diff --git a/garlic/fig/index.nix b/garlic/fig/index.nix index 63135f7..81244d0 100644 --- a/garlic/fig/index.nix +++ b/garlic/fig/index.nix @@ -42,8 +42,8 @@ in }; saiph = with exp.saiph; { - granularity-saiph = stdPlot ./saiph/granularity-saiph.R [ granularity-saiph ]; - scalability-saiph = stdPlot ./saiph/scalability-saiph.R [ scalability-saiph ]; + granularity = stdPlot ./saiph/granularity.R [ granularity ]; + ss = stdPlot ./saiph/ss.R [ ss ]; }; heat = with exp.heat; { diff --git a/garlic/fig/saiph/granularity-saiph.R b/garlic/fig/saiph/granularity-saiph.R deleted file mode 100644 index 4bdab6f..0000000 --- a/garlic/fig/saiph/granularity-saiph.R +++ /dev/null @@ -1,155 +0,0 @@ -library(ggplot2) -library(dplyr) -library(scales) -library(jsonlite) -library(viridis) - -args=commandArgs(trailingOnly=TRUE) - -# Read the timetable from args[1] -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() - - -# Create a data frame selecting the desired variables from the data set -df = select(dataset, config.nbly, config.nblz, config.nodes, time, total_time) %>% - rename(nbly=config.nbly, nblz=config.nblz, nnodes=config.nodes) - -# Declare variables as factors -# --> R does not allow to operate with factors: operate before casting to factors -df$nblPerProc = as.factor(round((df$nbly * df$nblz) / 24, digits = 2)) -df$biggernbly = as.factor(df$nbly > df$nblz) -df$nbly = as.factor(df$nbly) -df$nblz = as.factor(df$nblz) -df$nodes = as.factor(df$nnodes) - -# Create a new data frame including statistics -D=group_by(df, nbly, nblz, nblPerProc, nodes) %>% - mutate(tmedian = median(time)) %>% - mutate(ttmedian = median(total_time)) %>% - mutate(tnorm = time / tmedian - 1) %>% - mutate(bad = max(ifelse(abs(tnorm) >= 0.01, 1, 0))) %>% - mutate(tn = tmedian * nnodes) %>% - ungroup() - -D$bad = as.factor(D$bad) - -### Std output data frame D -print(D) - -### Output figure size -ppi=300 -h=5 -w=8 - -#################################################################### -### Boxplot -#################################################################### -png("box.png", width=w*ppi, height=h*ppi, res=ppi) -# -# -# Create the plot with the normalized time vs nblocks -p = ggplot(data=D, aes(x=nblPerProc, y=tnorm, color=bad)) + - - # Labels - labs(x="nblPerProc", y="Normalized time", - title=sprintf("Saiph-Heat3D normalized time"), - subtitle=input_file) + - # Add the maximum allowed error lines - geom_hline(yintercept=c(-0.01, 0.01), - linetype="dashed", color="gray") + - - # Draw boxplots - geom_boxplot() + - scale_color_manual(values=c("black", "brown")) + - theme_bw() + - theme(plot.subtitle=element_text(size=8)) + - theme(legend.position = "none") - - -# Render the plot -print(p) - -## Save the png image -dev.off() - -#################################################################### -### XY Scatter plot - measured_time & total_time vs tasks per cpu -#################################################################### - - -#################################################################### -### XY Scatter plot - time vs tasks per cpu -#################################################################### -png("scatter.png", width=w*ppi, height=h*ppi, res=ppi) -## Create the plot with the normalized time vs nblocks per proc -p = ggplot(D, aes(x=nblPerProc, y=time)) + - labs(x="nblPerProc", y="Time (s)", - title=sprintf("Saiph-Heat3D granularity"), - 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_y_continuous(trans=log2_trans()) - - -# Render the plot -print(p) - -## Save the png image -dev.off() - -#################################################################### -### XY Scatter plot - median time vs tasks per cpu -#################################################################### -png("scatter2.png", width=w*ppi, height=h*ppi, res=ppi) -## Create the plot with the normalized time vs nblocks per proc -p = ggplot(D, aes(x=nblPerProc, y=tmedian)) + - labs(x="nblPerProc", y="Median Time (s)", - title=sprintf("Saiph-Heat3D granularity"), - subtitle=input_file) + - theme_bw() + - theme(plot.subtitle=element_text(size=8)) + - theme(legend.position = c(0.5, 0.88)) + - geom_point(aes(color=biggernbly), shape=21, size=3) + - labs(color = "nbly > nblz") - scale_y_continuous(trans=log2_trans()) - -# Render the plot -print(p) - -# Save the png image -dev.off() - -#################################################################### -### Heatmap plot - median time vs tasks per cpu per dimension -#################################################################### -heatmap_plot = function(df, colname, title) { - p = ggplot(df, aes(x=nbly, y=nblz, fill=!!ensym(colname))) + - geom_raster() + - #scale_fill_gradient(high="black", low="white") + - scale_fill_viridis(option="plasma") + - coord_fixed() + - theme_bw() + - theme(axis.text.x=element_text(angle = -45, hjust = 0)) + - theme(plot.subtitle=element_text(size=8)) + - guides(fill = guide_colorbar(barwidth=12, title.vjust=0.8)) + - labs(x="nbly", y="nblz", - title=sprintf("Heat granularity: %s", title), - subtitle=input_file) + - theme(legend.position="bottom")+ - facet_wrap( ~ nodes) - - k=1 - ggsave(sprintf("%s.png", colname), plot=p, width=4.8*k, height=5*k, dpi=300) - ggsave(sprintf("%s.pdf", colname), plot=p, width=4.8*k, height=5*k, dpi=300) -} - -# call heatmap function with colname and legend title -heatmap_plot(D, "tmedian", "time") - diff --git a/garlic/fig/saiph/granularity.R b/garlic/fig/saiph/granularity.R new file mode 100644 index 0000000..b4ba304 --- /dev/null +++ b/garlic/fig/saiph/granularity.R @@ -0,0 +1,94 @@ +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" } + +df = jsonlite::stream_in(file(input_file), verbose=FALSE) %>% + + jsonlite::flatten() %>% + + select(unit, + config.nodes, + config.nblx, + config.nbly, + config.nblz, + config.gitBranch, + config.blocksPerCpu, + config.sizex, + time, + total_time) %>% + + rename(nodes=config.nodes, + nblx=config.nblx, + nbly=config.nbly, + nblz=config.nblz, + gitBranch=config.gitBranch, + blocksPerCpu=config.blocksPerCpu, + sizex=config.sizex) %>% + + # Remove the "garlic/" prefix from the gitBranch + mutate(branch = str_replace(gitBranch, "garlic/", "")) %>% + + # Computations before converting to factor + mutate(time.nodes = time * nodes) %>% + + # Convert to factors + mutate(unit = as.factor(unit)) %>% + mutate(nodes = as.factor(nodes)) %>% + mutate(gitBranch = as.factor(gitBranch)) %>% + mutate(nblx = as.factor(nblx)) %>% + mutate(nbly = as.factor(nbly)) %>% + mutate(nblz = as.factor(nblz)) %>% + mutate(sizex = as.factor(sizex)) %>% + 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)) %>% + ungroup() + +dpi = 300 +h = 5 +w = 8 + +maintitle = "Saiph-Heat3D granularity" + +# --------------------------------------------------------------------- + +p = ggplot(df, aes(x=nbly, y=normalized.time, fill=sizex)) + + geom_boxplot() + + geom_hline(yintercept=c(-0.01, 0.01), linetype="dashed", color="red") + + theme_bw() + + facet_wrap(branch ~ .) + + labs(y="Normalized time", + title=sprintf("%s: normalized time", maintitle), + subtitle=input_file) + + 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=blocksPerCpu, y=time, color=sizex)) + + geom_point(shape=21, size=3) + + geom_line(aes(y=median.time, group=sizex)) + + theme_bw() + + scale_x_continuous(trans=log2_trans()) + + labs(y="Time (s)", + title=sprintf("%s: time", maintitle), + subtitle=input_file) + + theme(plot.subtitle=element_text(size=8)) + +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/saiph/scalability-saiph.R b/garlic/fig/saiph/scalability-saiph.R deleted file mode 100644 index e29e720..0000000 --- a/garlic/fig/saiph/scalability-saiph.R +++ /dev/null @@ -1,156 +0,0 @@ -library(ggplot2) -library(dplyr) -library(scales) -library(jsonlite) -library(viridis) - -args=commandArgs(trailingOnly=TRUE) - -# Read the timetable from args[1] -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() - - -# Create a data frame selecting the desired variables from the data set -df = select(dataset, config.nbly, config.nblz, config.nodes, time, total_time) %>% - rename(nbly=config.nbly, nblz=config.nblz, nnodes=config.nodes) - -# Declare variables as factors -# --> R does not allow to operate with factors: operate before casting to factors -df$nblPerProc = as.factor(round((df$nbly * df$nblz) / 24, digits = 2)) -df$biggernbly = as.factor(df$nbly > df$nblz) -df$nbly = as.factor(df$nbly) -df$nblz = as.factor(df$nblz) -df$nodes = as.factor(df$nnodes) - -# Create a new data frame including statistics -D=group_by(df, nbly, nblz, nblPerProc, nodes) %>% - mutate(tmedian = median(time)) %>% - mutate(ttmedian = median(total_time)) %>% - mutate(tnorm = time / tmedian - 1) %>% - mutate(bad = max(ifelse(abs(tnorm) >= 0.01, 1, 0))) %>% - mutate(tn = tmedian * nnodes) %>% - ungroup() - -D$bad = as.factor(D$bad) - -### Std output data frame D -print(D) - -### Output figure size -ppi=300 -h=5 -w=8 - -#################################################################### -### Boxplot -#################################################################### -png("box.png", width=w*ppi, height=h*ppi, res=ppi) -# -# -# Create the plot with the normalized time vs nblocks -p = ggplot(data=D, aes(x=nblPerProc, y=tnorm, color=bad)) + - - # Labels - labs(x="nblPerProc", y="Normalized time", - title=sprintf("Saiph-Heat3D normalized time"), - subtitle=input_file) + - # Add the maximum allowed error lines - geom_hline(yintercept=c(-0.01, 0.01), - linetype="dashed", color="gray") + - - # Draw boxplots - geom_boxplot() + - scale_color_manual(values=c("black", "brown")) + - theme_bw() + - theme(plot.subtitle=element_text(size=8)) + - theme(legend.position = "none") - - -# Render the plot -print(p) - -## Save the png image -dev.off() - -#################################################################### -### XY Scatter plot - measured_time & total_time vs tasks per cpu -#################################################################### - - -#################################################################### -### XY Scatter plot - time vs tasks per cpu -#################################################################### -png("scatter.png", width=w*ppi, height=h*ppi, res=ppi) -## Create the plot with the normalized time vs nblocks per proc -p = ggplot(D, aes(x=nblPerProc, y=time)) + - labs(x="nblPerProc", y="Time (s)", - title=sprintf("Saiph-Heat3D granularity"), - subtitle=input_file) + - theme_bw() + - theme(plot.subtitle=element_text(size=8)) + - theme(legend.position = c(0.5, 0.88)) + - geom_point(aes(color=nodes), shape=21, size=3) + - scale_y_continuous(trans=log2_trans()) - - -# Render the plot -print(p) - -## Save the png image -dev.off() - - -#################################################################### -### XY Scatter plot - median time vs tasks per cpu -#################################################################### -png("scatter2.png", width=w*ppi, height=h*ppi, res=ppi) -## Create the plot with the normalized time vs nblocks per proc -p = ggplot(D, aes(x=nblPerProc, y=tn)) + - labs(x="nblPerProc", y="Median Time (s) * nodes", - title=sprintf("Saiph-Heat3D granularity"), - subtitle=input_file) + - theme_bw() + - theme(plot.subtitle=element_text(size=8)) + - theme(legend.position = c(0.5, 0.88)) + - geom_point(aes(color=nodes), shape=21, size=3) + - labs(color = "nbly > nblz") - scale_y_continuous(trans=log2_trans()) - -# Render the plot -print(p) - -# Save the png image -dev.off() - -#################################################################### -### Heatmap plot - median time vs tasks per cpu per dimension -#################################################################### -heatmap_plot = function(df, colname, title) { - p = ggplot(df, aes(x=nbly, y=nblz, fill=!!ensym(colname))) + - geom_raster() + - #scale_fill_gradient(high="black", low="white") + - scale_fill_viridis(option="plasma") + - coord_fixed() + - theme_bw() + - theme(axis.text.x=element_text(angle = -45, hjust = 0)) + - theme(plot.subtitle=element_text(size=8)) + - guides(fill = guide_colorbar(barwidth=12, title.vjust=0.8)) + - labs(x="nbly", y="nblz", - title=sprintf("Heat granularity: %s", title), - subtitle=input_file) + - theme(legend.position="bottom")+ - facet_wrap( ~ nodes) - - k=1 - ggsave(sprintf("%s.png", colname), plot=p, width=4.8*k, height=5*k, dpi=300) - ggsave(sprintf("%s.pdf", colname), plot=p, width=4.8*k, height=5*k, dpi=300) -} - -# call heatmap function with colname and legend title -heatmap_plot(D, "tmedian", "time") - diff --git a/garlic/fig/saiph/ss.R b/garlic/fig/saiph/ss.R new file mode 100644 index 0000000..2be666e --- /dev/null +++ b/garlic/fig/saiph/ss.R @@ -0,0 +1,109 @@ +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" } + +df = jsonlite::stream_in(file(input_file), verbose=FALSE) %>% + + jsonlite::flatten() %>% + + select(unit, + config.nodes, + config.nblx, + config.nbly, + config.nblz, + config.gitBranch, + config.blocksPerCpu, + config.sizex, + time, + total_time) %>% + + rename(nodes=config.nodes, + nblx=config.nblx, + nbly=config.nbly, + nblz=config.nblz, + gitBranch=config.gitBranch, + blocksPerCpu=config.blocksPerCpu, + sizex=config.sizex) %>% + + # Remove the "garlic/" prefix from the gitBranch + mutate(branch = str_replace(gitBranch, "garlic/", "")) %>% + + # Computations before converting to factor + mutate(time.nodes = time * nodes) %>% + + # Convert to factors + mutate(unit = as.factor(unit)) %>% + mutate(nodes = as.factor(nodes)) %>% + mutate(gitBranch = as.factor(gitBranch)) %>% + mutate(nblx = as.factor(nblx)) %>% + mutate(nbly = as.factor(nbly)) %>% + mutate(nblz = as.factor(nblz)) %>% + mutate(sizex = as.factor(sizex)) %>% + 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)) %>% + ungroup() + +dpi = 300 +h = 5 +w = 8 + +maintitle = "Saiph-Heat3D strong scaling" + +# --------------------------------------------------------------------- + +p = ggplot(df, aes(x=nodes, y=normalized.time, fill=sizex)) + + 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=sprintf("%s: normalized time", maintitle), + subtitle=input_file) + + 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=nodes, y=time, color=sizex)) + + geom_point(shape=21, size=3) + + geom_line(aes(y=median.time, group=sizex)) + + theme_bw() + +# facet_wrap(branch ~ .) + + labs(x="nodes", y="Time (s)", + title=sprintf("%s: time", maintitle), + subtitle=input_file) + + theme(plot.subtitle=element_text(size=8)) + +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=nodes, y=time.nodes, color=sizex)) + + geom_point(shape=21, size=3) + + geom_line(aes(y=median.time.nodes, group=sizex)) + + theme_bw() + + #facet_wrap(branch ~ .) + + labs(x="nodes", y="Time * nodes (s)", + title=sprintf("%s: time * nodes", maintitle), + subtitle=input_file) + + theme(plot.subtitle=element_text(size=8)) + +ggsave("time.nodes.png", plot=p, width=w, height=h, dpi=dpi) +ggsave("time.nodes.pdf", plot=p, width=w, height=h, dpi=dpi)