Import wiredtiger: a3325482022bc77846ffc0265097edfebccaadd3 from branch mongodb-4.2

ref: 315563f288..a332548202
for: 4.1.12

WT-4747       Python3: change optrack scripts to run under Python3
WT-4779       Disable new assertion related to timestamp consistency

5 files changed, 78 insertions, 62 deletions

diff --git a/src/third_party/wiredtiger/import.data b/src/third_party/wiredtiger/import.data
index 77c0a6a895c..8eaa6b77b0b 100644
--- a/src/third_party/wiredtiger/import.data
+++ b/src/third_party/wiredtiger/import.data
@@ -1,5 +1,5 @@
 {
-    "commit": "315563f28850026673ebb146b6f3d727178e58bc", 
+    "commit": "a3325482022bc77846ffc0265097edfebccaadd3", 
     "github": "wiredtiger/wiredtiger.git", 
     "vendor": "wiredtiger", 
     "branch": "mongodb-4.2"
diff --git a/src/third_party/wiredtiger/src/txn/txn_timestamp.c b/src/third_party/wiredtiger/src/txn/txn_timestamp.c
index c15d2043ee6..0e5fe4b53af 100644
--- a/src/third_party/wiredtiger/src/txn/txn_timestamp.c
+++ b/src/third_party/wiredtiger/src/txn/txn_timestamp.c
@@ -719,8 +719,12 @@ __wt_txn_set_commit_timestamp(
 			    __wt_timestamp_to_string(
 			    txn->first_commit_timestamp, ts_string[1]));
 
-		WT_RET(__txn_assert_after_reads(
-		    session, "commit", commit_ts, NULL));
+		/*
+		 * FIXME:
+		 * WT-4779 disabled to buy time to understand a test failure.
+		 * WT_RET(__txn_assert_after_reads(
+		 *   session, "commit", commit_ts, NULL));
+		 */
 	} else {
 		/*
 		 * For a prepared transaction, the commit timestamp should not
diff --git a/src/third_party/wiredtiger/tools/optrack/find-latency-spikes.py b/src/third_party/wiredtiger/tools/optrack/find-latency-spikes.py
index 93eed8fea8b..ca2b2d814a8 100755
--- a/src/third_party/wiredtiger/tools/optrack/find-latency-spikes.py
+++ b/src/third_party/wiredtiger/tools/optrack/find-latency-spikes.py
@@ -25,7 +25,6 @@
 # OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
 # ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 # OTHER DEALINGS IN THE SOFTWARE.
-#!/usr/bin/env python
 
 import argparse
 from bokeh.layouts import column
@@ -35,14 +34,12 @@ from bokeh.models import NumeralTickFormatter, OpenURL, Range1d, TapTool
 from bokeh.models.annotations import Label
 from bokeh.plotting import figure, output_file, reset_output, save, show
 from bokeh.resources import CDN
-import matplotlib
 from multiprocessing import Process, Queue, Array
 import multiprocessing
 import numpy as np
 import os
 import pandas as pd
 import sys
-import statvfs
 import traceback
 import time
 
@@ -120,21 +117,29 @@ timeUnitString = "nanoseconds";
 PERCENTILE = 0.999;
 
 def initColorList():
+    def hex2(n):
+        return hex(n)[2:].zfill(2)  # two digit hex string
 
     global colorList;
 
-    colorList = matplotlib.colors.cnames.keys();
-
-    for color in colorList:
-        # Some browsers break if you try to give them 'sage'
-        if (color == "sage"):
-            colorList.remove(color);
-        # We reserve red to highlight occurrences of functions
-        # that exceeded the user-defined latency threshold. Do
-        # not use red for regular function colors.
-        #
-        elif (color == "red"):
-            colorList.remove(color);
+    colorList = []
+    # Create a palette of 100 colors that are spaced around the RGB
+    # color wheel.  We advance R,G,B independently at different rates.
+    r = g = b = 0
+    while len(colorList) < 100:
+        r = (r + 87) % 256
+        g = (g + 153) % 256
+        b = (b + 61) % 256
+        # If the color is too close to red or white/grey/black, or
+        # too light, we'll choose a different color.  We reserve red
+        # to highlight occurrences of functions that exceeded the
+        # user-defined latency threshold. And white/grey/black and
+        # light colors do not stand out enough.
+        if (r > 128 and g < 20 and b < 20) or \
+           (abs(r - g) < 20 and abs(g - b) < 20 and abs(r - b) < 20) or \
+           (r > 246 and g > 246 and b > 246):
+            g = (g + 100) % 256
+        colorList.append('#' + hex2(r) + hex2(g) + hex2(b))
 
 #
 # Each unique function name gets a unique color.
@@ -147,7 +152,7 @@ def getColorForFunction(function):
     global lastColorUsed;
     global funcToColor;
 
-    if not funcToColor.has_key(function):
+    if not function in funcToColor:
         funcToColor[function] = colorList[lastColorUsed % len(colorList)];
         lastColorUsed += 1;
 
@@ -225,14 +230,14 @@ def plotOutlierHistogram(dataframe, maxOutliers, func,
                y_axis_label = "Number of outliers",
                tools = TOOLS, toolbar_location="above");
 
-    y_ticker_max = p.plot_height / pixelsPerHeightUnit;
-    y_ticker_step = max(1, (maxOutliers + 1)/y_ticker_max);
-    y_upper_bound = (maxOutliers / y_ticker_step + 2) * y_ticker_step;
+    y_ticker_max = p.plot_height // pixelsPerHeightUnit;
+    y_ticker_step = max(1, (maxOutliers + 1)//y_ticker_max);
+    y_upper_bound = (maxOutliers // y_ticker_step + 2) * y_ticker_step;
 
     p.yaxis.ticker = FixedTicker(ticks =
-                                 range(0, y_upper_bound, y_ticker_step));
+                                 list(range(0, y_upper_bound, y_ticker_step)));
     p.ygrid.ticker = FixedTicker(ticks =
-                                 range(0, y_upper_bound, y_ticker_step));
+                                 list(range(0, y_upper_bound, y_ticker_step)));
     p.xaxis.formatter = NumeralTickFormatter(format="0,");
 
     p.y_range = Range1d(0, y_upper_bound);
@@ -284,7 +289,7 @@ def normalizeIntervalData():
 
     print(color.BLUE + color.BOLD + "Normalizing data..." + color.END);
 
-    for file, df in perFileDataFrame.iteritems():
+    for file, df in perFileDataFrame.items():
         df['origstart'] = df['start'];
         df['start'] = df['start'] - firstTimeStamp;
         df['end'] = df['end'] - firstTimeStamp;
@@ -531,8 +536,8 @@ def generateBucketChartForFile(figureName, dataframe, y_max, x_min, x_max):
     p.yaxis.major_tick_line_color = None;
     p.yaxis.minor_tick_line_color = None;
     p.yaxis.major_label_text_font_size = '0pt';
-    p.yaxis.ticker = FixedTicker(ticks = range(0, y_max+1));
-    p.ygrid.ticker = FixedTicker(ticks = range(0, y_max+1));
+    p.yaxis.ticker = FixedTicker(ticks = list(range(0, y_max+1)));
+    p.ygrid.ticker = FixedTicker(ticks = list(range(0, y_max+1)));
 
     p.xaxis.formatter = NumeralTickFormatter(format="0,");
     p.title.text_font_style = "bold";
@@ -541,7 +546,7 @@ def generateBucketChartForFile(figureName, dataframe, y_max, x_min, x_max):
            top = 'stackdepthNext', color = 'color', line_color = "lightgrey",
            line_width = 0.5, source=cds);
 
-    for func, fColor in funcToColor.iteritems():
+    for func, fColor in funcToColor.items():
 
         # If this function is not present in this dataframe,
         # we don't care about it.
@@ -555,7 +560,7 @@ def generateBucketChartForFile(figureName, dataframe, y_max, x_min, x_max):
         # add it again to avoid redundancy in the charts and
         # in order not to waste space.
         #
-        if (colorAlreadyUsedInLegend.has_key(fColor)):
+        if fColor in colorAlreadyUsedInLegend:
             continue;
         else:
             colorAlreadyUsedInLegend[fColor] = True;
@@ -676,7 +681,7 @@ def generateCrossFilePlotsForBucket(i, lowerBound, upperBound, navigatorDF,
     save(column(figuresForAllFiles), filename = fileName,
          title=intervalTitle, resources=CDN);
 
-    retFilename.value = fileName;
+    retFilename.value = fileName.encode();
 
 
 # Generate a plot that shows a view of the entire timeline in a form of
@@ -718,8 +723,8 @@ def generateNavigatorFigure(dataframe, i, title):
     p.yaxis.major_tick_line_color = None;
     p.yaxis.minor_tick_line_color = None;
     p.yaxis.major_label_text_font_size = '0pt';
-    p.yaxis.ticker = FixedTicker(ticks = range(0, 1));
-    p.ygrid.ticker = FixedTicker(ticks = range(0, 1));
+    p.yaxis.ticker = FixedTicker(ticks = list(range(0, 1)));
+    p.ygrid.ticker = FixedTicker(ticks = list(range(0, 1)));
 
     p.xaxis.formatter = NumeralTickFormatter(format="0,");
 
@@ -780,7 +785,8 @@ def createIntervalNavigatorDF(numBuckets, timeUnitsPerBucket):
 def waitOnOneProcess(runningProcesses):
 
     success = False;
-    for i, p in runningProcesses.items():
+    # Use a copy since we will be deleting entries from the original
+    for i, p in runningProcesses.copy().items():
         if (not p.is_alive()):
             del runningProcesses[i];
             success = True;
@@ -797,7 +803,7 @@ def updatePercentComplete(runnableProcesses, runningProcesses,
 
     percentComplete = float(totalWorkItems - len(runnableProcesses) \
                         - len(runningProcesses)) / float(totalWorkItems) * 100;
-    print(color.BLUE + color.BOLD + " " + workName),
+    sys.stdout.write(color.BLUE + color.BOLD + "... " + workName);
     sys.stdout.write(" %d%% complete  \r" % (percentComplete) );
     sys.stdout.flush();
 
@@ -817,8 +823,8 @@ def generateTSSlicesForBuckets():
     returnValues = {};
     spawnedProcesses = {};
 
-    numBuckets = plotWidth / pixelsPerWidthUnit;
-    timeUnitsPerBucket = (lastTimeStamp - firstTimeStamp) / numBuckets;
+    numBuckets = plotWidth // pixelsPerWidthUnit;
+    timeUnitsPerBucket = (lastTimeStamp - firstTimeStamp) // numBuckets;
 
     navigatorDF = createIntervalNavigatorDF(numBuckets, timeUnitsPerBucket);
 
@@ -827,7 +833,7 @@ def generateTSSlicesForBuckets():
         + color.END);
 
     for i in range(numBuckets):
-        retFilename = Array('c', os.statvfs('/')[statvfs.F_NAMEMAX]);
+        retFilename = Array('c', os.statvfs('/').f_namemax)
         lowerBound = i * timeUnitsPerBucket;
         upperBound = (i+1) * timeUnitsPerBucket;
 
@@ -914,7 +920,7 @@ def checkForTimestampAndGetRowSkip(fname):
 
         if (len(words) == 1):
             try:
-                perFileTimeStamps[fname] = long(words[0]);
+                perFileTimeStamps[fname] = int(words[0]);
             except ValueError:
                 print(color.BOLD + color.RED +
                       "Could not parse seconds since Epoch on first line" +
@@ -952,7 +958,7 @@ def processFile(fname, dumpCleanDataBool):
         funcDF = iDF.loc[lambda iDF: iDF.function == func, :];
         funcDF = funcDF.drop(columns = ['function']);
 
-        if (not perFuncDF.has_key(func)):
+        if not func in perFuncDF:
             perFuncDF[func] = funcDF;
         else:
             perFuncDF[func] = pd.concat([perFuncDF[func], funcDF]);
@@ -974,7 +980,7 @@ def createOutlierHistogramForFunction(func, funcDF, bucketFilenames):
 
     statisticalOutlierThreshold = 0;
     statisticalOutlierThresholdDescr = "";
-    userLatencyThreshold = sys.maxint;
+    userLatencyThreshold = sys.maxsize;
     userLatencyThresholdDescr = None;
 
 
@@ -1007,10 +1013,10 @@ def createOutlierHistogramForFunction(func, funcDF, bucketFilenames):
     # we will highlight those bars that contain operations whose
     # duration exceeded the user-defined threshold.
     #
-    if (userDefinedLatencyThresholds.has_key(func)):
+    if (func in userDefinedLatencyThresholds):
         userLatencyThreshold = userDefinedLatencyThresholds[func];
         userLatencyThresholdDescr = userDefinedThresholdNames[func];
-    elif (userDefinedLatencyThresholds.has_key("*")):
+    elif ("*" in userDefinedLatencyThresholds):
         userLatencyThreshold = userDefinedLatencyThresholds["*"];
         userLatencyThresholdDescr = userDefinedThresholdNames["*"];
 
@@ -1022,8 +1028,8 @@ def createOutlierHistogramForFunction(func, funcDF, bucketFilenames):
                             "th percentile)";
 
 
-    numBuckets = plotWidth / pixelsPerWidthUnit;
-    timeUnitsPerBucket = (lastTimeStamp - firstTimeStamp) / numBuckets;
+    numBuckets = plotWidth // pixelsPerWidthUnit;
+    timeUnitsPerBucket = (lastTimeStamp - firstTimeStamp) // numBuckets;
 
     bucketHeights = [];
     markers = [];
@@ -1081,7 +1087,7 @@ def createOutlierHistogramForFunction(func, funcDF, bucketFilenames):
     dataframe = pd.DataFrame(data=dict);
     dataframe['markerX'] = dataframe['lowerbound'] +  \
                            (dataframe['upperbound'] -
-                            dataframe['lowerbound']) / 2 ;
+                            dataframe['lowerbound']) // 2 ;
     dataframe['markerY'] = dataframe['height'] + 0.2;
 
     return plotOutlierHistogram(dataframe, maxOutliers, func,
@@ -1172,9 +1178,9 @@ def parseConfigFile(fname):
         elif (firstNonCommentLine):
             try:
                 unitsPerSecond = int(line);
-                unitsPerMillisecond = unitsPerSecond / 1000;
-                unitsPerMicrosecond = unitsPerSecond / 1000000;
-                unitsPerNanosecond  = unitsPerSecond / 1000000000;
+                unitsPerMillisecond = unitsPerSecond // 1000;
+                unitsPerMicrosecond = unitsPerSecond // 1000000;
+                unitsPerNanosecond  = unitsPerSecond // 1000000000;
 
                 timeUnitString = getTimeUnitString(unitsPerSecond);
 
@@ -1321,7 +1327,8 @@ def main():
 
         i += 1;
         percentComplete = float(i) / float(totalFuncs) * 100;
-        print(color.BLUE + color.BOLD + " Generating outlier histograms... "),
+        sys.stdout.write(color.BLUE + color.BOLD +
+                         " Generating outlier histograms... ");
         sys.stdout.write("%d%% complete  \r" % (percentComplete) );
         sys.stdout.flush();
 
diff --git a/src/third_party/wiredtiger/tools/optrack/optrack_to_t2.py b/src/third_party/wiredtiger/tools/optrack/optrack_to_t2.py
index 80d004376f2..beb11627567 100755
--- a/src/third_party/wiredtiger/tools/optrack/optrack_to_t2.py
+++ b/src/third_party/wiredtiger/tools/optrack/optrack_to_t2.py
@@ -230,7 +230,7 @@ def checkForTimestampAndGetRowSkip(fname):
 
         if (len(words) == 1):
             try:
-                firstTimeStamp = long(words[0]);
+                firstTimeStamp = int(words[0]);
             except ValueError:
                 print(color.BOLD + color.RED +
                       "Could not parse seconds since Epoch on first line" +
@@ -308,7 +308,7 @@ def parseIntervals(df, firstTimeStamp, fname):
     firstIntervalTimestampSeconds = firstTimeStamp;
     lastIntervalTimestampSeconds = firstIntervalTimestampSeconds + \
                 (lastTimestampUnits - firstTimestampUnits) \
-                / unitsPerSecond;
+                // unitsPerSecond;
 
     if (lastIntervalTimestampSeconds < firstIntervalTimestampSeconds):
         print(color.BOLD + color.RED +
@@ -404,9 +404,9 @@ def parseIntervals(df, firstTimeStamp, fname):
 
         # Convert the durations to percentages and record them
         # in the output dictionary
-        for func, duration in thisIntDict.iteritems():
+        for func, duration in thisIntDict.items():
             outputDictKey =  columnNamePrefix + func;
-            percentDuration = float(duration) / \
+            percentDuration = float(duration) // \
                               float(intervalLength * unitsPerSecond) * 100;
             outputDict[outputDictKey].append(percentDuration);
 
@@ -415,7 +415,7 @@ def parseIntervals(df, firstTimeStamp, fname):
         # The list at each function's key should be as long as the list
         # at key 'time'.
         targetLen = len(outputDict['time']);
-        for key, theList in outputDict.iteritems():
+        for key, theList in outputDict.items():
             if len(theList) < targetLen:
                 theList.append(0);
 
@@ -427,7 +427,7 @@ def parseIntervals(df, firstTimeStamp, fname):
     #
     targetColumns = ['time'];
 
-    for key, value in outputDict.iteritems():
+    for key, value in outputDict.items():
         if key != 'time':
             targetColumns.append(key);
 
diff --git a/src/third_party/wiredtiger/tools/optrack/wt_optrack_decode.py b/src/third_party/wiredtiger/tools/optrack/wt_optrack_decode.py
index a00ab0d2c7b..06dec019fcd 100755
--- a/src/third_party/wiredtiger/tools/optrack/wt_optrack_decode.py
+++ b/src/third_party/wiredtiger/tools/optrack/wt_optrack_decode.py
@@ -70,7 +70,7 @@ def buildTranslationMap(mapFileName):
         print(color.BOLD + color.RED);
         print("Could not open " + mapFileName + " for reading");
         print(color.END);
-        return;
+        raise;
 
     # Read lines from the map file and build an in-memory map
     # of translations. Each line has a function ID followed by space and
@@ -97,7 +97,7 @@ def buildTranslationMap(mapFileName):
 
 def funcIDtoName(funcID):
 
-    if (functionMap.has_key(funcID)):
+    if funcID in functionMap:
         return functionMap[funcID];
     else:
        print("Could not find the name for func " + str(funcID));
@@ -147,10 +147,14 @@ def validateHeader(file):
     try:
         bytesRead = file.read(MIN_HEADER_SIZE);
     except:
-        return False, -1;
+        print(color.BOLD + color.RED +
+              "failed read of input file" + color.END);
+        raise;
 
     if (len(bytesRead) < MIN_HEADER_SIZE):
-        return False, -1;
+        print(color.BOLD + color.RED +
+              "unexpected sized input file" + color.END);
+        raise;
 
     version, threadType, tsc_nsec = struct.unpack('=III', bytesRead);
     print("VERSION IS " + str(version));
@@ -203,11 +207,11 @@ def parseFile(fileName):
 
     # Open the log file for reading
     try:
-        file = open(fileName, "r");
+        file = open(fileName, "rb");
     except:
         print(color.BOLD + color.RED +
               "Could not open " + fileName + " for reading" + color.END);
-        return;
+        raise;
 
     # Read and validate log header
     validVersion, threadType, tsc_nsec_ratio, sec_from_epoch = \
@@ -275,7 +279,8 @@ def parseFile(fileName):
 def waitOnOneProcess(runningProcesses):
 
     success = False;
-    for fname, p in runningProcesses.items():
+    # Use a copy since we will be deleting entries from the original
+    for fname, p in runningProcesses.copy().items():
         if (not p.is_alive()):
             del runningProcesses[fname];
             success = True;