This is a source code of a tool which allows running distributed algorithms for counting lattice animals.
Provided with the tool, are several implementations, which are based on Redelemeier's algorithm, that enumerate various classes of lattice animals and aggregating the results in defferent ways.
This system has two major parts:
-
Client - Each client can run in either a stand-alone mode, in which it executes a specific algorithm with a set of parameters. Or it can run as part of a distributed counting effort where it receives the jobs from a server.
-
Sever - The server manages the counting effort. It allocates jobs and returns then to clients on requests, it also receives the results and stores them in a database.
It is possible to extend the system to count additional classes of lattice animals without a lot of additional work.
Additional, a slightly modified version of Redelemeier is introduced. This version enumerates some classes of lattice animals by pruning some search trees instead of enumerating all the possible lattice animals and filtering those which are not inside the class.
The client code is written in C++. It does not use external libraries and is compiled with g++.
There are two targets you can build it for: Linux (native) and windows (cross compiled using MinGW). The target is determined using the PLAT parameter to the make file.
For example, to build a release version for Windows, run the following command:
make CFG=release PLAT=Linux
This will produce the following files:
client/bin/run_Linux_release
client/bin/unit_tests_Linux_release
As was mentioned, to build for windows, MinGW cross compiler needs to be installed.
sudo apt-get install mingw-w64
You can use a different cross compiler version. In this case, change the following line in the Makefile:
CXX=i686-w64-mingw32-g++
$client/bin/run_Linux_release -h
2017-06-09 23:16:07,541 INFO [default] Starting program. Client version: 2.4
2017-06-09 23:16:07,541 INFO [default] Parsing command line parameters...
Version 2.4
Usages:
./../client/bin/run_Linux_release -s <hostname>
./../client/bin/run_Linux_release -s <hostname> -p <port_number>
./../client/bin/run_Linux_release <n>
./../client/bin/run_Linux_release <n> -f <output_file_name>
./../client/bin/run_Linux_release <n> --algo_id <algo_id>
./../client/bin/run_Linux_release <n> <split_n> <low_id> <high_id>
./../client/bin/run_Linux_release
Available algorithms are:
0 fixed 2d (default)
1 fixed 3d
2 fixed 4d
3 fixed 5d
4 fixed 6d
5 weakly convex fixed 2d
6 weakly convex fixed 3d
7 weakly convex fixed 4d
8 weakly convex fixed 5d
9 count total adjacent cells 2d
10 count total adjacent cells 3d
11 count histo adjacent cells 2d
12 count hosto adjacent cells 3d
13 strongly convex fixed 2d
14 strongly convex fixed 3d
15 strongly convex fixed 4d
16 strongly convex fixed 5d
17 weakly convex fixed 2d simple algorithm using filter
18 weakly convex fixed 3d simple algorithm using filter
19 weakly convex fixed 4d simple algorithm using filter
20 trivial redelemeier weak convex 3d (obsolete)
First you need to add a new entry in the ALGORITHMS array in main.cpp:
vector< pair< string, CountingAlgorithm > > ALGORITHMS = {
make_pair("fixed 2d", redelemeier_main<LatticeAnimal, SimpleCounter, 2>),
make_pair("fixed 3d", redelemeier_main<LatticeAnimal, SimpleCounter, 3>),
make_pair("fixed 4d", redelemeier_main<LatticeAnimal, SimpleCounter, 4>),
...
make_pair("my new shiny implementation", pointer_to_afunction),
};The first paramter in the pair is a human readable description of the implementation.
The second parameter is a pointer to a function that runs the implementation.
The signature of the function is define in counting_algorithm.h:
/* Prototype for a counting algorithm entry point
*
* @param n The maximum size of the lattice animal to count
* @param n0
* @param low_id
* @param high_id
* @results
* @param dump_file Pointer to the dump stream. The stream should be already open for writing. If stream is
* open, the algorithm should dump all the polycubes that it has counted.
*/
typedef void (*CountingAlgorithm) (coord_t n,
coord_t n0,
count_t low_id,
count_t high_id,
std::map< std::string, count_t > *results,
std::ofstream* dump_file);Now, you have two options. You can either provide your own implementation ( a function with the above signature ), or instantiate the generic function redelemeier_main found in the same file.
For using your own function, you can look at redelemeier_3d_line_convex from the file redelemeier.cpp.
The reason that there are several implementations is because this work was done iteratively. In each iteration, a newer implementation was introduced, but the older implementations were retained for cross referencing the results.
If you want to use the already existing, modular infrastructure (this is the preferred way for newer implementations) look at the generic function redelemeier_main:
template <class A, class C, dim_t D>
void redelemeier_main (coord_t n,
coord_t n0,
count_t low_id,
count_t high_id,
std::map< std::string, count_t > *results,
std::ofstream* dump_file)In brief, the generic parameters are:
- A - A class which represents the model of the lattice animal.
- C - A class which represents the entity which counts and aggregates the results.
- D - The dimension at which the counter needs to operate.
Suppose you want to count convex lattice animals.
A starting point would be to look at the LatticeAnimal class. In most scenarios, it is possible to derive from this class and override only some of it's methods.
In this particular example, a trivial implementation would override is_in_class with a method that tests if the lattice animal is convex or not.
Checking convexity is a heavy operation, and it will run for each lattice animal found by the Redelemeier algorithm (which is exponentialy large number). A more sophisticated approach would be to override add and remove methods as well. Each time a new lattice animal is constructed by adding or removing a cell, it's convexity can be calculated much fasted if the convexity of the lattice animal it is basen on. So the idea here is to keep track of convexity and perform a relatively lightweight operation each time a new lattice animal is constructed.
This example can be found in the wc_lattice_animal.h file (wc stands for weakly convex).
If all that you want is to count the total perimeter of all lattice animal of size n, then it is enough to provide a custom implementation of class A (change to the get_count() method). But if you want to count the number of lattice animals for each perimeter, you will also have to use non default class C implementation.
The default implementation is SimpleCounter from simple_counter.h, you can use it as an example. It is advisable to derive from it and override the functions. More advanced example is the HistogramCounter which can be used exactly for the propose that was described above.
Notice that the increment method is called for every counted object. Therefore it must be as efficient as possible.
Some legacy implementations do not have an option to scale the dimension dynamically, therefore the prototype CountingAlgorithm can not have a dimension parameter.
Since redelemeier_main must comply with that prototype, the dimension is passed through a generic parameter.
This is not an intrinsic limitation and the code can be rewritten in a way that would allow receiving the dimension as part of a job configuration, independently of the algorithm id.
TBD
The source code of the server is located in /counting_site. Do not be confused with /server which is an obsolete version which is powered by Google's app engine.
The server is powered by Django framework and it uses MySQL as a database.
The framework used for the server is Django 1.9.4 running with Python 2.7. It might work with newer versions of Django, but for older versions the chances are low.
To allow connections with MySQL server I installed the following:
pip install django-ipware
sudo apt-get install libmysqlclient-dev
sudo pip install MySQL-python
pip install mysqlclient
I did not install local instance of MySQL server. I opened a tet db using the same cloud provider that I used to host the production db and application. I use (www.pythonanywhere.com)[www.pythonanywhere.com], but any cloud provider that have MySQL and Django is suitable.
There is no subsitute for learning how Django works. I suggest trying the official tutorial.
Here is a quick list of commands that I found usefull. This list can be used as a cheat sheet.
-
ssh -L 3306:clown.mysql.pythonanywhere-services.com:3306 [email protected] -
python manage.py makemigrations counting_app -
python manage.py migrate -
python manage.py createsuperuser -
python manage.py collectstatic
Browse to the /admin page.
The /info page will display all Configs in the system:
It is possible to view information about progress and other statistics by going to the info page of an individual config:
TBD
The communication between the server and the client is based on HTTP. The servers runs an HTTP server and the client is the one responisble to initiates the communication.
Client's version can be changed by editing the line in main.cpp.
#define CLIENT_VERSION "2.4"
Client's version must match the version specified in the server's active Config.
To obtain a new job, the client sends a GET request to /allocate.
In the body of the response, will contain a line of the following structure:
<client_version> <secret_hash> <algo_id> <n> <n0> <low_id> <high_id>
- client_version - The version of the client that the server requires. If the client version is different from this value, it should not process the job.
- secret_hash - Client should use it to identify the job when reporting it back to the server.
- algo_id - The algorithm implementation to run. The mapping between the id and the actual implementation is decided by the client and is version dependent.
- n - The maximal size of the lattice animal we want to count.
- n0 - The size at which to split the counting.
- low_id, high_id - The range of the lattice animals not to prune at the n0 level.
If the server can not allocate any job at the time, it will send the following response:
0 0 0 0 0 0 0
After completing the computation, the client is required to send a GET request that looks like this:
/report?secret=<secret_hash>&res=1:<count_1>+2:<count_2>+...
Life is short and waiting for results is a useless waste of it, so here are some tips that can speed the counting a bit. Some of these are already in the code.
[x] Use good compiler flags.
[x] Precalculate anything you can (for example neighbor of each cell are calculated in LatticeAnimal constructor)
[ ] Determine the best n0 depending on the number of available clients.
[ ] Redelemeier algorithm can be implemented without recursion!
[x] Use iterative approach to determine whether a lattice animal is inside a class (not implemented for strongly convex yet)
[x] Make sure values are passed by reference and there is no implicit copy constructor invocation in the recursive call of the Redelemeier implementation.
Lattice animal classes can have the following characteristics:
- Fixed or free - whether or not two symmetrical lattice animals are considered distinct.
- Dimension - polycubes and higher dimensions.
- Common property - for example all the convex, column convex, directed, strongly convex in higher dimensions etc.
- Lattice - for example polyiamond (triangle lattice) or polyhex (hexagonal lattice).
- Neighbor connections - for example polyknights
Here is an article with some ideas: Some problems in counting of lattice animals, polyominoes, polygons and walks / Andrew Daniel Rechnitzer