move some files around

scripts/build.pl

@@ -5,7 +5,7 @@ use warnings;
 use diagnostics;
 
 use FindBin;
-use lib $FindBin::Bin;
+use lib "$FindBin::Bin/Modules";
 
 use Util;
 use TUI;

scripts/charts/combined_sankey.r

@@ -0,0 +1,80 @@
+library(ggplot2)
+library(ggalluvial)
+
+# Usage: Rscript combined_comparion.r exp_abspath1 exp_abspath2 ...
+
+args <- commandArgs(trailingOnly = TRUE)
+argc <- length(args)
+
+if (argc != 2) {
+  print("Expecting two input files")
+  stop()
+}
+
+for (experiment in args) {
+  datafile <- paste(experiment, "/faults.csv", sep = "")
+  if (!file.exists(datafile)) {
+    print(paste("Input file", datafile, "is missing"))
+    stop()
+  }
+}
+
+resulttype_labels <- c(
+  OK_MARKER = "OK",
+  FAIL_MARKER = "FAIL",
+  DETECTED_MARKER = "DETECTED",
+  TIMEOUT = "TIMEOUT",
+  TRAP = "TRAP",
+  ACCESS_OUTERSPACE = "OUTERSPC",
+  WRITE_TEXTSEGMENT = "WRITETXT"
+)
+
+# Read data
+datafile1 <- paste(args[1], "/faults.csv", sep = "")
+data1 <- readr::read_csv(datafile1)
+data1$fault_address <- strtoi(data1$fault_address)
+data1$resulttype <- resulttype_labels[data1$resulttype]
+# tibble::glimpse(data1)
+
+datafile2 <- paste(args[2], "/faults.csv", sep = "")
+data2 <- readr::read_csv(datafile2)
+data2$fault_address <- strtoi(data2$fault_address)
+data2$resulttype <- resulttype_labels[data2$resulttype]
+# tibble::glimpse(data2)
+
+# https://corybrunson.github.io/ggalluvial/
+joined <- merge(
+  data1[, c("fault_address", "resulttype", "faults")],
+  data2[, c("fault_address", "resulttype", "faults")],
+  by = "fault_address",
+  suffixes = c("_bench1", "_bench2")
+)
+
+streams <- aggregate(
+  faults_bench2 ~ resulttype_bench1 + resulttype_bench2,
+  data = joined,
+  sum
+)
+names(streams) <- c("bench1", "bench2", "faults")
+
+plot <- ggplot(
+  data = streams,
+  aes(axis1 = bench1, axis2 = bench2, y = faults)
+) +
+  scale_x_discrete(
+    # TODO: Name the benchmarks
+    # limits = c(args[1], args[2])
+    limits = c("Bench A", "Bench B")
+  ) +
+  labs(x = "Benchmark", y = "Faults") +
+  geom_alluvium(aes(fill = bench1)) +
+  geom_stratum() +
+  geom_text(stat = "stratum", aes(label = after_stat(stratum))) +
+  theme_minimal() +
+  theme(legend.position = "none")
+
+# TODO: Name the file according to the benchmarks
+ggsave(
+  paste(args[2], "/../sankey.svg", sep = ""),
+  plot = plot,
+)

scripts/charts/single_result.r

@@ -0,0 +1,26 @@
+library(ggplot2)
+
+# Usage: Rscript single_result.r exp_abspath
+
+args <- commandArgs(trailingOnly = TRUE)
+experiment <- args[1]
+datafile <- paste(experiment, "/resultsdata.csv", sep = "")
+
+if (!file.exists(datafile)) {
+  print(paste("Input file", datafile, "is missing"))
+  stop()
+}
+
+data <- readr::read_csv(datafile)
+tibble::glimpse(data)
+
+plot <- ggplot(data, aes(x = benchmark, y = faults, fill = resulttype)) +
+  geom_col(position = "dodge") +
+  scale_y_log10() +
+  labs(x = "Benchmark", y = "Faults", fill = "Result Type") +
+  theme_minimal()
+
+ggsave(
+  paste(experiment, "/single_result.svg", sep = ""),
+  plot = plot,
+)

scripts/charts/single_scatter.r

@@ -0,0 +1,32 @@
+library(ggplot2)
+
+# Usage: Rscript single_scatter.r exp_abspath
+
+# TODO: Allow filtering resulttypes (or at least exclude OK_MARKER)
+
+args <- commandArgs(trailingOnly = TRUE)
+experiment <- args[1]
+datafile <- paste(experiment, "/faults.csv", sep = "")
+
+if (!file.exists(datafile)) {
+  print(paste("Input file", datafile, "is missing"))
+  stop()
+}
+
+data <- readr::read_csv(datafile)
+data$fault_address <- strtoi(data$fault_address)
+tibble::glimpse(data)
+
+plot <- ggplot(data, aes(x = fault_address, y = faults)) +
+  geom_point(aes(color = resulttype)) +
+  scale_x_continuous(
+    labels = function(x) sprintf("0x%X", as.integer(x))
+  ) +
+  scale_y_log10() +
+  labs(x = "Address", y = "Faults", color = "Type") +
+  theme_minimal()
+
+ggsave(
+  paste(experiment, "/scatter.svg", sep = ""),
+  plot = plot,
+)

scripts/compile.pl

@@ -7,7 +7,7 @@ use File::Copy qw(copy);
 use File::Path qw(rmtree make_path);
 use Cwd        qw(abs_path);
 use FindBin;
-use lib $FindBin::Bin;
+use lib "$FindBin::Bin/Modules";
 use Util;
 
 # ========================================================================================= #

scripts/deploy.pl

@@ -5,7 +5,7 @@ use warnings;
 use diagnostics;
 
 use FindBin;
-use lib $FindBin::Bin;
+use lib "$FindBin::Bin/Modules";
 
 use Util;
 use Mars;

scripts/explore.pl

@@ -5,7 +5,7 @@ use warnings;
 use diagnostics;
 
 use FindBin;
-use lib $FindBin::Bin;
+use lib "$FindBin::Bin/Modules";
 
 use Util;
 use Mars;

scripts/ghidra/ImportMarkersAsBookmarks.java

@@ -0,0 +1,115 @@
+import ghidra.app.script.GhidraScript;
+import ghidra.program.model.address.Address;
+import ghidra.program.model.listing.BookmarkManager;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+
+public class ImportMarkersAsBookmarks extends GhidraScript {
+
+  @Override
+  public void run() throws Exception {
+    // Can't do this in headless mode
+    // File input = askFile("Select CSV file", "Import");
+
+    String[] args = getScriptArgs();
+    if (args.length < 1) {
+      throw new IllegalArgumentException(
+          "Missing CSV file path.\nUsage: ImportMarkersAsBookmarks <markers.csv>");
+    }
+
+    File input = new File(args[0]);
+    if (!input.isFile()) {
+      throw new IllegalArgumentException(
+          "CSV file does not exist or is not a regular file: " + input.getAbsolutePath());
+    }
+
+    println("Importing bookmarks from: " + input.getAbsolutePath());
+
+    // https://ghidra.re/ghidra_docs/api/ghidra/program/model/listing/BookmarkManager.html
+    BookmarkManager bm = currentProgram.getBookmarkManager();
+
+    int imported = 0;
+    int skipped = 0;
+    int lineNo = 0;
+
+    // CSV columns: (benchmark, resulttype, faults, fault_address)
+    // Example:     (ip       , OK_MARKER , 4311  , 0x10001B     )
+    try (BufferedReader br = new BufferedReader(new FileReader(input))) {
+      String line;
+      while ((line = br.readLine()) != null) {
+        lineNo++;
+
+        line = line.trim();
+        if (line.isEmpty() || line.startsWith("#") || line.startsWith("benchmark")) {
+          continue;
+        }
+
+        // Make sure to always use "," delimiter and never quotations
+        String[] parts = line.split(",");
+        if (parts.length != 4) {
+          skipped++;
+          printerr("Line " + lineNo + ": malformed");
+          continue;
+        }
+
+        String benchText = parts[0].trim();
+        String typeText = parts[1].trim();
+        String countText = parts[2].trim();
+        String addrText = parts[3].trim();
+
+        if (benchText.isEmpty()
+            || typeText.isEmpty()
+            || countText.isEmpty()
+            || addrText.isEmpty()) {
+          skipped++;
+          printerr("Line " + lineNo + ": malformed");
+          continue;
+        }
+
+        Address addr = parseAddress(addrText);
+        if (addr == null) {
+          skipped++;
+          printerr("Line " + lineNo + ": invalid address: " + addrText);
+          continue;
+        }
+
+        println(
+            "Adding bookmark at "
+                + addr
+                + " with type "
+                + benchText
+                + " with category "
+                + benchText // ip, mem or regs
+                + " - "
+                + typeText
+                + " description "
+                + countText
+                + "x");
+
+        //                   TYPE       CATEGORY                      DESCRIPTION
+        bm.setBookmark(addr, benchText, benchText + " - " + typeText, countText + "x");
+        imported++;
+      }
+    }
+
+    println("Imported " + imported + " bookmarks.");
+    if (skipped > 0) {
+      println("Skipped " + skipped + " lines.");
+    }
+  }
+
+  public Address parseAddress(String text) {
+    text = text.trim();
+
+    if (text.startsWith("0x") || text.startsWith("0X")) {
+      text = text.substring(2);
+    }
+
+    try {
+      return toAddr(text);
+    } catch (Exception e) {
+      return null;
+    }
+  }
+}

scripts/ghidra/RemapSourcePaths.java

@@ -0,0 +1,36 @@
+import ghidra.program.database.sourcemap.UserDataPathTransformer;
+import ghidra.program.model.sourcemap.SourcePathTransformer;
+
+// Remap:
+// /build/source/core (libiwasm)
+// /home/christoph/Notes/TU/MastersThesis/FailNix/build-sum2_repl_cored_late/module_host.c
+public class RemapSourcePaths extends GhidraScript {
+
+  @Override
+  protected void run() throws Exception {
+    String[] args = getScriptArgs();
+    if (args.length < 2) {
+      throw new IllegalArgumentException(
+          "Missing file paths.\nUsage: RemapSourcePaths <libiwasm> <host>");
+    }
+
+    // https://ghidra.re/ghidra_docs/api/ghidra/program/model/sourcemap/SourcePathTransformer.html
+    SourcePathTransformer tx = UserDataPathTransformer.getPathTransformer(currentProgram);
+
+    String oldIwasmDir = "/build/source/core";
+    String newIwasmDir = args[0];
+
+    tx.addDirectoryTransform(oldIwasmDir, newIwasmDir);
+    println("Added transform:");
+    println("  " + oldIwasmDir + " -> " + newIwasmDir);
+
+    // TODO: What to do here? Need to know the build dir name...
+    String failNix = "/home/christoph/Notes/TU/MastersThesis/FailNix";
+    String oldHostDir = failNix + "/build-.../module_host.c";
+    String newHostDir = args[1];
+
+    tx.addDirectoryTransform(oldHostDir, newHostDir);
+    println("Added transform:");
+    println("  " + oldHostDir + " -> " + newHostDir);
+  }
+}

scripts/menu.pl

@@ -5,7 +5,7 @@ use warnings;
 use diagnostics;
 
 use FindBin;
-use lib $FindBin::Bin;
+use lib "$FindBin::Bin/Modules";
 
 use Util;
 use Mars;
@@ -25,9 +25,9 @@ my $local_wamr            = "$local_root/wamr";
 my $local_scripts_dir     = "$local_root/scripts";
 my $local_builds_dir      = "$local_root/builds";
 my $local_archive_dir     = "$local_root/injections";
-my $local_charts_dir      = "$local_root/charts";
-my $local_ghidra_projects = "$local_root/ghidra/projects";
-my $local_ghidra_scripts  = "$local_root/ghidra/scripts";
+my $local_charts_dir      = "$local_root/scripts/charts";
+my $local_ghidra_projects = "$local_root/ghidra";
+my $local_ghidra_scripts  = "$local_root/scripts/ghidra";
 my $local_db_conf         = "$local_root/db.conf";
 
 my $resultbrowser_port = '5000';

scripts/multi_runner.pl

@@ -5,7 +5,7 @@ use warnings;
 use diagnostics;
 
 use FindBin;
-use lib $FindBin::Bin;
+use lib "$FindBin::Bin/Modules";
 
 use Util;
 

scripts/runner.pl

@@ -6,7 +6,7 @@ use diagnostics;
 
 use FindBin;
 use lib $FindBin::Bin;
-use lib "$FindBin::Bin/../../scripts";
+use lib "$FindBin::Bin/../../scripts/Modules";
 
 use Util;