Re: [graph-tool] Multiprocessing.Process bug

13 Nov 2016


      As a side note, the MWE I provide calls graph_tool.topology.shortest_path
without specifying the target., but the logs refer to the target, this is
counterintuitive, sorry about that. However, the behavior is as described
above when one does specify the target to graph_tool.topology.shortest_path.

François

On Sun, Nov 13, 2016 at 6:03 PM, François Kawala <francois.kawala@gmail.com>
wrote:
...
To be comprehensive, I add here the MWE source. Note that I fixed the
vertices so that the output is reproducible. However, one could select
randomly the vertices and would end with the same behavior.
Bests,
François.
import multiprocessing
import graph_tool as gt
import graph_tool.topology as gtt
import hashlib
import sys
class MyProcess(multiprocessing.Process):
    """
    A process that computes shortest paths and shortest distances in a
graph tool graph.
    """
    def __init__(self, graph, test):
        super(MyProcess, self).__init__()
        self.graph = graph
        self.test = test
def run(self):
        while True:
            # Operation is repeated so that the bug is cristal clear.
            source, target = self.test
            source = self.graph.vertex(source)
            target = self.graph.vertex(target)
# We start the work.
            print('{} does shortest_distance from {} to {}'.format(self,
source, target))
gtt.shortest_distance(self.graph,
                                  source=source,
                                  weights=self.graph.ep['weight'],
                                  max_dist=1400,
                                  pred_map=True)
# We end the work.
            print('{} done.'.format(self))
def hash_graphs(*args):
    """
    Provides an edge based graph digest that can be used to invalidate old
cache.
:type args: tuple of :class:`graph_tool.GraphView`
    :param args: the graphs to be hashed.
:rtype: str
    :return: a hash digest of the input graph.
    """
    graph_hash = hashlib.md5()
    for graph in args:
        graph_hash.update(gt.edge_endpoint_property(graph,
graph.vp['id'], "source").a.tobytes())
        graph_hash.update(gt.edge_endpoint_property(graph,
graph.vp['id'], "target").a.tobytes())
    return graph_hash.hexdigest()
if __name__ == '__main__':
# Unserialize the graph.
    graph = gt.load_graph('./mwe/graph.gt.gz')
# Bug switch.
    if sys.argv[-1] == 'DO_HASH':
        graph_hash = hash_graphs(graph)
# Repetable inputs.
    tests = [(452946, 391015),
             (266188, 207342),
             (514127, 290838),
             (439705, 87897),
             (223098, 440593),
             (279880, 368550),
             (108357, 199593),
             (273888, 275937)]
# Actual work.
    procs = [MyProcess(graph, tests[i]) for i in range(8)]
for proc in procs:
        proc.start()
for proc in procs:
        proc.join()
On Thu, Nov 10, 2016 at 7:24 PM, François Kawala <
francois.kawala@gmail.com> wrote:
...
Hello,
I observe a quite strange bug that involves python's multiprocessing
library. I try to use (read only) one graph instance with several
*Multithreading.Process*. The graph is unserialized in the parent
process. Each child receives a reference to the graph. Then each child does
simple repetitive calls to *graph_tool.topology.shortest_distance*.
Everything great each child process works as fast as it can. However when
the main process executes the *hash_graphs* function presented below,
each child process hangs infinitely. The *hash_graphs* is executed prior
to the children start.
def hash_graphs(*args):
    """
    Provides an edge based graph digest that can be used to invalidate
old cache.
:type args: tuple of :class:`graph_tool.GraphView`
    :param args: the graphs to be hashed.
:rtype: str
    :return: a hash digest of the input graph.
    """
    graph_hash = hashlib.md5()
    for graph in args:
        graph_hash.update(gt.edge_endpoint_property(graph,
graph.vp['id'], "source").a.tobytes())
        graph_hash.update(gt.edge_endpoint_property(graph,
graph.vp['id'], "target").a.tobytes())
    return graph_hash.hexdigest()
I package a MWE, it is available here : https://drive.google.com/file/
d/0B5GhhBKHOKOxVnpfYTBwNDZxODA/view?usp=sharing. To run it simply do :
tar xzf mwe.tar.gz
# run the buggy version
python3 -m mwe DO_HASH
# run as expected
python3 -m mwe
The buggy output looks like :
<MyProcess(MyProcess-1, started)> does shortest_distance from 452946 to
391015
<MyProcess(MyProcess-2, started)> does shortest_distance from 266188 to
207342
<MyProcess(MyProcess-3, started)> does shortest_distance from 514127 to
290838
<MyProcess(MyProcess-4, started)> does shortest_distance from 439705 to
87897
<MyProcess(MyProcess-5, started)> does shortest_distance from 223098 to
440593
<MyProcess(MyProcess-6, started)> does shortest_distance from 279880 to
368550
<MyProcess(MyProcess-7, started)> does shortest_distance from 108357 to
199593
<MyProcess(MyProcess-8, started)> does shortest_distance from 273888 to
275937
The expected output looks like :
<MyProcess(MyProcess-1, started)> does shortest_distance from 452946 to
391015
<MyProcess(MyProcess-2, started)> does shortest_distance from 266188 to
207342
<MyProcess(MyProcess-3, started)> does shortest_distance from 514127 to
290838
<MyProcess(MyProcess-5, started)> does shortest_distance from 223098 to
440593
<MyProcess(MyProcess-6, started)> does shortest_distance from 279880 to
368550
<MyProcess(MyProcess-1, started)> done.
<MyProcess(MyProcess-1, started)> does shortest_distance from 452946 to
391015
<MyProcess(MyProcess-2, started)> done.
<MyProcess(MyProcess-2, started)> does shortest_distance from 266188 to
207342
<MyProcess(MyProcess-4, started)> does shortest_distance from 439705 to
87897
<MyProcess(MyProcess-7, started)> does shortest_distance from 108357 to
199593
<MyProcess(MyProcess-3, started)> done.
<MyProcess(MyProcess-1, started)> done.
<MyProcess(MyProcess-3, started)> does shortest_distance from 514127 to
290838
<MyProcess(MyProcess-1, started)> does shortest_distance from 452946 to
391015
<MyProcess(MyProcess-8, started)> does shortest_distance from 273888 to
275937
<MyProcess(MyProcess-2, started)> done.
<MyProcess(MyProcess-2, started)> does shortest_distance from 266188 to
207342
<MyProcess(MyProcess-3, started)> done.
<MyProcess(MyProcess-3, started)> does shortest_distance from 514127 to
290838
<MyProcess(MyProcess-1, started)> done.
<MyProcess(MyProcess-1, started)> does shortest_distance from 452946 to
391015
<MyProcess(MyProcess-6, started)> done.
<MyProcess(MyProcess-6, started)> does shortest_distance from 279880 to
368550
<MyProcess(MyProcess-4, started)> done.
<MyProcess(MyProcess-4, started)> does shortest_distance from 439705 to
87897
<MyProcess(MyProcess-8, started)> done.
<MyProcess(MyProcess-8, started)> does shortest_distance from 273888 to
275937
<MyProcess(MyProcess-1, started)> done.
<MyProcess(MyProcess-1, started)> does shortest_distance from 452946 to
391015
<MyProcess(MyProcess-2, started)> done.
<MyProcess(MyProcess-2, started)> does shortest_distance from 266188 to
207342
<MyProcess(MyProcess-3, started)> done.
<MyProcess(MyProcess-3, started)> does shortest_distance from 514127 to
290838
<MyProcess(MyProcess-5, started)> done.
<MyProcess(MyProcess-5, started)> does shortest_distance from 223098 to
440593
<MyProcess(MyProcess-1, started)> done.
<MyProcess(MyProcess-1, started)> does shortest_distance from 452946 to
391015
<MyProcess(MyProcess-8, started)> done.
<MyProcess(MyProcess-8, started)> does shortest_distance from 273888 to
275937
<MyProcess(MyProcess-7, started)> done.
<MyProcess(MyProcess-7, started)> does shortest_distance from 108357 to
199593
<MyProcess(MyProcess-3, started)> done.
<MyProcess(MyProcess-3, started)> does shortest_distance from 514127 to
290838
...
How could I explain this behavior ?
Bests,
François.
--
François Kawala
-- 
François Kawala