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Ubuntu 20.04 #670

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merged 7 commits into from
Jun 7, 2022
Merged

Ubuntu 20.04 #670

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31bd83c
update to ubuntu 20.04 (from docker-openstudio)
brianlball May 21, 2022
b0126d1
Merge remote-tracking branch 'origin/develop' into ubuntu-20
brianlball May 24, 2022
b225102
update morris.R for 4.2.0
brianlball May 24, 2022
a04d841
update morris for R 4.2.0, part of 20.04 update
brianlball May 25, 2022
7ca177d
use openstudio:dev-3.4.1-alpha and openstudio-r:latest
brianlball Jun 6, 2022
f7c6745
update test for new R version
brianlball Jun 7, 2022
aecf02c
openstudio-r:4.2.0
brianlball Jun 7, 2022
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7 changes: 3 additions & 4 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -5,15 +5,15 @@

#may include suffix
ARG OPENSTUDIO_VERSION=3.4.0
FROM nrel/openstudio:$OPENSTUDIO_VERSION as base
FROM nrel/openstudio:dev-3.4.1-alpha as base
MAINTAINER Nicholas Long nicholas.long@nrel.gov

ENV DEBIAN_FRONTEND=noninteractive
# Install required libaries.
# realpath - needed for wait-for-it
RUN apt-get update && apt-get install -y wget gnupg \
&& wget -qO - https://www.mongodb.org/static/pgp/server-4.4.asc | apt-key add - \
#RUN sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 0C49F3730359A14518585931BC711F9BA15703C6 && \
&& echo "deb http://repo.mongodb.org/apt/ubuntu xenial/mongodb-org/4.4 multiverse" | \
&& echo "deb http://repo.mongodb.org/apt/ubuntu focal/mongodb-org/4.4 multiverse" | \
tee /etc/apt/sources.list.d/mongodb-org-4.4.list \
&& apt-get update \
&& apt-get install -y --no-install-recommends \
Expand All @@ -33,7 +33,6 @@ RUN apt-get update && apt-get install -y wget gnupg \
libbz2-dev \
libcurl4-openssl-dev \
libdbus-glib-1-2 \
libgdbm5 \
libgdbm-dev \
libglib2.0-dev \
libglu1 \
Expand Down
2 changes: 1 addition & 1 deletion docker/R/Dockerfile
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Expand Up @@ -2,7 +2,7 @@
# DESCRIPTION: OpenStudio Server R Container
# TO_BUILD_AND_RUN: docker-compose up

FROM nrel/openstudio-r:3.6.1-1
FROM nrel/openstudio-r:4.2.0
MAINTAINER Nicholas Long nicholas.long@nrel.gov

# Add in the additional R packages
Expand Down
47 changes: 26 additions & 21 deletions docker/R/lib/morris.R
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Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,9 @@ print(paste("vartypes:",vartypes))
print(paste("varnames:",varnames))
print(paste("vardisplaynames:",vardisplaynames))
print(paste("objnames:",objnames))
colnames(vars) <- varnames
print(paste("vars:",vars))
print(vars)

# Setup a bunch of variables for the analysis based on passed variables
# From Ruby
Expand Down Expand Up @@ -148,7 +151,7 @@ if (check_boundary == 1) {
print(paste("logical(ncol(vars):",logical(ncol(vars))))
}
for (i in 1:ncol(vars)){
if (is.nan(m$X[,i])) {
if (all(is.nan(m$X[,i]))) {
print(paste("m$X[,i] is NaN:",m$X[,i]))
print(paste("i:",i))
}
Expand All @@ -168,10 +171,12 @@ if (check_boundary == 1) {
}
try(results <- clusterApplyLB(cl, m1, f),silent=FALSE)
if (debug_messages == 1) {
print(paste("nrow(results):",nrow(results)))
print(paste("ncol(results):",ncol(results)))
print(paste("length(results):",length(results)))
print(paste("lengths(results):",lengths(results)))
}
result <- as.data.frame(results)
print(paste("results:",results))
#result <- as.data.frame(results)
result <- as.data.frame(results, row.name=objnames)
if (debug_messages == 1) {
print(paste("length(objnames):",length(objnames)))
print(paste("nrow(result):",nrow(result)))
Expand Down Expand Up @@ -202,6 +207,8 @@ if (nrow(result) > 0) {
var_mu_star[i] <- mean(abs(n$ee[,i]))
var_sigma[i] <- sd(n$ee[,i])
}
print(paste("var_mu_star:",var_mu_star))
print(paste("var_sigma:",var_sigma))
answer <- paste('"',gsub(" ","_",objnames[j],fixed=TRUE),'":{',paste('"',gsub(".","|",varnames, fixed=TRUE),'":','{"var_mu": ',var_mu,',"var_mu_star": ',var_mu_star,',"var_sigma": ',var_sigma,'}',sep='', collapse=','),'}',sep='')
#answer <- paste('{',paste('"',gsub(".","|",varnames, fixed=TRUE),'":','{"var_mu": ',var_mu,',"var_mu_star": ',var_mu_star,',"var_sigma": ',var_sigma,'}',sep='', collapse=','),'}',sep='')
if (j < nrow(result)) {
Expand All @@ -214,13 +221,17 @@ if (nrow(result) > 0) {
file_names_R[j] <- paste(analysis_dir,"/m_",gsub(" ","_",objnames[j], fixed=TRUE),".RData",sep="")
save(n, file=file_names_R[j])
if (all(is.finite(var_mu_star))) {
file_names_png[j] <- paste(analysis_dir,"/morris_",gsub(" ","_",objnames[j],fixed=TRUE),"_sigma_mu.png",sep="")
png(file_names_png[j], width=8, height=8, units="in", pointsize=10, res=200, type="cairo")
plot(n)
#axis(1, las=2)
#axis(2, las=1)
dev.off()

if (all(!is.na(var_sigma))) {
print('plot(n)')
file_names_png[j] <- paste(analysis_dir,"/morris_",gsub(" ","_",objnames[j],fixed=TRUE),"_sigma_mu.png",sep="")
png(file_names_png[j], width=8, height=8, units="in", pointsize=10, res=200, type="cairo")
plot(n)
#axis(1, las=2)
#axis(2, las=1)
dev.off()
}

print('barplot var_mu_star')
file_names_bar_png[j] <- paste(analysis_dir,"/morris_",gsub(" ","_",objnames[j],fixed=TRUE),"_bar.png",sep="")
png(file_names_bar_png[j], width=8, height=8, units="in", pointsize=10, res=200, type="cairo")
op <- par(mar = c(14,4,4,2) + 0.1)
Expand All @@ -229,14 +240,16 @@ if (nrow(result) > 0) {
#axis(2, las=1)
dev.off()
#sorted
print('barplot var_mu_star sorted')
file_names_bar_sorted_png[j] <- paste(analysis_dir,"/morris_",gsub(" ","_",objnames[j],fixed=TRUE),"_bar_sorted.png",sep="")
png(file_names_bar_sorted_png[j], width=8, height=8, units="in", pointsize=10, res=200, type="cairo")
op <- par(mar = c(14,4,4,2) + 0.1)
mp <- barplot(height=sort(var_mu_star), ylab="mu.star", main="Mu Star of Elementary Effects", xaxt="n")
axis(1, at=mp, labels=vardisplaynames[order(var_mu_star)], las=2, cex.axis=0.9)
#axis(2, las=1)
dev.off()


print('boxplot n$ee')
file_names_box_png[j] <- paste(analysis_dir,"/morris_",gsub(" ","_",objnames[j],fixed=TRUE),"_box.png",sep="")
png(file_names_box_png[j], width=8, height=8, units="in", pointsize=10, res=200, type="cairo")
bottommar <- max(strwidth(vardisplaynames[which.max(nchar(vardisplaynames))], "inch")+0.1, na.rm = TRUE)
Expand All @@ -245,15 +258,7 @@ if (nrow(result) > 0) {
mp <- boxplot(n$ee, las=2, names=vardisplaynames, cex.axis=0.9, main="BoxPlot of Elementary Effects", ylab=paste("EE of",objnames[j]))
axis(1, at=seq(1,length(vardisplaynames)), labels=vardisplaynames, las=2, cex.axis=0.9)
dev.off()

file_names_box_sorted_png[j] <- paste(analysis_dir,"/morris_",gsub(" ","_",objnames[j],fixed=TRUE),"_box_sorted.png",sep="")
png(file_names_box_sorted_png[j], width=8, height=8, units="in", pointsize=10, res=200, type="cairo")
bottommar <- max(strwidth(vardisplaynames[which.max(nchar(vardisplaynames))], "inch")+0.1, na.rm = TRUE)
leftmar <- max(strwidth(nchar(max(n$ee)), "inch")+0.25, na.rm = TRUE)
par(mai=c(bottommar,leftmar, 0.25,0.25))
mp <- boxplot(n$ee[,order(colMeans(abs(n$ee)))], las=2, names=vardisplaynames[order(var_mu_star)], cex.axis=0.9, main="BoxPlot of Elementary Effects", ylab=paste("EE of",objnames[j]))
axis(1, at=seq(1,length(vardisplaynames)), labels=vardisplaynames[order(var_mu_star)], las=2, cex.axis=0.9)
dev.off()

file_zip <- c(file_names_jsons,file_names_R,file_names_bar_png,file_names_bar_sorted_png,file_names_png,file_names_box_png,file_names_box_sorted_png,paste(analysis_dir,"/vardisplaynames.json",sep=''))

#file_zip <- c(file_names_jsons,file_names_R,file_names_bar_png,file_names_bar_sorted_png,file_names_png,file_names_box_png,paste(analysis_dir,"/vardisplaynames.json",sep=''))
Expand Down