I am trying to implement a modified parallel depth-first search algorithm in Erlang (let's call it *dfs_mod*).
All I want to get is all the 'dead-end paths' which are basically the paths that are returned when *dfs_mod* visits a vertex without neighbours or a vertex with neighbours which were already visited. I save each path to ets_table1 if my custom function fun1(Path) returns true and to ets_table2 if fun1(Path) returns false(I need to filter the resulting 'dead-end' paths with some customer filter).
I have implemented a sequential version of this algorithm and for some strange reason it performs better than the parallel one.
The idea behind the parallel implementation is simple:
visit a Vertex from [Vertex|Other_vertices] = Unvisited_neighbours,
add this Vertex to the current path;
send {self(), wait} to the 'collector' process;
run *dfs_mod* for Unvisited_neighbours of the current Vertex in a new process;
continue running *dfs_mod* with the rest of the provided vertices (Other_vertices);
when there are no more vertices to visit - send {self(), done} to the collector process and terminate;
So, basically each time I visit a vertex with unvisited neighbours I spawn a new depth-first search process and then continue with the other vertices.
Right after spawning a first *dfs_mod* process I start to collect all {Pid, wait} and {Pid, done} messages (wait message is to keep the collector waiting for all the done messages). In N milliseconds after waiting the collector function returns ok.
For some reason, this parallel implementation runs from 8 to 160 seconds while the sequential version runs just 4 seconds (the testing was done on a fully-connected digraph with 5 vertices on a machine with Intel i5 processor).
Here are my thoughts on such a poor performance:
I pass the digraph Graph to each new process which runs *dfs_mod*. Maybe doing digraph:out_neighbours(Graph) against one digraph from many processes causes this slowness?
I accumulate the current path in a list and pass it to each new spawned *dfs_mod* process, maybe passing so many lists is the problem?
I use an ETS table to save a path each time I visit a new vertex and add it to the path. The ETS properties are ([bag, public,{write_concurrency, true}), but maybe I am doing something wrong?
each time I visit a new vertex and add it to the path, I check a path with a custom function fun1() (it basically checks if the path has vertices labeled with letter "n" occurring before vertices with "m" and returns true/false depending on the result). Maybe this fun1() slows things down?
I have tried to run *dfs_mod* without collecting done and wait messages, but htop shows a lot of Erlang activity for quite a long time after *dfs_mod* returns ok in the shell, so I do not think that the active message passing slows things down.
How can I make my parallel dfs_mod run faster than its sequential counterpart?
Edit: when I run the parallel *dfs_mod*, pman shows no processes at all, although htop shows that all 4 CPU threads are busy.
There is no quick way to know without the code, but here's a quick list of why this might fail:
You might be confusing parallelism and concurrency. Erlang's model is shared-nothing and aims for concurrency first (running distinct units of code independently). Parallelism is only an optimization of this (running some of the units of code at the same time). Usually, parallelism will take form at a higher level, say you want to run your sorting function on 50 different structures -- you then decide to run 50 of the sequential sort functions.
You might have synchronization problems or sequential bottlenecks, effectively changing your parallel solution into a sequential one.
The overhead of copying data, context switching and whatnot dwarfs the gains you have in terms of parallelism. This former is especially true of large data sets that you break into sub data sets, then join back into a large one. The latter is especially true of highly sequential code, as seen is the process ring benchmarks.
If I wanted to optimize this, I would try to reduce message passing and data copying to a minimum.
If I were the one working on this, I would keep the sequential version. It does what it says it should do, and when part of a larger system, as soon as you have more processes than core, parallelism will come from the many calls to the sort function rather than branches of the sort function. In the long run, if part of a server or service, using the sequential version N times should have no more negative impact than a parallel one that ends up creating many, many more processes to do the same task, and risk overloading the system more.
Related
I am working on some fairly complex application that is making use of Dask framework, trying to increase the performance. To that end I am looking at the diagnostics dashboard. I have two use-cases. On first I have a 1GB parquet file split in 50 parts, and on second use case I have the first part of the above file, split over 5 parts, which is what used for the following charts:
The red node is called "memory:list" and I do not understand what it is.
When running the bigger input this seems to block the whole operation.
Finally this is what I see when I go inside those nodes:
I am not sure where I should start looking to understand what is generating this memory:list node, especially given how there is no stack button inside the task as it often happens. Any suggestions ?
Red nodes are in memory. So this computation has occurred, and the result is sitting in memory on some machine.
It looks like the type of the piece of data is a Python list object. Also, the name of the task is list-159..., so probably this is the result of calling the list Python function.
I have a function which returns a dataframe to me. I am trying to use this function in parallel by using dask.
I append the delayed objects of the dataframes into a list. However, the run-time of my code is the same with and without dask.delayed.
I use the reduce function from functools along with pd.merge to merge my dataframes.
Any suggestions on how to improve the run-time?
The visualized graph and code are as below.
from functools import reduce
d = []
for lot in lots:
lot_data = data[data["LOTID"]==lot]
trmat = delayed(LOT)(lot, lot_data).transition_matrix(lot)
d.append(trmat)
df = delayed(reduce)(lambda x, y: x.merge(y, how='outer', on=['from', "to"]), d)
Visualized graph of the operations
General rule: if your data comfortable fits into memory (including the base size times a small number for possible intermediates), then there is a good chance that Pandas is fast and efficient for your use case.
Specifically for your case, there is a good chance that the tasks you are trying to parallelise do not release python's internal lock, the GIL, in which case although you have independent threads, only one can run at a time. The solution would be to use the "distributed" scheduler instead, which can have any mix of multiple threads and processed; however using processes comes at a cost for moving data between client and processes, and you may find that the extra cost dominates any time saving. You would certainly want to ensure that you load the data within the workers rather than passing from the client.
Short story, you should do some experimentation, measure well, and read the data-frame and distributed scheduler documentation carefully.
I have some large files in a local binary format, which contains many 3D (or 4D) arrays as a series of 2D chunks. The order of the chunks in the files is random (could have chunk 17 of variable A, followed by chunk 6 of variable B, etc.). I don't have control over the file generation, I'm just using the results. Fortunately the files contain a table of contents, so I know where all the chunks are without having to read the entire file.
I have a simple interface to lazily load this data into dask, and re-construct the chunks as Array objects. This works fine - I can slice and dice the array, do calculations on them, and when I finally compute() the final result the chunks get loaded from file appropriately.
However, the order that the chunks are loaded is not optimal for these files. If I understand correctly, for tasks where there is no difference of cost (in terms of # of dependencies?), the local threaded scheduler will use the task keynames as a tie-breaker. This seems to cause the chunks to be loaded in their logical order within the Array. Unfortunately my files do not follow the logical order, so this results in many seeks through the data (e.g. seek halfway through the file to get chunk (0,0,0) of variable A, then go back near the beginning to get chunk (0,0,1) of variable A, etc.). What I would like to do is somehow control the order that these chunks get read, so they follow the order in the file.
I found a kludge that works for simple cases, by creating a callback function on the start_state. It scans through the tasks in the 'ready' state, looking for any references to these data chunks, then re-orders those tasks based on the order of the data on disk. Using this kludge, I was able to speed up my processing by a factor of 3. I'm guessing the OS is doing some kind of read-ahead when the file is being read sequentially, and the chunks are small enough that several get picked up in a single disk read. This kludge is sufficient for my current usage, however, it's ugly and brittle. It will probably work against dask's optimization algorithm for complex calculations. Is there a better way in dask to control which tasks win in a tie-breaker, in particular for loading chunks from disk? I.e., is there a way to tell dask, "all things being equal, here's the relative order I'd like you to process this group of chunks?"
Your assessment is correct. As of 2018-06-16 there is not currently any way to add in a final tie breaker. In the distributed scheduler (which works fine on a single machine) you can provide explicit priorities with the priority= keyword, but these take precedence over all other considerations.
I understand that dask work well in batch mode like this
def load(filename):
...
def clean(data):
...
def analyze(sequence_of_data):
...
def store(result):
with open(..., 'w') as f:
f.write(result)
dsk = {'load-1': (load, 'myfile.a.data'),
'load-2': (load, 'myfile.b.data'),
'load-3': (load, 'myfile.c.data'),
'clean-1': (clean, 'load-1'),
'clean-2': (clean, 'load-2'),
'clean-3': (clean, 'load-3'),
'analyze': (analyze, ['clean-%d' % i for i in [1, 2, 3]]),
'store': (store, 'analyze')}
from dask.multiprocessing import get
get(dsk, 'store') # executes in parallel
Can we use dask to process streaming channel , where the number of chunks is unknown or even endless?
Can it perform the computation in an incremental way. for example can the 'analyze' step above could process ongoing chunks?
must we call the "get" operation only after all the data chunks are known , could we add new chunks after the "get" was called
Edit: see newer answer below
No
The current task scheduler within dask expects a single computational graph. It does not support dynamically adding to or removing from this graph. The scheduler is designed to evaluate large graphs in a small amount of memory; knowing the entire graph ahead of time is critical for this.
However, this doesn't stop one from creating other schedulers with different properties. One simple solution here is just to use a module like conncurrent.futures on a single machine or distributed on multiple machines.
Actually Yes
The distributed scheduler now operates fully asynchronously and you can submit tasks, wait on a few of them, submit more, cancel tasks, add/remove workers etc. all during computation. There are several ways to do this, but the simplest is probably the new concurrent.futures interface described briefly here:
http://dask.pydata.org/en/latest/futures.html
Let's say we implement Pregel with Erlang. Why do we actually need supersteps? Isn't it better to just send messages from one supervisor to processes that represent nodes? They could just apply the calculation function to themselves, send messages to each other and then send a 'done' message to the supervisor.
What is the whole purpose of supersteps in concurrent Erlang implementation of Pregel?
The SuperStep concept as espoused by the Pregel model could be viewed as sort of a Barrier for parallel-y executing entities. At the end of each superstep, each worker, flushes it state to the persistent store.
The algorithm is check-pointed at the end of each SuperStep so that in case of failure, when a new node has to take over the function of a failed peer, it has a point to start from. Pregel guarantees that since the data of the node has been flushed to disk before the SuperStep started, it can reliably start from exactly that point.
It also in a way signifies "progress" of the algorithm. A pregel algorithm/job can be provided with a "max number of supersteps" after which the algorithm should terminate.
What you specified in your question (about superisors sending worker a calculation function and waiting for a "done") can definitely be implemented (although I dont think the current supervisor packaged with OTP can do stuff like that out of the box) but I guess the concept of a SuperStep is just a requirement of a Pregel model. If on the other hand, you were implementing something like a parallel mapper (like what Joe implements in his book) you wont need supersteps/