geom_line(aes(y=median.time)) +
+  theme_bw() +
+  facet_wrap(~ attachToSocket, labeller=label_both) +
+  labs(x="Blocksize", y="Time (s)",
+    title=sprintf("NBody NUMA (%s | %d Nodes): Time",
+      branch, nodes), 
+    subtitle=input_file) + 
+  theme(plot.subtitle=element_text(size=8)) +
+  theme(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)

garlic/fig/nbody/ss.R

@@ -10,8 +10,10 @@ 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, config.numNodes, unit, time) %>%
+  select(config.blocksize, config.gitBranch, config.nodes, unit, time) %>%
-  rename(nodes = config.numNodes, blocksize=config.blocksize, branch=config.gitBranch) %>%
+  rename(nodes = config.nodes, blocksize=config.blocksize, branch=config.gitBranch) %>%
+
+  mutate(time.nodes = time * nodes) %>%
 
   mutate(blocksize = as.factor(blocksize)) %>%
   mutate(nodes = as.factor(nodes)) %>%
@@ -21,6 +23,7 @@ df = jsonlite::stream_in(file(input_file), verbose=FALSE) %>%
   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)) %>%
 
@@ -32,21 +35,6 @@ w = 8
 
 # ---------------------------------------------------------------------
 
-p = ggplot(df, aes(x=nodes, y=median.time, color=branch)) +
-  geom_point() +
-  geom_line(aes(group=branch)) +
-  theme_bw() +
-  labs(x="Nodes", y="Median time (s)", title="NBody Scaling: 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=nodes, y=normalized.time, color=branch)) +
   geom_boxplot() +
   geom_hline(yintercept=c(-0.01, 0.01), linetype="dashed", color="red") +
@@ -63,31 +51,15 @@ ggsave("normalized.time.pdf", plot=p, width=w, height=h, dpi=dpi)
 
 # ---------------------------------------------------------------------
 
-p = ggplot(df, aes(x=nodes, y=time, color=branch)) +
+p = ggplot(df, aes(x=nodes, y=time.nodes, color=branch)) +
   geom_point(shape=21, size=3) +
+  geom_line(aes(y=median.time.nodes, group=branch)) +
   theme_bw() +
-  labs(x="Nodes", y="Time (s)", title="NBody Scaling: Time", 
+  labs(x="Nodes", y="Time * nodes (s)", title="NBody Scaling: Time * nodes", 
     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.nodes.png", plot=p, width=w, height=h, dpi=dpi)
-ggsave("time.pdf", plot=p, width=w, height=h, dpi=dpi)
+ggsave("time.nodes.pdf", plot=p, width=w, height=h, dpi=dpi)
-
-
-# ---------------------------------------------------------------------
-
-p = ggplot(df, aes(x=nodes, y=branch, fill=median.time)) +
-  geom_raster() + 
-  scale_fill_viridis(option="plasma") +
-  coord_fixed() +
-  theme_bw() +
-  labs(x="Nodes", y="Branch", title="NBody Scaling: 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)