Opened 5 years ago

Closed 5 years ago

#16083 closed enhancement (fixed)

MCQD to compute max cliques

Reported by: ncohen Owned by:
Priority: major Milestone: sage-6.3
Component: graph theory Keywords:
Cc: azi Merged in:
Authors: Nathann Cohen Reviewers: Jernej Azarija
Report Upstream: N/A Work issues:
Branch: c0158ed (Commits) Commit: c0158edff1516bbca93ff330acbec1d1a5238049
Dependencies: Stopgaps:

Description (last modified by ncohen)

Jernej reported that this solver was faster than cliquer on some instances.

So we need it :-P

Nathann

Install the new (optional) spkg : mcqd-1.0.tar.bz2

Attachments (1)

mcqd-1.0.tar.bz2 (246.1 KB) - added by ncohen 5 years ago.

Download all attachments as: .zip

Change History (30)

Changed 5 years ago by ncohen

comment:1 Changed 5 years ago by git

  • Commit changed from 66d0e3b709bdf9d06014b487e54ee1e9c0d3e595 to c2dc8ce055b4005bc68f59d90e24f835f9ff9b1e

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

c2dc8cetrac #16083: mcqd solver for max cliques

comment:2 Changed 5 years ago by git

  • Commit changed from c2dc8ce055b4005bc68f59d90e24f835f9ff9b1e to ad90443749baad49c5b0e0919b7fed13cf2324cc

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

ad90443trac #16083: mcqd solver for max cliques

comment:3 Changed 5 years ago by azi

Hello,

how do I install the mcqd package? The attached tar.bz2 for one appears to be corrupt..

azi@bodysnatcher:/tmp$ mv mcqd-1.0.tar.bz2.1 mcqd-1.0.tar.bz2
azi@bodysnatcher:/tmp$ tar -xf mcqd-1.0.tar.bz2 
bzip2: (stdin) is not a bzip2 file.

comment:4 Changed 5 years ago by ncohen

The file looks good to me ...

/tmp$ tar -xf mcqd-1.0.tar.bz2 
/tmp$ 

Nathann

comment:5 Changed 5 years ago by ncohen

  • Status changed from new to needs_review

God. I had forgotten to set it to needs_review.. That's dangerous O_O;;;;

comment:6 Changed 5 years ago by vbraun_spam

  • Milestone changed from sage-6.2 to sage-6.3

comment:7 follow-up: Changed 5 years ago by azi

Nathann,

as promised here are my comments !

  1. I was not able to test the code since I cannot figure out how to install the module. What am I supposed to do with the tar.bz2?
  1. Following are some comments about the code/politics:

2.1. The program mcqd consists of a single .h file. Since the author of the code agrees that we can use the program in Sage, is there any reason not to simply put this .h file along with the .pyx module? This way we can also tweak the file a bit (I'd like to remove debug stuff and unnecessary verbosity counters that are present in the code)

2.2 (mcqd.pyx) The variable c0 is a pointer to c. Hence I am wondering, why do you need to allocate memory ? On line 39 you assign the ptr c to it and lose the reference to the allocated space.

2.3 (mcqd.pyx) Lines 30-37. Can they be made shorter by using the fact (is it true ????) that sage_free(NULL) is legal?

2.4 (mcqd.pyx) Can we get rid of the memset by using sage_calloc on c?

2.5 (mcqd.pyx) At the very end C should be deleted.

comment:8 in reply to: ↑ 7 ; follow-up: Changed 5 years ago by ncohen

Yoooooooooooo !

  1. I was not able to test the code since I cannot figure out how to install the module. What am I supposed to do with the tar.bz2?

Save it in SAGE_ROOT/upstream/ and run "sage -f mcqd" (on the right branch)

2.1. The program mcqd consists of a single .h file. Since the author of the code agrees that we can use the program in Sage, is there any reason not to simply put this .h file along with the .pyx module?

Yes : the code has not been reviewed. And it "may" be updated, which is why we try not to change third-party code.

2.2 (mcqd.pyx) The variable c0 is a pointer to c.

?... No, it is not O_o

c0 is a pointer to n*n booleans.

2.3 (mcqd.pyx) Lines 30-37. Can they be made shorter by using the fact (is it true ????) that sage_free(NULL) is legal?

Right. Done

2.4 (mcqd.pyx) Can we get rid of the memset by using sage_calloc on c?

Done.

2.5 (mcqd.pyx) At the very end C should be deleted.

Why ? This is done automatically, isn't it ? You don't have to dealloc objects when nothing else points toward them.

Nathann

comment:9 Changed 5 years ago by git

  • Commit changed from ad90443749baad49c5b0e0919b7fed13cf2324cc to 303de8966e0c76f31f33b135370cee22edb12b9b

Branch pushed to git repo; I updated commit sha1. New commits:

55e2922trac #16083: Merged with 6.3.beta2
303de89trac #16083: Reviewer's comments

comment:10 in reply to: ↑ 8 Changed 5 years ago by azi

Replying to ncohen:

Yoooooooooooo !

  1. I was not able to test the code since I cannot figure out how to install the module. What am I supposed to do with the tar.bz2?

Save it in SAGE_ROOT/upstream/ and run "sage -f mcqd" (on the right branch)

Thanks I'll check that out and report back!

2.1. The program mcqd consists of a single .h file. Since the author of the code agrees that we can use the program in Sage, is there any reason not to simply put this .h file along with the .pyx module?

Yes : the code has not been reviewed. And it "may" be updated, which is why we try not to change third-party code.

2.2 (mcqd.pyx) The variable c0 is a pointer to c.

?... No, it is not O_o

Nevermind about that I was talking nonsense.

c0 is a pointer to n*n booleans.

2.3 (mcqd.pyx) Lines 30-37. Can they be made shorter by using the fact (is it true ????) that sage_free(NULL) is legal?

Right. Done

2.4 (mcqd.pyx) Can we get rid of the memset by using sage_calloc on c?

Done.

2.5 (mcqd.pyx) At the very end C should be deleted.

Why ? This is done automatically, isn't it ? You don't have to dealloc objects when nothing else points toward them.

No I am not sure this is done. In C++ there is no garbage collector so whatever you allocate with new you have to dealocate with delete()

Nathann

comment:11 Changed 5 years ago by git

  • Commit changed from 303de8966e0c76f31f33b135370cee22edb12b9b to a555604888f8f5fd3ab4846a379c8719ae7a7de6

Branch pushed to git repo; I updated commit sha1. New commits:

a555604trac #16083: "del C"

comment:12 follow-up: Changed 5 years ago by azi

BTW, are you sure del is good? Shouldn't you use C++'s delete?

comment:13 in reply to: ↑ 12 Changed 5 years ago by ncohen

BTW, are you sure del is good? Shouldn't you use C++'s delete?

http://docs.cython.org/src/userguide/wrapping_CPlusPlus.html C++ objects can now be dynamically allocated with new and del keywords.

Nathann

comment:14 Changed 5 years ago by azi

I am still not able to run the code :-(

azi@bodysnatcher:~/sage$ sage -f mcqd
Found local metadata for mcqd-1.0
Found local sources at /home/azi/sage/upstream/mcqd-1.0.tar.bz2
.......blahblah............
Finished installing mcqd-1.0.spkg

and then

azi@bodysnatcher:~/sage$ sage
.........blahblah............
Done updating paths.
sage: G = graphs.PetersenGraph()
sage: G.clique_number(algorithm='mcqd')
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-2-99d3195b7504> in <module>()
----> 1 G.clique_number(algorithm='mcqd')


ImportError: Please install the mcqd package

The new code looks good except for a minor question:

Why you use double variables for the adjacency matrix? Is there any benefit from allocating a n*n matrix and using a nested for loop to fill it?

comment:15 follow-up: Changed 5 years ago by azi

Okay, so I was missing the step of running sage -b. Thanks Nathann for the private email.

As for this ticket I'd just like to hear the answer to

Why you use double variables for the adjacency matrix? Is there any benefit from allocating a n*n matrix and using a nested for loop to fill it?

(as posted above) and if sage -t works for you then we are good to go!!

comment:16 in reply to: ↑ 15 Changed 5 years ago by ncohen

Yo !

As for this ticket I'd just like to hear the answer to

Why you use double variables for the adjacency matrix? Is there any benefit from allocating a n*n matrix and using a nested for loop to fill it?

What do you mean by "double variables" ? Do you mean that I allocate both "c" (linear size) and "c0" (quadratic size) ?

If so, that is because what MCQD expects is the vector c, which points toward the entries of c0.

Nathann

comment:17 follow-ups: Changed 5 years ago by azi

Yes, I am quite confused by that. Following is how I used to (successfully) call mcqd from a *.pyx file, but I don't seem to be using the same convention as you say. I hope I am not bothering you with this I'd just like to understand what I was doing here and what you're doing in your code :)))

def clique_number_fast(G):
    n = G.order()

    cpdef bool **adj
    cpdef int clorder
    cpdef int *clverts

    adj= <bool **> malloc(sizeof(bool *)*n)
    for i in xrange(n):
        adj[i] = <bool *> calloc(n, sizeof(bool))    
    
    # Warning we are assuming the vertices are labeled from 0...n-1
    for i,j in G.edges(labels=False):
        adj[i][j] = True
        adj[j][i] = True

    cpdef Maxclique *m = new_Maxclique(adj,n,0.025)
    m.mcqdyn(clverts, clorder); 
    # Yes, I am supposed to free the entire array but the above is just an indication of what is causing the error
    for i in xrange(n): free(adj[i])
    
    free(adj)

    return clorder

comment:18 in reply to: ↑ 17 Changed 5 years ago by ncohen

Hello !

Yes, I am quite confused by that. Following is how I used to (successfully) call mcqd from a *.pyx file, but I don't seem to be using the same convention as you say. I hope I am not bothering you with this I'd just like to understand what I was doing here and what you're doing in your code :)))

I do exactly what you did. The only difference is that I only do ONE memory allocation while you allocate n vectors (all your adj[i]). Now, you should write a check that all vectors have been correctly allocated, and if not deallocate them all, and this is what I wanted to avoid by allocating just one big vector of size n*n and making adj point toward pieces of it.

Nathann

comment:19 in reply to: ↑ 17 Changed 5 years ago by ncohen

I hope I am not bothering you with this I'd just like to understand what I was doing here and what you're doing in your code :)))

This is precisely the reviewer's job :-P

Nathann

comment:20 Changed 5 years ago by azi

Oh I see it now. OK.

Then as far as I am concerned the code is good to go once you confirm that sage -t passes through for you!

comment:21 Changed 5 years ago by ncohen

Well, it does in the graph/ folder, and clearly no other code calls that.

Nathann

comment:22 Changed 5 years ago by azi

  • Reviewers set to Jernej Azarija
  • Status changed from needs_review to positive_review

comment:23 Changed 5 years ago by ncohen

  • Description modified (diff)

Thaaaaaaaaaaaaanks! :-)

comment:24 follow-up: Changed 5 years ago by azi

Actually, thank you for doing all this patches and stuff !!!!!!

comment:25 in reply to: ↑ 24 Changed 5 years ago by ncohen

Actually, thank you for doing all this patches and stuff !!!!!!

:-D

Nathann

comment:26 Changed 5 years ago by vbraun

  • Status changed from positive_review to needs_work
sage -t --long src/sage/graphs/mcqd.pyx
**********************************************************************
File "src/sage/graphs/mcqd.pyx", line 15, in sage.graphs.mcqd.mcqd
Failed example:
    from sage.graphs.mcqd import mcqd
Exception raised:
    Traceback (most recent call last):
      File "/home/release/Sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 480, in _run
        self.execute(example, compiled, test.globs)
      File "/home/release/Sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 839, in execute
        exec compiled in globs
      File "<doctest sage.graphs.mcqd.mcqd[0]>", line 1, in <module>
        from sage.graphs.mcqd import mcqd
    ImportError: No module named mcqd
**********************************************************************

comment:27 Changed 5 years ago by git

  • Commit changed from a555604888f8f5fd3ab4846a379c8719ae7a7de6 to c0158edff1516bbca93ff330acbec1d1a5238049

Branch pushed to git repo; I updated commit sha1. New commits:

c0158edtrac #16083: Broken doctest

comment:28 Changed 5 years ago by ncohen

  • Status changed from needs_work to positive_review

Sorry.. All the lines except the import statement were tagged with "optional" :-/

Nathann

comment:29 Changed 5 years ago by vbraun

  • Branch changed from public/mcqd to c0158edff1516bbca93ff330acbec1d1a5238049
  • Resolution set to fixed
  • Status changed from positive_review to closed
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