Optimization

paper/main.tex

@@ -136,25 +136,26 @@ Check time series algorithms:
 \section{Evaluation}
 \label{sec:evaluation}
 
-Two study examples (two reference jobs):
+In the following, we assume a job is given and we aim to identify similar jobs.
+We chose several reference jobs with different compute and IO characteristics visualized in \Cref{fig:refJobs}:
 \begin{itemize}
-	\item job-short: shorter length, e.g. 5-10, that has a little bit IO in at least two metadata metrics (more better).
-  \item job-mixed:
-	\item job-long: a very IO intensive longer job, e.g., length $>$ 20, with IO read or write and maybe one other metrics.
+	\item Job-S: performs postprocessing on a single node. This is a typical process in climate science where data products are reformatted and annotated with metadata to a standard representation (so called CMORization). The post-processing is IO intensive.
+  \item Job-M: a typical MPI parallel 8-hour compute job on 128 nodes which writes time series data after some spin up.   %CHE.ws12
+	\item Job-L: a 66-hour 20-node job.
+  The initialization data is read at the beginning.
+  Then only a single master node writes constantly a small volume of data; in fact, the generated data is too small to be categorized as IO relevant.
 \end{itemize}
 
-For each reference job: create CSV file which contains all jobs with:
-\begin{itemize}
-	\item JOB ID, for each algorithm: the coding and the computed ranking $\rightarrow$ thus one long row.
-\end{itemize}
-Alternatively, could be one CSV for each algorithm that contains JOB ID, coding + rank
+For each reference job and algorithm, we created a CSV files with the computed similarity for all other jobs.
+
+
+Sollte man was zur Laufzeit der Algorithmen sagen? Denke Daten zu haben wäre sinnvoll.
 
 Create histograms + cumulative job distribution for all algorithms.
 Insert job profiles for closest 10 jobs.
 
 Potentially, analyze how the rankings of different similarities look like.
 
-\Cref{fig:refJobs}
 
 \begin{figure}
 \begin{subfigure}{0.8\textwidth}

scripts/create-paper-vis.sh

@@ -7,7 +7,8 @@ for job in 5024292 4296426 7488914 ; do
 ./scripts/plot-single-job.py $job "fig/job-"
 done
 
-for file in fig/*.pdf ; do
-  pdfcrop $file output.pdf
-  mv output.pdf $file
-done
+# Remove whitespace around jobs
+# for file in fig/*.pdf ; do
+#   pdfcrop $file output.pdf
+#   mv output.pdf $file
+# done

scripts/plot-single-job.py

@@ -7,8 +7,8 @@ from pandas import Grouper
 from matplotlib import pyplot
 import matplotlib.cm as cm
 
-jobs = [sys.argv[1]]
-prefix = sys.argv[2]
+jobs = sys.argv[1].split(",")
+prefix = sys.argv[2].split(",")
 
 print("Plotting the job: " + str(jobs))
 
@@ -80,7 +80,9 @@ def plot(prefix, header, row):
     colors.append(colorMap[name])
 
   fsize = (8, 1 + 1.5 * len(labels))
-  fsizeFixed = (8, 3)
+  fsizeFixed = (8, 2)
+  
+  pyplot.close('all')
 
   if len(labels) < 4 :
     ax = metrics.plot(legend=True, sharex=True, grid = True,  sharey=True, markersize=10, figsize=fsizeFixed, color=colors, style=style)
@@ -91,7 +93,7 @@ def plot(prefix, header, row):
       ax[i].set_ylabel(l)
 
   pyplot.xlabel("Segment number")
-  pyplot.savefig(prefix + "timeseries" + jobid + ".pdf")
+  pyplot.savefig(prefix + "timeseries" + jobid + ".pdf", bbox_inches='tight')
 
   # Plot first 30 segments
   if len(timeseries) <= 50:
@@ -107,7 +109,7 @@ def plot(prefix, header, row):
       ax[i].set_ylabel(l)
 
   pyplot.xlabel("Segment number")
-  pyplot.savefig(prefix + "timeseries" + jobid + "-30.pdf")
+  pyplot.savefig(prefix + "timeseries" + jobid + "-30.pdf", bbox_inches='tight')
 
 ### end plotting function
 
@@ -116,6 +118,7 @@ def plot(prefix, header, row):
 with open('job-io-datasets/datasets/job_codings.csv') as csv_file:
     csv_reader = csv.reader(csv_file, delimiter=',')
     line_count = 0
+    job = 0
     for row in csv_reader:
       if line_count == 0:
         header = row
@@ -125,4 +128,5 @@ with open('job-io-datasets/datasets/job_codings.csv') as csv_file:
       if not row[0].strip() in jobs:
         continue
       else:
-        plot(prefix, header, row)
+        plot(prefix[job], header, row)
+        job += 1

scripts/plot.R

@@ -19,10 +19,8 @@ data = read.csv(file)
 # Columns are: jobid alg_id alg_name similarity
 
 data$alg_id = as.factor(data$alg_id)
-print(nrow(data))
-
-# FILTER, TODO
-data = data %>% filter(similarity <= 1.0)
+cat("Job count:")
+cat(nrow(data))
 
 # empirical cummulative density function (ECDF)
 ggplot(data, aes(similarity, color=alg_name, group=alg_name)) + stat_ecdf(geom = "step") + xlab("SIM") + ylab("Fraction of jobs") + theme(legend.position="bottom") + scale_color_brewer(palette = "Set2")
@@ -51,13 +49,10 @@ plotJobs = function(jobs){
     md = metadata[metadata$jobid %in% jobs,]
     print(summary(md))
 
-    # print the job timeline
+    # print the job timelines
     r = e[ordered, ]
-    for (row in 1:length(jobs)) {
-      prefix = sprintf("%s-%f-%.0f-", level, r[row, "similarity"], row)
-      job = r[row, "jobid"]
-      system(sprintf("scripts/plot-single-job.py %s %s", job, prefix))
-    }
+    prefix = do.call("sprintf", list("%s-%.0f-", level, r$similarity))
+    system(sprintf("scripts/plot-single-job.py %s %s", paste(r$jobid, collapse=","), paste(prefix, collapse=",")))
   }
 
 # Store the job ids in a table, each column is one algorithm