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saiph: update scaling exp and figures

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Sandra 2021-03-12 15:15:53 +01:00 committed by Rodrigo Arias Mallo
parent 8406c1c4e5
commit 46536548ca
8 changed files with 684 additions and 36 deletions
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2
garlic/exp/index.nix
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@ -35,6 +35,8 @@
numcomm = callPackage ./saiph/numcomm.nix { }; numcomm = callPackage ./saiph/numcomm.nix { };
granularity = callPackage ./saiph/granularity.nix { }; granularity = callPackage ./saiph/granularity.nix { };
scaling = callPackage ./saiph/scaling.nix { }; scaling = callPackage ./saiph/scaling.nix { };
scaling2 = callPackage ./saiph/scaling2.nix { };
debug = callPackage ./saiph/debug.nix { };
blockingY = callPackage ./saiph/blocking_Y.nix { }; blockingY = callPackage ./saiph/blocking_Y.nix { };
blockingZ = callPackage ./saiph/blocking_Z.nix { }; blockingZ = callPackage ./saiph/blocking_Z.nix { };
blockingYZ = callPackage ./saiph/blocking_YZ.nix { }; blockingYZ = callPackage ./saiph/blocking_YZ.nix { };

89
garlic/exp/saiph/debug.nix Normal file
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@ -0,0 +1,89 @@
{
stdenv
, stdexp
, bsc
, targetMachine
, stages
}:
with stdenv.lib;
let
# Initial variable configuration
varConf = with bsc; {
};
# Generate the complete configuration for each unit
genConf = with bsc; c: targetMachine.config // rec {
expName = "saiph";
unitName = "${expName}-debug";
# unitName = if (gitCommit == "3b52a616d44f4b86880663e2d951ad89c1dcab4f")
# then "${expName}-N${toString nodes}" + "-nblx${toString nblx}-nbly${toString nbly}" + "-par-init"
# else "${expName}-N${toString nodes}" + "-nblx${toString nblx}-nbly${toString nbly}" + "-seq-init";
inherit (targetMachine.config) hw;
# saiph options
manualDist = 1;
nbgx = 1;
nbgy = 1;
nbgz = 8;
nblx = 1;
nbly = 4;
nblz = 96;
nbltotal = 384;
mpi = impi;
gitBranch = "garlic/tampi+isend+oss+task+simd";
gitCommit = "3fa116620f1c7fbd1127d785c8bdc5d2372837b3";
#gitCommit = c.gitCommit; # if exp involves more than 1 commit
#inherit (c) gitCommit; # if exp fixes the commit
# Repeat the execution of each unit 50 times
loops = 1;
# Resources
qos = "debug";
ntasksPerNode = hw.socketsPerNode;
nodes = 4;
cpusPerTask = hw.cpusPerSocket;
jobName = "${unitName}";
# Compile flags
debugFlags = 1;
asanFlags = 0;
};
# Compute the array of configurations
configs = stdexp.buildConfigs {
inherit varConf genConf;
};
exec = {nextStage, conf, ...}: with conf; stages.exec {
inherit nextStage;
env = ''
export OMP_NUM_THREADS=${toString hw.cpusPerSocket}
export ASAN_SYMBOLIZER_PATH=${bsc.clangOmpss2Unwrapped}/bin/llvm-symbolizer
'';
pre = ''
ulimit -c unlimited
'';
};
valgrind = {nextStage, ...}: stages.valgrind {
inherit nextStage;
};
program = {nextStage, conf, ...}:
let
customPkgs = stdexp.replaceMpi conf.mpi;
in
customPkgs.apps.saiph.override {
inherit (conf) manualDist nbgx nbgy nbgz nblx nbly nblz nbltotal mpi gitBranch gitCommit debugFlags asanFlags;
};
pipeline = stdexp.stdPipeline ++ [ exec valgrind program ];
in
stdexp.genExperiment { inherit configs pipeline; }

45
garlic/exp/saiph/scaling.nix
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@ -11,9 +11,29 @@ with stdenv.lib;
let let
# Initial variable configuration # Initial variable configuration
varConf = with bsc; { varConf = with bsc; {
nbl = [ 1 2 4 8 16 32 64 ]; #nbl = [ 1 2 4 8 16 32 64 ];
nodes = [ 1 2 4 8 ]; nodes = [ 1 2 4 8 ];
#gitCommit = [ "3ecae7c209ec3e33d1108ae4783d7e733d54f2ca" "3b52a616d44f4b86880663e2d951ad89c1dcab4f" ];
input = [
{ nbly=12 ; nblz=1; nbltotal=12 ; }
{ nbly=24 ; nblz=1; nbltotal=24 ; }
{ nbly=48 ; nblz=1; nbltotal=48 ; }
{ nbly=96 ; nblz=1; nbltotal=96 ; }
{ nbly=6 ; nblz=2; nbltotal=12 ; }
{ nbly=12 ; nblz=2; nbltotal=24 ; }
{ nbly=24 ; nblz=2; nbltotal=48 ; }
{ nbly=48 ; nblz=2; nbltotal=96 ; }
{ nbly=96 ; nblz=2; nbltotal=192 ; }
{ nbly=3 ; nblz=4; nbltotal=12 ; }
{ nbly=6 ; nblz=4; nbltotal=24 ; }
{ nbly=12 ; nblz=4; nbltotal=48 ; }
{ nbly=24 ; nblz=4; nbltotal=96 ; }
{ nbly=48 ; nblz=4; nbltotal=192 ; }
{ nbly=96 ; nblz=4; nbltotal=384 ; }
];
}; };
# Generate the complete configuration for each unit # Generate the complete configuration for each unit
@ -30,31 +50,33 @@ let
manualDist = 1; manualDist = 1;
nbgx = 1; nbgx = 1;
nbgy = 1; nbgy = 1;
nbgz = nodes; nbgz = nodes*2;
nblx = 1; nblx = 1;
nbly = c.nbl; #nbly = c.nbl;
nblz = c.nbl; #nblz = c.nbl;
mpi = impi; mpi = impi;
gitBranch = "garlic/tampi+isend+oss+task+simd"; gitBranch = "garlic/tampi+isend+oss+task+simd";
#gitCommit = c.gitCommit; # if exp involves more than 1 commit #gitCommit = c.gitCommit; # if exp involves more than 1 commit
gitCommit = "3fa116620f1c7fbd1127d785c8bdc5d2372837b3";
#inherit (c) gitCommit; # if exp fixes the commit #inherit (c) gitCommit; # if exp fixes the commit
inherit (c.input) nbly nblz nbltotal ;
# Repeat the execution of each unit 50 times # Repeat the execution of each unit 50 times
loops = 10; loops = 10;
# Resources # Resources
qos = "bsc_cs"; qos = "bsc_cs";
ntasksPerNode = 1; ntasksPerNode = hw.socketsPerNode;
nodes = c.nodes; nodes = c.nodes;
cpusPerTask = hw.cpusPerSocket; cpusPerTask = hw.cpusPerSocket;
jobName = "${unitName}"; jobName = "${unitName}";
}; };
# Compute the array of configurations # Compute the array of configurations
configs = stdexp.buildConfigs { configsAll = stdexp.buildConfigs {
inherit varConf genConf; inherit varConf genConf;
}; };
#configs = filter (el: if el.nbly == 1 && el.nblz == 1 && el.nodes == 1 && el.gitCommit == "3b52a616d44f4b86880663e2d951ad89c1dcab4f" then false else true) configsAll; configs = filter (el: if (el.nbly == 24 && el.nblz == 4) && el.nodes == 4 then false else true) configsAll;
exec = {nextStage, conf, ...}: with conf; stages.exec { exec = {nextStage, conf, ...}: with conf; stages.exec {
inherit nextStage; inherit nextStage;
@ -69,11 +91,14 @@ let
customPkgs = stdexp.replaceMpi conf.mpi; customPkgs = stdexp.replaceMpi conf.mpi;
in in
customPkgs.apps.saiph.override { customPkgs.apps.saiph.override {
inherit (conf) manualDist nbgx nbgy nbgz nblx nbly nblz mpi gitBranch; inherit (conf) manualDist nbgx nbgy nbgz nblx nbly nblz nbltotal mpi gitBranch gitCommit;
}; };
pipeline = stdexp.stdPipeline ++ [ exec program ]; pipeline = stdexp.stdPipeline ++ [ exec program ];
in in
stdexp.genExperiment { inherit configs pipeline; } stdexp.genExperiment { inherit configs pipeline; }
# last plot hash: f5xb7jv1c4mbrcy6d9s9j10msfz3kkj0-plot

104
garlic/exp/saiph/scaling2.nix Normal file
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@ -0,0 +1,104 @@
{
stdenv
, stdexp
, bsc
, targetMachine
, stages
}:
with stdenv.lib;
let
# Initial variable configuration
varConf = with bsc; {
#nbl = [ 1 2 4 8 16 32 64 ];
nodes = [ 1 2 4 8 ];
input = [
{ nblz=12 ; nbly=1; nbltotal=12 ; }
{ nblz=24 ; nbly=1; nbltotal=24 ; }
{ nblz=48 ; nbly=1; nbltotal=48 ; }
{ nblz=96 ; nbly=1; nbltotal=96 ; }
{ nblz=6 ; nbly=2; nbltotal=12 ; }
{ nblz=12 ; nbly=2; nbltotal=24 ; }
{ nblz=24 ; nbly=2; nbltotal=48 ; }
{ nblz=48 ; nbly=2; nbltotal=96 ; }
{ nblz=96 ; nbly=2; nbltotal=192 ; }
{ nblz=3 ; nbly=4; nbltotal=12 ; }
{ nblz=6 ; nbly=4; nbltotal=24 ; }
{ nblz=12 ; nbly=4; nbltotal=48 ; }
{ nblz=24 ; nbly=4; nbltotal=96 ; }
{ nblz=48 ; nbly=4; nbltotal=192 ; }
{ nblz=96 ; nbly=4; nbltotal=384 ; }
];
};
# Generate the complete configuration for each unit
genConf = with bsc; c: targetMachine.config // rec {
expName = "saiph";
unitName = "${expName}-N${toString nodes}" + "-nblx${toString nblx}-nbly${toString nbly}" + "-par-init-One-dimensionalDistribution";
# unitName = if (gitCommit == "3b52a616d44f4b86880663e2d951ad89c1dcab4f")
# then "${expName}-N${toString nodes}" + "-nblx${toString nblx}-nbly${toString nbly}" + "-par-init"
# else "${expName}-N${toString nodes}" + "-nblx${toString nblx}-nbly${toString nbly}" + "-seq-init";
inherit (targetMachine.config) hw;
# saiph options
manualDist = 1;
nbgx = 1;
nbgy = 1;
nbgz = nodes*2;
nblx = 1;
#nbly = c.nbl;
#nblz = c.nbl;
mpi = impi;
gitBranch = "garlic/tampi+isend+oss+task+simd";
#gitCommit = c.gitCommit; # if exp involves more than 1 commit
gitCommit = "3fa116620f1c7fbd1127d785c8bdc5d2372837b3";
#inherit (c) gitCommit; # if exp fixes the commit
inherit (c.input) nbly nblz nbltotal ;
# Repeat the execution of each unit 50 times
loops = 10;
# Resources
qos = "bsc_cs";
ntasksPerNode = hw.socketsPerNode;
nodes = c.nodes;
cpusPerTask = hw.cpusPerSocket;
jobName = "${unitName}";
};
# Compute the array of configurations
configs = stdexp.buildConfigs {
inherit varConf genConf;
};
#configs = filter (el: if (el.nbly == 24 && el.nblz == 4) && el.nodes == 4 then false else true) configsAll;
exec = {nextStage, conf, ...}: with conf; stages.exec {
inherit nextStage;
env = ''
export OMP_NUM_THREADS=${toString hw.cpusPerSocket}
export ASAN_SYMBOLIZER_PATH=${bsc.clangOmpss2Unwrapped}/bin/llvm-symbolizer
'';
};
program = {nextStage, conf, ...}:
let
customPkgs = stdexp.replaceMpi conf.mpi;
in
customPkgs.apps.saiph.override {
inherit (conf) manualDist nbgx nbgy nbgz nblx nbly nblz nbltotal mpi gitBranch gitCommit;
};
pipeline = stdexp.stdPipeline ++ [ exec program ];
in
stdexp.genExperiment { inherit configs pipeline; }
# last plot hash: f5xb7jv1c4mbrcy6d9s9j10msfz3kkj0-plot

14
garlic/fig/index.nix
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@ -42,12 +42,14 @@ in
}; };
saiph = with exp.saiph; { saiph = with exp.saiph; {
granularity = rPlotExp ./saiph/granularity.R [ granularity ]; granularity = stdPlot ./saiph/granularity.R [ granularity ];
scaling = rPlotExp ./saiph/scaling.R [ scaling ]; scaling = stdPlot ./saiph/scaling.R [ scaling ];
blockingY = rPlotExp ./saiph/granularityY.R [ blockingY ]; scaling2 = stdPlot ./saiph/scaling2.R [ scaling2 ];
blockingZ = rPlotExp ./saiph/granularityZ.R [ blockingZ ]; scalingnblyz = stdPlot ./saiph/scalingnblyz.R [ scaling scaling2 ];
blockingYZ = rPlotExp ./saiph/granularityYZ.R [ blockingYZ ]; blockingY = stdPlot ./saiph/granularityY.R [ blockingY ];
blockingZY = rPlotExp ./saiph/granularityZY.R [ blockingZY ]; blockingZ = stdPlot ./saiph/granularityZ.R [ blockingZ ];
blockingYZ = stdPlot ./saiph/granularityYZ.R [ blockingYZ ];
blockingZY = stdPlot ./saiph/granularityZY.R [ blockingZY ];
}; };
heat = with exp.heat; { heat = with exp.heat; {

94
garlic/fig/saiph/scaling.R
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@ -15,15 +15,22 @@ dataset = jsonlite::stream_in(file(input_file)) %>%
# We only need the nblocks and time # We only need the nblocks and time
df = select(dataset, config.nby, config.nodes, time, total_time, config.gitCommit) %>% #df = select(dataset, config.nbly, config.nodes, time, total_time, config.gitCommit) %>%
rename(nby=config.nby, nnodes=config.nodes, gitCommit=config.gitCommit) # rename(nbly=config.nbly, nnodes=config.nodes, gitCommit=config.gitCommit)
df$nby = as.factor(df$nby) df = select(dataset, config.nbly, config.nblz, config.nbltotal, config.nodes, time, total_time) %>%
rename(nbly=config.nbly, nblz=config.nblz, nbltotal=config.nbltotal, nnodes=config.nodes)
df$nbly = as.factor(df$nbly)
df$nblz = as.factor(df$nblz)
df$nblPerProc = as.factor(df$nbltotal / 24)
df$nbltotal = as.factor(df$nbltotal)
df$nodes = as.factor(df$nnodes) df$nodes = as.factor(df$nnodes)
df$gitCommit = as.factor(df$gitCommit) #df$gitCommit = as.factor(df$gitCommit)
# Normalize the time by the median # Normalize the time by the median
D=group_by(df, nby, nodes, gitCommit) %>% #D=group_by(df, nbly, nodes, gitCommit) %>%
D=group_by(df, nbly, nblz, nbltotal, nodes) %>%
mutate(tmedian = median(time)) %>% mutate(tmedian = median(time)) %>%
mutate(ttmedian = median(total_time)) %>% mutate(ttmedian = median(total_time)) %>%
mutate(tnorm = time / tmedian - 1) %>% mutate(tnorm = time / tmedian - 1) %>%
@ -33,7 +40,6 @@ D=group_by(df, nby, nodes, gitCommit) %>%
D$bad = as.factor(D$bad) D$bad = as.factor(D$bad)
print(D) print(D)
ppi=300 ppi=300
@ -45,10 +51,10 @@ png("box.png", width=w*ppi, height=h*ppi, res=ppi)
# #
# #
# Create the plot with the normalized time vs nblocks # Create the plot with the normalized time vs nblocks
p = ggplot(data=D, aes(x=nby, y=tnorm, color=bad)) + p = ggplot(data=D, aes(x=nbly, y=tnorm, color=bad)) +
# Labels # Labels
labs(x="nby", y="Normalized time", labs(x="nbly", y="Normalized time",
title=sprintf("Saiph-Heat3D normalized time"), title=sprintf("Saiph-Heat3D normalized time"),
subtitle=input_file) + subtitle=input_file) +
@ -86,9 +92,9 @@ dev.off()
png("scatter.png", width=w*ppi, height=h*ppi, res=ppi) png("scatter.png", width=w*ppi, height=h*ppi, res=ppi)
# #
## Create the plot with the normalized time vs nblocks ## Create the plot with the normalized time vs nblocks
p = ggplot(D, aes(x=nby, y=time)) + p = ggplot(D, aes(x=nbltotal, y=time)) +
labs(x="nby", y="Time (s)", labs(x="nbltotal", y="Time (s)",
title=sprintf("Saiph-Heat3D granularity"), title=sprintf("Saiph-Heat3D granularity"),
subtitle=input_file) + subtitle=input_file) +
theme_bw() + theme_bw() +
@ -97,8 +103,8 @@ p = ggplot(D, aes(x=nby, y=time)) +
geom_point(aes(color=nodes), shape=21, size=3) + geom_point(aes(color=nodes), shape=21, size=3) +
#scale_x_continuous(trans=log2_trans()) + #scale_x_continuous(trans=log2_trans()) +
scale_y_continuous(trans=log2_trans()) + scale_y_continuous(trans=log2_trans())
facet_wrap( ~ gitCommit) # facet_wrap( ~ gitCommit)
# Render the plot # Render the plot
@ -107,12 +113,37 @@ print(p)
# Save the png image # Save the png image
dev.off() dev.off()
png("scatter1.png", width=w*ppi, height=h*ppi, res=ppi)
#
## Create the plot with the normalized time vs nblocks
p = ggplot(D, aes(x=nblPerProc, y=time)) +
labs(x="nblPerProc", y="Time (s)",
title=sprintf("Saiph-Heat3D granularity per nodes"),
subtitle=input_file) +
theme_bw() +
theme(plot.subtitle=element_text(size=8)) +
theme(legend.position = c(0.5, 0.5)) +
geom_point(aes(color=nblz), shape=21, size=3) +
#scale_x_continuous(trans=log2_trans()) +
scale_y_continuous(trans=log2_trans()) +
facet_wrap( ~ nodes)
# Render the plot
print(p)
# Save the png image
dev.off()
png("wasted.png", width=w*ppi, height=h*ppi, res=ppi) png("wasted.png", width=w*ppi, height=h*ppi, res=ppi)
# #
## Create the plot with the normalized time vs nblocks ## Create the plot with the normalized time vs nblocks
p = ggplot(D, aes(x=nby, y=time)) + p = ggplot(D, aes(x=nbly, y=time)) +
labs(x="nby", y="Time (s)", labs(x="nbly", y="Time (s)",
title=sprintf("Saiph-Heat3D granularity"), title=sprintf("Saiph-Heat3D granularity"),
subtitle=input_file) + subtitle=input_file) +
theme_bw() + theme_bw() +
@ -123,8 +154,8 @@ p = ggplot(D, aes(x=nby, y=time)) +
geom_line(aes(y=tmedian, color=nodes, group=nodes)) + geom_line(aes(y=tmedian, color=nodes, group=nodes)) +
geom_line(aes(y=ttmedian, color=nodes, group=nodes)) + geom_line(aes(y=ttmedian, color=nodes, group=nodes)) +
#scale_x_continuous(trans=log2_trans()) + #scale_x_continuous(trans=log2_trans()) +
scale_y_continuous(trans=log2_trans()) + scale_y_continuous(trans=log2_trans())
facet_wrap( ~ gitCommit) # facet_wrap( ~ gitCommit)
# Render the plot # Render the plot
print(p) print(p)
@ -135,9 +166,9 @@ dev.off()
png("test.png", width=w*ppi, height=h*ppi, res=ppi) png("test.png", width=w*ppi, height=h*ppi, res=ppi)
# #
## Create the plot with the normalized time vs nblocks ## Create the plot with the normalized time vs nblocks
p = ggplot(D, aes(x=nby, y=tn)) + p = ggplot(D, aes(x=nbltotal, y=tn)) +
labs(x="nby", y="Time (s) * nodes", labs(x="nbltotal", y="Time (s) * nodes",
title=sprintf("Saiph-Heat3D granularity"), title=sprintf("Saiph-Heat3D granularity"),
subtitle=input_file) + subtitle=input_file) +
theme_bw() + theme_bw() +
@ -146,8 +177,31 @@ p = ggplot(D, aes(x=nby, y=tn)) +
geom_point(shape=21, size=3) + geom_point(shape=21, size=3) +
geom_line(aes(color=nodes, group=nodes)) + geom_line(aes(color=nodes, group=nodes)) +
#scale_x_continuous(trans=log2_trans()) + #scale_x_continuous(trans=log2_trans()) +
scale_y_continuous(trans=log2_trans()) + scale_y_continuous(trans=log2_trans())
facet_wrap( ~ gitCommit) # facet_wrap( ~ gitCommit)
# Render the plot
print(p)
# Save the png image
dev.off()
png("test1.png", width=w*ppi, height=h*ppi, res=ppi)
#
## Create the plot with the normalized time vs nblocks
p = ggplot(D, aes(x=nblPerProc, y=tn)) +
labs(x="nblPerProc", y="Time (s) * nodes",
title=sprintf("Saiph-Heat3D granularity per nblz blocks"),
subtitle=input_file) +
theme_bw() +
theme(plot.subtitle=element_text(size=8)) +
geom_point(shape=21, size=3) +
geom_line(aes(color=nodes, group=nodes)) +
#scale_x_continuous(trans=log2_trans()) +
scale_y_continuous(trans=log2_trans()) +
facet_wrap( ~ nblz)
# Render the plot # Render the plot
print(p) print(p)

210
garlic/fig/saiph/scaling2.R Normal file
View File

@ -0,0 +1,210 @@
library(ggplot2)
library(dplyr)
library(scales)
library(jsonlite)
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()
# We only need the nblocks and time
#df = select(dataset, config.nbly, config.nodes, time, total_time, config.gitCommit) %>%
# rename(nbly=config.nbly, nnodes=config.nodes, gitCommit=config.gitCommit)
df = select(dataset, config.nbly, config.nblz, config.nbltotal, config.nodes, time, total_time) %>%
rename(nbly=config.nbly, nblz=config.nblz, nbltotal=config.nbltotal, nnodes=config.nodes)
df$nbly = as.factor(df$nbly)
df$nblz = as.factor(df$nblz)
df$nblPerProc = as.factor(df$nbltotal / 24)
df$nbltotal = as.factor(df$nbltotal)
df$nodes = as.factor(df$nnodes)
#df$gitCommit = as.factor(df$gitCommit)
# Normalize the time by the median
#D=group_by(df, nbly, nodes, gitCommit) %>%
D=group_by(df, nbly, nblz, nbltotal, 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)
print(D)
ppi=300
h=5
w=8
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=nbly, y=tnorm, color=bad)) +
# Labels
labs(x="nbly", y="Normalized time",
title=sprintf("Saiph-Heat3D normalized time"),
subtitle=input_file) +
# Center the title
#theme(plot.title = element_text(hjust = 0.5)) +
# Black and white mode (useful for printing)
#theme_bw() +
# 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")) +
#scale_y_continuous(breaks = scales::pretty_breaks(n = 10)) +
theme_bw() +
theme(plot.subtitle=element_text(size=8)) +
theme(legend.position = "none")
#theme(legend.position = c(0.85, 0.85))
# Render the plot
print(p)
## Save the png image
dev.off()
#
png("scatter.png", width=w*ppi, height=h*ppi, res=ppi)
#
## Create the plot with the normalized time vs nblocks
p = ggplot(D, aes(x=nbltotal, y=time)) +
labs(x="nbltotal", 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_x_continuous(trans=log2_trans()) +
scale_y_continuous(trans=log2_trans())
# facet_wrap( ~ gitCommit)
# Render the plot
print(p)
# Save the png image
dev.off()
png("scatter1.png", width=w*ppi, height=h*ppi, res=ppi)
#
## Create the plot with the normalized time vs nblocks
p = ggplot(D, aes(x=nblPerProc, y=time)) +
labs(x="nblPerProc", y="Time (s)",
title=sprintf("Saiph-Heat3D granularity per nodes"),
subtitle=input_file) +
theme_bw() +
theme(plot.subtitle=element_text(size=8)) +
theme(legend.position = c(0.5, 0.5)) +
geom_point(aes(color=nbly), shape=21, size=3) +
#scale_x_continuous(trans=log2_trans()) +
scale_y_continuous(trans=log2_trans()) +
facet_wrap( ~ nodes)
# Render the plot
print(p)
# Save the png image
dev.off()
png("wasted.png", width=w*ppi, height=h*ppi, res=ppi)
#
## Create the plot with the normalized time vs nblocks
p = ggplot(D, aes(x=nbly, y=time)) +
labs(x="nbly", y="Time (s)",
title=sprintf("Saiph-Heat3D granularity"),
subtitle=input_file) +
theme_bw() +
theme(plot.subtitle=element_text(size=8)) +
geom_point(shape=21, size=3) +
geom_point(aes(y=total_time), shape=1, size=3, color="red") +
geom_line(aes(y=tmedian, color=nodes, group=nodes)) +
geom_line(aes(y=ttmedian, color=nodes, group=nodes)) +
#scale_x_continuous(trans=log2_trans()) +
scale_y_continuous(trans=log2_trans())
# facet_wrap( ~ gitCommit)
# Render the plot
print(p)
# Save the png image
dev.off()
png("test.png", width=w*ppi, height=h*ppi, res=ppi)
#
## Create the plot with the normalized time vs nblocks
p = ggplot(D, aes(x=nbltotal, y=tn)) +
labs(x="nbltotal", y="Time (s) * nodes",
title=sprintf("Saiph-Heat3D granularity"),
subtitle=input_file) +
theme_bw() +
theme(plot.subtitle=element_text(size=8)) +
geom_point(shape=21, size=3) +
geom_line(aes(color=nodes, group=nodes)) +
#scale_x_continuous(trans=log2_trans()) +
scale_y_continuous(trans=log2_trans())
# facet_wrap( ~ gitCommit)
# Render the plot
print(p)
# Save the png image
dev.off()
png("test1.png", width=w*ppi, height=h*ppi, res=ppi)
#
## Create the plot with the normalized time vs nblocks
p = ggplot(D, aes(x=nblPerProc, y=tn)) +
labs(x="nblPerProc", y="Time (s) * nodes",
title=sprintf("Saiph-Heat3D granularity per nbly blocks"),
subtitle=input_file) +
theme_bw() +
theme(plot.subtitle=element_text(size=8)) +
geom_point(shape=21, size=3) +
geom_line(aes(color=nodes, group=nodes)) +
#scale_x_continuous(trans=log2_trans()) +
scale_y_continuous(trans=log2_trans()) +
facet_wrap( ~ nbly)
# Render the plot
print(p)
# Save the png image
dev.off()

162
garlic/fig/saiph/scalingnblyz.R Normal file
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@ -0,0 +1,162 @@
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()
# We only need the nblocks and time
#df = select(dataset, config.nbly, config.nodes, time, total_time, config.gitCommit) %>%
# rename(nbly=config.nbly, nnodes=config.nodes, gitCommit=config.gitCommit)
df = select(dataset, config.nbly, config.nblz, config.nbltotal, config.nodes, time, total_time) %>%
rename(nbly=config.nbly, nblz=config.nblz, nbltotal=config.nbltotal, nnodes=config.nodes)
df2 = df[df$nblz == 1 | df$nblz == 2 | df$nblz == 4, ]
df3 = df[df$nbly == 1 | df$nbly == 2 | df$nbly == 4, ]
# df2 data frame
df2$nblsetZ = as.factor(df2$nblz)
df2$nblPerProcZ = as.factor(df2$nbltotal / 24)
df2$nbltotal = as.factor(df2$nbltotal)
df2$nodes = as.factor(df2$nnodes)
# df3 data frame
df3$nblsetY = as.factor(df3$nbly)
df3$nblPerProcY = as.factor(df3$nbltotal / 24)
df3$nbltotalY = as.factor(df3$nbltotal)
df3$nodes = as.factor(df3$nnodes)
df$nbly = as.factor(df$nbly)
df$nblz = as.factor(df$nblz)
df$nblPerProc = as.factor(df$nbltotal / 24)
df$nbltotal = as.factor(df$nbltotal)
df$nodes = as.factor(df$nnodes)
#df$gitCommit = as.factor(df$gitCommit)
# Normalize the time by the median
#D=group_by(df, nbly, nodes, gitCommit) %>%
D=group_by(df, nbly, nblz, nbltotal, 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)
print(D)
ppi=300
h=5
w=8
png("scatter_nbly.png", width=w*ppi, height=h*ppi, res=ppi)
#
## Create the plot with the normalized time vs nblocks
p = ggplot() +
geom_point(data=df2, aes(x=nblPerProcZ, y=time, color=nblsetZ), shape=21, size=3, show.legend=TRUE) +
geom_point(data=df3, aes(x=nblPerProcY, y=time, color=nblsetY), shape=4, size=2, show.legend=TRUE) +
labs(x="nblPerProc", y="Time (s)",
title=sprintf("Saiph-Heat3D granularity per nodes"),
subtitle=input_file) +
theme_bw() +
theme(plot.subtitle=element_text(size=8)) +
theme(legend.position = c(0.5, 0.5)) +
scale_y_continuous(trans=log2_trans()) +
facet_wrap( ~ nodes)
# Render the plot
print(p)
# Save the png image
dev.off()
png("scatter_nbly.png", width=w*ppi, height=h*ppi, res=ppi)
#
## Create the plot with the normalized time vs nblocks
p = ggplot() +
geom_point(data=df2, aes(x=nblPerProcZ, y=time, color=nblsetZ), shape=21, size=3, show.legend=TRUE) +
geom_point(data=df3, aes(x=nblPerProcY, y=time, color=nblsetY), shape=4, size=2, show.legend=TRUE) +
labs(x="nblPerProc", y="Time (s)",
title=sprintf("Saiph-Heat3D granularity per nodes"),
subtitle=input_file) +
theme_bw() +
theme(plot.subtitle=element_text(size=8)) +
theme(legend.position = c(0.5, 0.5)) +
scale_y_continuous(trans=log2_trans()) +
facet_wrap( ~ nodes)
# Render the plot
print(p)
# Save the png image
dev.off()
png("test1.png", width=w*ppi, height=h*ppi, res=ppi)
#
## Create the plot with the normalized time vs nblocks
p = ggplot(D, aes(x=nblPerProc, y=tn)) +
labs(x="nblPerProc", y="Time (s) * nodes",
title=sprintf("Saiph-Heat3D granularity per nbly blocks"),
subtitle=input_file) +
theme_bw() +
theme(plot.subtitle=element_text(size=8)) +
geom_point(shape=21, size=3) +
geom_line(aes(color=nodes, group=nodes)) +
#scale_x_continuous(trans=log2_trans()) +
scale_y_continuous(trans=log2_trans()) +
facet_wrap( ~ nbly)
# Render the plot
print(p)
# Save the png image
dev.off()
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=15, title.position="top")) +
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)
}
heatmap_plot(D, "tmedian", "time")