forked from broadgsa/gatk
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge remote-tracking branch 'unstable/master'
- Loading branch information
Showing
434 changed files
with
19,932 additions
and
14,329 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,169 @@ | ||
| library(gsalib) | ||
| require("ggplot2") | ||
| require("gplots") | ||
|
|
||
| # | ||
| # Standard command line switch. Can we loaded interactively for development | ||
| # or executed with RScript | ||
| # | ||
| args = commandArgs(TRUE) | ||
| onCMDLine = ! is.na(args[1]) | ||
| if ( onCMDLine ) { | ||
| inputFileName = args[1] | ||
| outputPDF = args[2] | ||
| } else { | ||
| #inputFileName = "~/Desktop/broadLocal/GATK/unstable/report.txt" | ||
| inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/[email protected]" | ||
| #inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/rodPerformanceGoals/history/report.082711.txt" | ||
| outputPDF = NA | ||
| } | ||
|
|
||
| RUNTIME_UNITS = "(sec)" | ||
| ORIGINAL_UNITS_TO_SECONDS = 1/1000 | ||
|
|
||
| # | ||
| # Helper function to aggregate all of the jobs in the report across all tables | ||
| # | ||
| allJobsFromReport <- function(report) { | ||
| names <- c("jobName", "startTime", "analysisName", "doneTime", "exechosts") | ||
| sub <- lapply(report, function(table) table[,names]) | ||
| do.call("rbind", sub) | ||
| } | ||
|
|
||
| # | ||
| # Creates segmentation plots of time (x) vs. job (y) with segments for the duration of the job | ||
| # | ||
| plotJobsGantt <- function(gatkReport, sortOverall) { | ||
| allJobs = allJobsFromReport(gatkReport) | ||
| if ( sortOverall ) { | ||
| title = "All jobs, by analysis, by start time" | ||
| allJobs = allJobs[order(allJobs$analysisName, allJobs$startTime, decreasing=T), ] | ||
| } else { | ||
| title = "All jobs, sorted by start time" | ||
| allJobs = allJobs[order(allJobs$startTime, decreasing=T), ] | ||
| } | ||
| allJobs$index = 1:nrow(allJobs) | ||
| minTime = min(allJobs$startTime) | ||
| allJobs$relStartTime = allJobs$startTime - minTime | ||
| allJobs$relDoneTime = allJobs$doneTime - minTime | ||
| allJobs$ganttName = paste(allJobs$jobName, "@", allJobs$exechosts) | ||
| maxRelTime = max(allJobs$relDoneTime) | ||
| p <- ggplot(data=allJobs, aes(x=relStartTime, y=index, color=analysisName)) | ||
| p <- p + geom_segment(aes(xend=relDoneTime, yend=index), size=2, arrow=arrow(length = unit(0.1, "cm"))) | ||
| p <- p + geom_text(aes(x=relDoneTime, label=ganttName, hjust=-0.2), size=2) | ||
| p <- p + xlim(0, maxRelTime * 1.1) | ||
| p <- p + xlab(paste("Start time (relative to first job)", RUNTIME_UNITS)) | ||
| p <- p + ylab("Job") | ||
| p <- p + opts(title=title) | ||
| print(p) | ||
| } | ||
|
|
||
| # | ||
| # Plots scheduling efficiency at job events | ||
| # | ||
| plotProgressByTime <- function(gatkReport) { | ||
| allJobs = allJobsFromReport(gatkReport) | ||
| nJobs = dim(allJobs)[1] | ||
| allJobs = allJobs[order(allJobs$startTime, decreasing=F),] | ||
| allJobs$index = 1:nrow(allJobs) | ||
|
|
||
| minTime = min(allJobs$startTime) | ||
| allJobs$relStartTime = allJobs$startTime - minTime | ||
| allJobs$relDoneTime = allJobs$doneTime - minTime | ||
|
|
||
| times = sort(c(allJobs$relStartTime, allJobs$relDoneTime)) | ||
|
|
||
| countJobs <- function(p) { | ||
| s = allJobs$relStartTime | ||
| e = allJobs$relDoneTime | ||
| x = c() # I wish I knew how to make this work with apply | ||
| for ( time in times ) | ||
| x = c(x, sum(p(s, e, time))) | ||
| x | ||
| } | ||
|
|
||
| pending = countJobs(function(s, e, t) s > t) | ||
| done = countJobs(function(s, e, t) e < t) | ||
| running = nJobs - pending - done | ||
|
|
||
| d = data.frame(times=times, pending=pending, running=running, done=done) | ||
|
|
||
| p <- ggplot(data=melt(d, id.vars=c("times")), aes(x=times, y=value, color=variable)) | ||
| p <- p + facet_grid(variable ~ ., scales="free") | ||
| p <- p + geom_line(size=2) | ||
| p <- p + xlab(paste("Time since start of first job", RUNTIME_UNITS)) | ||
| p <- p + opts(title = "Job scheduling") | ||
| print(p) | ||
| } | ||
|
|
||
| # | ||
| # Creates tables for each job in this group | ||
| # | ||
| standardColumns = c("jobName", "startTime", "formattedStartTime", "analysisName", "intermediate", "exechosts", "formattedDoneTime", "doneTime", "runtime") | ||
| plotGroup <- function(groupTable) { | ||
| name = unique(groupTable$analysisName)[1] | ||
| groupAnnotations = setdiff(names(groupTable), standardColumns) | ||
| sub = groupTable[,c("jobName", groupAnnotations, "runtime")] | ||
| sub = sub[order(sub$iteration, sub$jobName, decreasing=F), ] | ||
|
|
||
| # create a table showing each job and all annotations | ||
| textplot(sub, show.rownames=F) | ||
| title(paste("Job summary for", name, "full itemization"), cex=3) | ||
|
|
||
| # create the table for each combination of values in the group, listing iterations in the columns | ||
| sum = cast(melt(sub, id.vars=groupAnnotations, measure.vars=c("runtime")), ... ~ iteration, fun.aggregate=mean) | ||
| textplot(as.data.frame(sum), show.rownames=F) | ||
| title(paste("Job summary for", name, "itemizing each iteration"), cex=3) | ||
|
|
||
| # histogram of job times by groupAnnotations | ||
| if ( length(groupAnnotations) == 1 && dim(sub)[1] > 1 ) { | ||
| # todo -- how do we group by annotations? | ||
| p <- ggplot(data=sub, aes(x=runtime)) + geom_histogram() | ||
| p <- p + xlab("runtime in seconds") + ylab("No. of jobs") | ||
| p <- p + opts(title=paste("Job runtime histogram for", name)) | ||
| print(p) | ||
| } | ||
|
|
||
| # as above, but averaging over all iterations | ||
| groupAnnotationsNoIteration = setdiff(groupAnnotations, "iteration") | ||
| if ( dim(sub)[1] > 1 ) { | ||
| sum = cast(melt(sub, id.vars=groupAnnotationsNoIteration, measure.vars=c("runtime")), ... ~ ., fun.aggregate=c(mean, sd)) | ||
| textplot(as.data.frame(sum), show.rownames=F) | ||
| title(paste("Job summary for", name, "averaging over all iterations"), cex=3) | ||
| } | ||
| } | ||
|
|
||
| # print out some useful basic information | ||
| print("Report") | ||
| print(paste("Project :", inputFileName)) | ||
|
|
||
| convertUnits <- function(gatkReportData) { | ||
| convertGroup <- function(g) { | ||
| g$runtime = g$runtime * ORIGINAL_UNITS_TO_SECONDS | ||
| g$startTime = g$startTime * ORIGINAL_UNITS_TO_SECONDS | ||
| g$doneTime = g$doneTime * ORIGINAL_UNITS_TO_SECONDS | ||
| g | ||
| } | ||
| lapply(gatkReportData, convertGroup) | ||
| } | ||
|
|
||
|
|
||
| # read the table | ||
| gatkReportData <- gsa.read.gatkreport(inputFileName) | ||
| gatkReportData <- convertUnits(gatkReportData) | ||
| #print(summary(gatkReportData)) | ||
|
|
||
| if ( ! is.na(outputPDF) ) { | ||
| pdf(outputPDF, height=8.5, width=11) | ||
| } | ||
|
|
||
| plotJobsGantt(gatkReportData, T) | ||
| plotJobsGantt(gatkReportData, F) | ||
| plotProgressByTime(gatkReportData) | ||
| for ( group in gatkReportData ) { | ||
| plotGroup(group) | ||
| } | ||
|
|
||
| if ( ! is.na(outputPDF) ) { | ||
| dev.off() | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.