diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java
index 10183f091d72da27ca5d9e5c0fe0467064d368af..c08c18d07ec090a9d02ebfc908960a1b11f6f41c 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java
@@ -1,11 +1,17 @@
package cz.it4i.fiji.haas_spim_benchmark.core;
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.InvalidPathException;
import java.nio.file.Path;
import java.nio.file.Paths;
+import java.text.MessageFormat;
import java.util.Arrays;
import java.util.Collection;
+import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.function.Predicate;
@@ -27,7 +33,6 @@ import net.imagej.updater.util.Progress;
public class BenchmarkJobManager {
- @SuppressWarnings("unused")
private static Logger log = LoggerFactory
.getLogger(cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.class);
@@ -42,10 +47,10 @@ public class BenchmarkJobManager {
}
public void startJob(Progress progress) throws IOException {
- jobInfo.uploadFilesByName(Arrays.asList(CONFIG_YAML), progress);
- String outputName = getOutputName(jobInfo.openLocalFile(CONFIG_YAML));
+ jobInfo.uploadFilesByName(Arrays.asList(Constants.CONFIG_YAML), progress);
+ String outputName = getOutputName(jobInfo.openLocalFile(Constants.CONFIG_YAML));
jobInfo.submit();
- jobInfo.setProperty(SPIM_OUTPUT_FILENAME_PATTERN, outputName);
+ jobInfo.setProperty(Constants.SPIM_OUTPUT_FILENAME_PATTERN, outputName);
}
public JobState getState() {
@@ -56,7 +61,7 @@ public class BenchmarkJobManager {
JobInfo ji = jobInfo;
if (ji.needsDownload()) {
if (ji.getState() == JobState.Finished) {
- String filePattern = ji.getProperty(SPIM_OUTPUT_FILENAME_PATTERN);
+ String filePattern = ji.getProperty(Constants.SPIM_OUTPUT_FILENAME_PATTERN);
ji.downloadData(downloadFinishedData(filePattern), progress, false);
} else if (ji.getState() == JobState.Failed) {
ji.downloadData(downloadFailedData(), progress, false);
@@ -67,6 +72,9 @@ public class BenchmarkJobManager {
public void downloadStatistics(Progress progress) throws IOException {
JobInfo ji = jobInfo;
ji.downloadData(BenchmarkJobManager.downloadStatistics(), progress, true);
+ Path resultFile = ji.getDirectory().resolve(Constants.BENCHMARK_RESULT_FILE);
+ if (resultFile != null)
+ BenchmarkJobManager.formatResultFile(resultFile);
}
public List<String> getOutput(List<JobSynchronizableFile> files) {
@@ -130,15 +138,6 @@ public class BenchmarkJobManager {
}
}
- private static final String HAAS_JOB_NAME = "HaaSSPIMBenchmark";
- private static final int HAAS_CLUSTER_NODE_TYPE = 6;
- private static final int HAAS_TEMPLATE_ID = 4;
- private static final String HAAS_PROJECT_ID = "DD-17-31";
- private static final int HAAS_TIMEOUT = 9600;
-
- private static final String SPIM_OUTPUT_FILENAME_PATTERN = "spim.outputFilenamePattern";
- private static final String CONFIG_YAML = "config.yaml";
-
private JobManager jobManager;
public BenchmarkJobManager(BenchmarkSPIMParameters params) throws IOException {
@@ -157,7 +156,7 @@ public class BenchmarkJobManager {
}
private HaaSClient.UploadingFile getUploadingFile() {
- return new UploadingFileFromResource("", CONFIG_YAML);
+ return new UploadingFileFromResource("", Constants.CONFIG_YAML);
}
private Job convertJob(JobInfo jobInfo) {
@@ -185,30 +184,114 @@ public class BenchmarkJobManager {
}
- private Predicate<String> downloadFinishedData(String filePattern) {
+ private static Predicate<String> downloadFinishedData(String filePattern) {
return name -> {
- Path p = Paths.get(name);
- String fileName = p.getFileName().toString();
+ Path path = getPathSafely(name);
+ if (path == null)
+ return false;
+
+ String fileName = path.getFileName().toString();
return fileName.startsWith(filePattern) && fileName.endsWith("h5") || fileName.equals(filePattern + ".xml")
- || fileName.equals("benchmark_result.csv");
+ || fileName.equals(Constants.BENCHMARK_RESULT_FILE);
};
}
- static private Predicate<String> downloadStatistics() {
+ private static Predicate<String> downloadStatistics() {
return name -> {
- Path p = Paths.get(name);
- String fileName = p.getFileName().toString();
- return fileName.equals("benchmark_result.csv");
+ Path path = getPathSafely(name);
+ if (path == null)
+ return false;
+
+ String fileName = path.getFileName().toString();
+ return fileName.equals(Constants.BENCHMARK_RESULT_FILE);
};
}
- private Predicate<String> downloadFailedData() {
+ private static Predicate<String> downloadFailedData() {
return name -> {
- Path p = Paths.get(name);
- return p.getFileName().toString().startsWith("snakejob.")
- || p.getParent().getFileName().toString().equals("logs");
+ Path path = getPathSafely(name);
+ if (path == null)
+ return false;
+
+ return path.getFileName().toString().startsWith("snakejob.")
+ || path.getParent().getFileName().toString().equals("logs");
};
}
+
+ private static Path getPathSafely(String name) {
+ try {
+ return Paths.get(name);
+ } catch(InvalidPathException ex) {
+ return null;
+ }
+ }
+
+ private static void formatResultFile(Path filename) throws FileNotFoundException {
+
+ List<ResultFileTask> identifiedTasks = new LinkedList<ResultFileTask>();
+
+ try {
+ String line = null;
+ final String separator = ";";
+
+ ResultFileTask processedTask = null;
+ List<ResultFileJob> jobs = new LinkedList<>();
+
+ BufferedReader reader = Files.newBufferedReader(filename);
+ while (null != (line = reader.readLine())) {
+
+ line = line.trim();
+ if (line.isEmpty()) {
+ continue;
+ }
+
+ String[] columns = line.split(separator);
+
+ if (columns[0].equals(Constants.STATISTICS_TASK_NAME)) {
+
+ // If there is a task being processed, add all cached jobs to it and wrap it up
+ if (null != processedTask ) {
+ processedTask.jobs.addAll(jobs);
+ identifiedTasks.add(processedTask);
+ }
+
+ // Start processing a new task
+ processedTask = new ResultFileTask(columns[1]);
+ jobs.clear();
+
+ } else if (columns[0].equals(Constants.STATISTICS_JOB_IDS)) {
+
+ // Cache all found jobs
+ for (int i = 1; i < columns.length; i++) {
+ jobs.add(new ResultFileJob(columns[i]));
+ }
+
+ } else if (!columns[0].equals(Constants.STATISTICS_JOB_COUNT)) {
+
+ // Save values of a given property to cached jobs
+ for (int i = 1; i < columns.length; i++) {
+ jobs.get(i - 1).setValue(columns[0], columns[i]);
+ }
+
+ }
+ }
+
+ // If there is a task being processed, add all cached jobs to it and wrap it up
+ if (null != processedTask ) {
+ processedTask.jobs.addAll(jobs);
+ identifiedTasks.add(processedTask);
+ }
+
+ } catch (IOException e) {
+ log.error(e.getMessage(), e);
+ }
+
+ for (ResultFileTask task : identifiedTasks) {
+ Object[] args = {Constants.STATISTICS_TASK_NAME_MAP.get(task.name), task.getJobCount(), task.getAverageMemoryUsage()};
+ MessageFormat fmt = new MessageFormat(Constants.STATISTICS_OUTPUT_MESSAGE);
+ System.out.println(fmt.format(args));
+ }
+ }
private static Settings constructSettingsFromParams(BenchmarkSPIMParameters params) {
// TODO Auto-generated method stub
@@ -221,17 +304,17 @@ public class BenchmarkJobManager {
@Override
public int getTimeout() {
- return HAAS_TIMEOUT;
+ return Constants.HAAS_TIMEOUT;
}
@Override
public long getTemplateId() {
- return HAAS_TEMPLATE_ID;
+ return Constants.HAAS_TEMPLATE_ID;
}
@Override
public String getProjectId() {
- return HAAS_PROJECT_ID;
+ return Constants.HAAS_PROJECT_ID;
}
@Override
@@ -246,7 +329,7 @@ public class BenchmarkJobManager {
@Override
public String getJobName() {
- return HAAS_JOB_NAME;
+ return Constants.HAAS_JOB_NAME;
}
@Override
@@ -256,7 +339,7 @@ public class BenchmarkJobManager {
@Override
public long getClusterNodeType() {
- return HAAS_CLUSTER_NODE_TYPE;
+ return Constants.HAAS_CLUSTER_NODE_TYPE;
}
};
}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Constants.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Constants.java
index 367ef54df3ca69b2dc82e879f4c0088737adf470..0e4f436ca65c9eb2174a0d2d91496394c1bf2248 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Constants.java
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Constants.java
@@ -1,5 +1,41 @@
package cz.it4i.fiji.haas_spim_benchmark.core;
+import java.util.HashMap;
+import java.util.Map;
+
public interface Constants {
long HAAS_UPDATE_TIMEOUT = 1000;
+ String HAAS_JOB_NAME = "HaaSSPIMBenchmark";
+ int HAAS_CLUSTER_NODE_TYPE = 6;
+ int HAAS_TEMPLATE_ID = 4;
+ String HAAS_PROJECT_ID = "DD-17-31";
+ int HAAS_TIMEOUT = 9600;
+
+ String SPIM_OUTPUT_FILENAME_PATTERN = "spim.outputFilenamePattern";
+ String CONFIG_YAML = "config.yaml";
+ String BENCHMARK_RESULT_FILE = "benchmark_result.csv";
+
+ String STATISTICS_TASK_NAME = "Task name";
+ String STATISTICS_JOB_IDS = "job ids";
+ String STATISTICS_JOB_COUNT = "jobs #";
+ String STATISTICS_RESOURCES_MEMORY_USAGE = "resources_used.mem";
+ String STATISTICS_RESOURCES_WALL_TIME = "resources_used.walltime";
+ String STATISTICS_RESOURCES_CPU_PERCENTAGE = "resources_used.cpupercent";
+
+ Map<String, String> STATISTICS_TASK_NAME_MAP = new HashMap<String, String>() {
+ private static final long serialVersionUID = 1L;
+ {
+ put("define_xml_tif", "Define dataset");
+ put("hdf5_xml", "Define hdf5 dataset");
+ put("resave_hdf5", "Resave to hdf5");
+ put("registration", "Detection and registration");
+ put("xml_merge", "Merge xml");
+ put("timelapse", "Time lapse registration");
+ put("fusion", "Average fusion");
+ put("deconvolution", "Deconvolution GPU");
+ put("define_output", "Define output");
+ put("hdf5_xml_output", "Define hdf5 output");
+ put("resave_hdf5_output", "Resave output to hdf5");
+ }};
+ String STATISTICS_OUTPUT_MESSAGE = "{0} needed {1} {1,choice,0#jobs|1#job|1<jobs} and {2} MB of memory in average.";
}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/ResultFileJob.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/ResultFileJob.java
new file mode 100644
index 0000000000000000000000000000000000000000..f67fee23997feb9a8782eab46e65ebd43e1b7a21
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/ResultFileJob.java
@@ -0,0 +1,21 @@
+package cz.it4i.fiji.haas_spim_benchmark.core;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class ResultFileJob {
+ String id;
+ Map<String, String> values = new HashMap<>();
+
+ public ResultFileJob(String id) {
+ this.id = id;
+ }
+
+ public String getValue(String key) {
+ return values.get(key);
+ }
+
+ public void setValue(String key, String value) {
+ values.put(key, value);
+ }
+}
\ No newline at end of file
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/ResultFileTask.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/ResultFileTask.java
new file mode 100644
index 0000000000000000000000000000000000000000..88767ed9748b70ddd2cf921d2733e05e7b73824d
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/ResultFileTask.java
@@ -0,0 +1,36 @@
+package cz.it4i.fiji.haas_spim_benchmark.core;
+
+import java.util.LinkedList;
+import java.util.stream.Collectors;
+
+public class ResultFileTask {
+ String name;
+ LinkedList<ResultFileJob> jobs;
+
+ public ResultFileTask(String name) {
+ this.name = name;
+ this.jobs = new LinkedList<ResultFileJob>();
+ }
+
+ public int getJobCount() {
+ return this.jobs.size();
+ }
+
+ public double getAverageMemoryUsage() {
+ return getAverage(Constants.STATISTICS_RESOURCES_MEMORY_USAGE);
+ }
+
+ public double getAverageWallTime() {
+ return getAverage(Constants.STATISTICS_RESOURCES_WALL_TIME);
+ }
+
+ public double getAverageCpuPercentage() {
+ return getAverage(Constants.STATISTICS_RESOURCES_CPU_PERCENTAGE);
+ }
+
+ private Double getAverage(String propertyName) {
+ return jobs.stream().map(job -> job.getValue(propertyName))
+ .map(memStr -> Double.parseDouble(memStr))
+ .collect(Collectors.averagingDouble(d->d)).doubleValue();
+ }
+}
\ No newline at end of file