SERVER-27874 Display locks and generate digraph for threads using LockManager locks and/or pthread_mutexes

(cherry picked from commit 5fe822f53e4bb28e15af2541c0ca931fa05a0e20)

5 files changed, 365 insertions, 18 deletions

diff --git a/.gdbinit b/.gdbinit
index d82d81f02ba..66d56149410 100644
--- a/.gdbinit
+++ b/.gdbinit
@@ -2,5 +2,7 @@
 set python print-stack full
 
 # Load the mongodb pretty printers
-#
 source buildscripts/gdb/mongo.py
+
+# Load the mongodb lock analysis
+source buildscripts/gdb/mongo_lock.py
diff --git a/buildscripts/gdb/mongo.py b/buildscripts/gdb/mongo.py
index ecf2f1469fe..ce0835c4fbd 100644
--- a/buildscripts/gdb/mongo.py
+++ b/buildscripts/gdb/mongo.py
@@ -4,6 +4,7 @@ from __future__ import print_function
 
 import gdb.printing
 import os
+import re
 import sys
 
 try:
@@ -29,6 +30,27 @@ def get_process_name():
     return os.path.splitext(os.path.basename(main_binary_name))[0]
 
 
+def get_thread_id():
+    """Returns the thread_id of the current GDB thread"""
+    # GDB thread example:
+    #  RHEL
+    #   [Current thread is 1 (Thread 0x7f072426cca0 (LWP 12867))]
+    thread_info = gdb.execute("thread", from_tty=False, to_string=True)
+
+    if sys.platform.startswith("linux"):
+        match = re.search(r"Thread (?P<pthread_id>0x[0-9a-f]+)", thread_info)
+        if match:
+            return int(match.group("pthread_id"), 16)
+    elif sys.platform.startswith("sunos"):
+        match = re.search(r"Thread (?P<pthread_id>[0-9]+)", thread_info)
+        if match:
+            return int(match.group("pthread_id"), 10)
+        lwpid = gdb.selected_thread().ptid[1]
+        if lwpid != 0:
+            return lwpid
+    raise ValueError("Failed to find thread id in {}".format(thread_info))
+
+
 ###################################################################################################
 #
 # Pretty-Printers
@@ -336,35 +358,34 @@ class DumpGlobalServiceContext(gdb.Command):
 DumpGlobalServiceContext()
 
 
-class MongoDBAnalyze(gdb.Command):
-    """Analyze MongoDB process"""
+class MongoDBDumpLocks(gdb.Command):
+    """Dump locks in mongod process"""
 
     def __init__(self):
-        register_mongo_command(self, "mongodb-analyze", gdb.COMMAND_STATUS)
+        register_mongo_command(self, "mongodb-dump-locks", gdb.COMMAND_DATA)
 
     def invoke(self, arg, _from_tty):
         print("Running Hang Analyzer Supplement")
 
         main_binary_name = get_process_name()
-        if main_binary_name.endswith('mongod'):
-            self.analyze_mongod()
+        if main_binary_name == 'mongod':
+            self.dump_mongod_locks()
         else:
-            print("No process specific analysis done for: %s" % (main_binary_name))
+            print("Not invoking mongod lock dump for: %s" % (main_binary_name))
 
-    def analyze_mongod(self):
+    def dump_mongod_locks(self):
         """GDB in-process python supplement"""
 
         try:
-
             # Call into mongod, and dump the state of lock manager
             # Note that output will go to mongod's standard output, not the debugger output window
             gdb.execute("call ('mongo::(anonymous namespace)::globalLockManager').dump()",
                         from_tty=False, to_string=False)
         except gdb.error as gdberr:
-            print("Ignoring error '%s'" % str(gdberr))
+            print("Ignoring error '%s' in dump_mongod_locks" % str(gdberr))
 
 # Register command
-MongoDBAnalyze()
+MongoDBDumpLocks()
 
 
 class MongoDBUniqueStack(gdb.Command):
@@ -394,7 +415,7 @@ class MongoDBUniqueStack(gdb.Command):
         thread_info = {}  # thread dict to hold per thread data
         thread_info['frames'] = []  # the complete backtrace per thread from gdb
         thread_info['functions'] = []  # list of function names from frames
-        thread_info['pthread'] = hex(int(gdb.parse_and_eval("(uint64_t)pthread_self()")))
+        thread_info['pthread'] = hex(get_thread_id())
 
         frame = gdb.newest_frame()
         while frame:
@@ -480,7 +501,7 @@ class MongoDBHelp(gdb.Command):
     """Dump list of mongodb commands"""
 
     def __init__(self):
-        gdb.Command.__init__(self, "mongodb-help", gdb.COMMAND_DATA)
+        gdb.Command.__init__(self, "mongodb-help", gdb.COMMAND_SUPPORT)
 
     def invoke(self, arg, _from_tty):
         print("Command - Description")
diff --git a/buildscripts/gdb/mongo_lock.py b/buildscripts/gdb/mongo_lock.py
new file mode 100644
index 00000000000..5fbde9c3e8f
--- /dev/null
+++ b/buildscripts/gdb/mongo_lock.py
@@ -0,0 +1,311 @@
+from __future__ import print_function
+
+import gdb
+import gdb.printing
+import re
+import sys
+
+if sys.version_info[0] >= 3:
+    # GDB only permits converting a gdb.Value instance to its numerical address when using the
+    # long() constructor in Python 2 and not when using the int() constructor. We define the
+    # 'long' class as an alias for the 'int' class in Python 3 for compatibility.
+    long = int
+
+
+class Thread(object):
+    def __init__(self, thread_id, lwpid):
+        self.thread_id = thread_id
+        self.lwpid = lwpid
+
+    def __eq__(self, other):
+        if isinstance(other, Thread):
+            return self.thread_id == other.thread_id
+        return NotImplemented
+
+    def __ne__(self, other):
+        return not self == other
+
+    def __str__(self):
+        return "Thread 0x{:012x} (LWP {})".format(self.thread_id, self.lwpid)
+
+    def key(self):
+        return "Thread 0x{:012x}".format(self.thread_id)
+
+
+class Lock(object):
+    def __init__(self, addr, resource):
+        self.addr = addr
+        self.resource = resource
+
+    def __eq__(self, other):
+        if isinstance(other, Lock):
+            return self.addr == other.addr
+        return NotImplemented
+
+    def __ne__(self, other):
+        return not self == other
+
+    def __str__(self):
+        return "Lock 0x{:012x} ({})".format(self.addr, self.resource)
+
+    def key(self):
+        return "Lock 0x{:012x}".format(self.addr)
+
+
+class Graph(object):
+    # The Graph is a dict with the following structure:
+    #   {'node_key': {'node': {id: val}, 'next_nodes': [node_key_1, ...]}}
+    # Example graph:
+    #   {
+    #    'Lock 1': {'node': {1: 'MongoDB lock'}, 'next_nodes': ['Thread 1']},
+    #    'Lock 2': {'node': {1: 'MongoDB lock'}, 'next_nodes': ['Thread 2']},
+    #    'Thread 1': {'node': {1: 123}, 'next_nodes': ['Lock 2']},
+    #    'Thread 2': {'node': {2: 456}, 'next_nodes': ['Lock 1']}
+    #   }
+    def __init__(self):
+        self.nodes = {}
+
+    def add_node(self, node):
+        if not self.find_node(node):
+            self.nodes[node.key()] = {'node': node, 'next_nodes': []}
+
+    def find_node(self, node):
+        if node.key() in self.nodes:
+            return self.nodes[node.key()]
+        return None
+
+    def find_from_node(self, from_node):
+        for node_key in self.nodes:
+            node = self.nodes[node_key]
+            for next_node in node['next_nodes']:
+                if next_node == from_node['node'].key():
+                    return node
+        return None
+
+    def remove_nodes_without_edge(self):
+        # Rebuild graph by removing any nodes which do not have any incoming or outgoing any edges.
+        temp_nodes = {}
+        for node_key in self.nodes:
+            node = self.nodes[node_key]
+            if node['next_nodes'] or self.find_from_node(node) is not None:
+                temp_nodes[node_key] = self.nodes[node_key]
+        self.nodes = temp_nodes
+
+    def add_edge(self, from_node, to_node):
+        f = self.find_node(from_node)
+        if f is None:
+            self.add_node(from_node)
+            f = self.nodes[from_node.key()]
+
+        t = self.find_node(to_node)
+        if t is None:
+            self.add_node(to_node)
+            t = self.nodes[to_node.key()]
+
+        for n in f['next_nodes']:
+            if n == to_node.key():
+                return
+        self.nodes[from_node.key()]['next_nodes'].append(to_node.key())
+
+    def print(self):
+        for node_key in self.nodes:
+            print("Node", self.nodes[node_key]['node'])
+            for to in self.nodes[node_key]['next_nodes']:
+                print(" ->", to)
+
+    def to_graph(self):
+        sb = []
+        sb.append('digraph "mongod+lock-status" {')
+        for node_key in self.nodes:
+            for next_node_key in self.nodes[node_key]['next_nodes']:
+                sb.append('    "%s" -> "%s";' % (node_key, next_node_key))
+        for node_key in self.nodes:
+            sb.append('    "%s" [label="%s"]' % (node_key, self.nodes[node_key]['node']))
+        sb.append("}")
+        return "\n".join(sb)
+
+
+def find_lwpid(thread_dict, search_thread_id):
+    for (lwpid, thread_id) in thread_dict.items():
+        if thread_id == search_thread_id:
+            return lwpid
+    return None
+
+
+def find_func_block(block):
+    while block:
+        if block.function:
+            return block
+        block = block.superblock
+    return None
+
+
+def find_frame(function_name_pattern):
+    frame = gdb.newest_frame()
+    while frame:
+        block = None
+        try:
+            block = frame.block()
+        except RuntimeError as err:
+            if err.args[0] != "Cannot locate block for frame.":
+                raise
+
+        block = find_func_block(block)
+        if block and re.match(function_name_pattern, block.function.name):
+            return frame
+        frame = frame.older()
+    return None
+
+
+def find_mutex_holder(graph, thread_dict, show):
+    frame = find_frame(r'std::mutex::lock\(\)')
+    if frame is None:
+        return
+
+    frame.select()
+
+    # Waiting for mutex locking!
+    mutex_this, _ = gdb.lookup_symbol("this", frame.block())
+    mutex_value = mutex_this.value(frame)
+    # The mutex holder is a LWPID
+    mutex_holder = int(mutex_value["_M_mutex"]["__data"]["__owner"])
+    mutex_holder_id = thread_dict[mutex_holder]
+
+    (_, mutex_waiter_lwpid, _) = gdb.selected_thread().ptid
+    mutex_waiter_id = thread_dict[mutex_waiter_lwpid]
+    if show:
+        print("Mutex at {} held by thread 0x{:x} (LWP {}) "
+              " waited on by thread 0x{:x} (LWP {})".format(mutex_value,
+                                                            mutex_holder_id,
+                                                            mutex_holder,
+                                                            mutex_waiter_id,
+                                                            mutex_waiter_lwpid))
+    if graph:
+        graph.add_edge(Thread(mutex_waiter_id, mutex_waiter_lwpid),
+                       Lock(long(mutex_value), "Mutex"))
+        graph.add_edge(Lock(long(mutex_value), "Mutex"), Thread(mutex_holder_id, mutex_holder))
+
+
+def find_lock_manager_holders(graph, thread_dict, show):
+    frame = find_frame(r'mongo::LockerImpl\<.*\>::')
+    if not frame:
+        return
+
+    frame.select()
+
+    (_, lwpid, _) = gdb.selected_thread().ptid
+
+    locker_ptr_type = gdb.lookup_type("mongo::LockerImpl<false>").pointer()
+    lock_head = gdb.parse_and_eval(
+        "mongo::getGlobalLockManager()->_getBucket(resId)->findOrInsert(resId)")
+
+    grantedList = lock_head.dereference()["grantedList"]
+    lock_request_ptr = grantedList["_front"]
+    while lock_request_ptr:
+        lock_request = lock_request_ptr.dereference()
+        locker_ptr = lock_request["locker"]
+        locker_ptr = locker_ptr.cast(locker_ptr_type)
+        locker = locker_ptr.dereference()
+        lock_thread_id = int(locker["_threadId"]["_M_thread"])
+        lock_thread_lwpid = find_lwpid(thread_dict, lock_thread_id)
+        if show:
+            print("MongoDB Lock at {} ({}) held by thread id 0x{:x} (LWP {})".format(
+                lock_head, lock_request["mode"], lock_thread_id, lock_thread_lwpid) +
+                " waited on by thread 0x{:x} (LWP {})".format(thread_dict[lwpid], lwpid))
+        if graph:
+            graph.add_edge(Thread(thread_dict[lwpid], lwpid), Lock(long(lock_head), "MongoDB lock"))
+            graph.add_edge(Lock(long(lock_head), "MongoDB lock"),
+                           Thread(lock_thread_id, lock_thread_lwpid))
+        lock_request_ptr = lock_request["next"]
+
+
+def get_locks(graph, thread_dict, show=False):
+    for thread in gdb.selected_inferior().threads():
+        try:
+            if not thread.is_valid():
+                continue
+            thread.switch()
+            find_mutex_holder(graph, thread_dict, show)
+            find_lock_manager_holders(graph, thread_dict, show)
+        except gdb.error as err:
+            print("Ignoring GDB error '%s' in get_locks" % str(err))
+
+
+def get_threads_info(graph=None):
+    thread_dict = {}
+    for thread in gdb.selected_inferior().threads():
+        try:
+            if not thread.is_valid():
+                continue
+            thread.switch()
+            # PTID is a tuple: Process ID (PID), Lightweight Process ID (LWPID), Thread ID (TID)
+            (_, lwpid, _) = thread.ptid
+            thread_num = thread.num
+            thread_id = get_thread_id()
+            if not thread_id:
+                print("Unable to retrieve thread_info for thread %d" % thread_num)
+                continue
+            thread_dict[lwpid] = thread_id
+        except gdb.error as err:
+            print("Ignoring GDB error '%s' in get_threads_info" % str(err))
+
+    return thread_dict
+
+
+class MongoDBShowLocks(gdb.Command):
+    """Show MongoDB locks"""
+    def __init__(self):
+        register_mongo_command(self, "mongodb-show-locks", gdb.COMMAND_DATA)
+
+    def invoke(self, arg, _from_tty):
+        main_binary_name = get_process_name()
+        if main_binary_name.endswith('mongod') or main_binary_name.endswith('mongo'):
+            self.mongodb_show_locks()
+        else:
+            print("No show MongoDB locks done for: %s" % (main_binary_name))
+
+    def mongodb_show_locks(self):
+        """GDB in-process python supplement"""
+        try:
+            thread_dict = get_threads_info()
+            get_locks(graph=None, thread_dict=thread_dict, show=True)
+        except gdb.error as err:
+            print("Ignoring GDB error '%s' in mongodb_show_locks" % str(err))
+
+MongoDBShowLocks()
+
+
+class MongoDBWaitsForGraph(gdb.Command):
+    """Create MongoDB WaitsFor graph [graph_file]"""
+    def __init__(self):
+        register_mongo_command(self, "mongodb-waitsfor-graph", gdb.COMMAND_DATA)
+
+    def invoke(self, arg, _from_tty):
+        main_binary_name = get_process_name()
+        if main_binary_name.endswith('mongod') or main_binary_name.endswith('mongo'):
+            self.mongodb_waitsfor_graph(arg)
+        else:
+            print("No create MongoDB WaitsFor graph done for: %s" % (main_binary_name))
+
+    def mongodb_waitsfor_graph(self, file=None):
+        """GDB in-process python supplement"""
+
+        graph = Graph()
+        try:
+            thread_dict = get_threads_info(graph=graph)
+            get_locks(graph=graph, thread_dict=thread_dict, show=False)
+            graph.remove_nodes_without_edge()
+            if file:
+                print("Saving digraph to %s" % file)
+                with open(file, 'w') as f:
+                    f.write(graph.to_graph())
+            else:
+                print(graph.to_graph())
+
+        except gdb.error as err:
+            print("Ignoring GDB error '%s' in mongod_deadlock_graph" % str(err))
+
+
+MongoDBWaitsForGraph()
+
+print("MongoDB Lock analysis commands loaded")
diff --git a/buildscripts/hang_analyzer.py b/buildscripts/hang_analyzer.py
index f46e8702ccb..87afaeacc09 100755
--- a/buildscripts/hang_analyzer.py
+++ b/buildscripts/hang_analyzer.py
@@ -336,8 +336,12 @@ class GDBDumper(object):
         root_logger.info("dir %s" % script_dir)
         gdb_dir = os.path.join(script_dir, "gdb")
         printers_script = os.path.join(gdb_dir, "mongo.py")
+        mongo_lock_script = os.path.join(gdb_dir, "mongo_lock.py")
 
         bt_command = "mongodb-uniqstack bt"
+        mongodb_show_locks = "mongodb-show-locks"
+        mongodb_deadlock = "mongodb-waitsfor-graph debugger_deadlock_%s_%d.gv" % \
+            (process_name, pid)
         if sys.platform.startswith("sunos"):
             '''
             On Solaris, currently calling mongo-uniqstack leads to an error:
@@ -353,20 +357,29 @@ class GDBDumper(object):
             When the function is done executing, GDB will silently stop.
             '''
             bt_command = "thread apply all bt"
+            mongodb_show_locks = ""
+            mongodb_deadlock = ""
 
         cmds = [
-            "set pagination off",
+            "set interactive-mode off",
+            "set print thread-events off",  # Python calls to gdb.parse_and_eval may cause threads
+                                            # to start and finish. This suppresses those messages
+                                            # from appearing in the return output.
+            "file %s" % process_name,  # Solaris must load the process to read the symbols.
             "attach %d" % pid,
             "info sharedlibrary",
             "info threads",  # Dump a simple list of commands to get the thread name
             "set python print-stack full",
-            "source " + printers_script,
+            "source %s" % printers_script,
+            "source %s" % mongo_lock_script,
             bt_command,
             dump_command,
-            "mongodb-analyze",
+            "mongodb-dump-locks",
+            mongodb_show_locks,
+            mongodb_deadlock,
             "mongodb-javascript-stack",  # The mongodb-javascript-stack command executes code in
                                          # order to dump JavaScript backtraces and should therefore
-                                         # should be one of the last analysis commands.
+                                         # be one of the last analysis commands.
             "set confirm off",
             "quit",
             ]
diff --git a/etc/evergreen.yml b/etc/evergreen.yml
index 8e1303be758..59646a3be5e 100644
--- a/etc/evergreen.yml
+++ b/etc/evergreen.yml
@@ -1057,7 +1057,7 @@ post:
       target: "src/mongo-hanganalyzer.tgz"
       source_dir: "src"
       include:
-        - "./debugger*.log"
+        - "./debugger*.*"
   - command: s3.put
     params:
       aws_key: ${aws_key}