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YupingLu / biclique

Maximal Biclique Enumeration in Bipartite Graphs
https://github.com/YupingLu/biclique
GNU General Public License v2.0
21 stars 10 forks source link

'memory not mapped' #7

Open onmikula opened 5 years ago

onmikula commented 5 years ago

Hi, I wanted to use bi.clique function on a bit larger data set (matrix of dimension 12481 x 24: mat_12481x24.txt), but got the following error:

caught segfault address 0x111ea6000, cause 'memory not mapped'

The function worked well with fewer columns (matrix of dimension 12481 x 10: mat_12481x10.txt ), but not with fewer rows (5200 x 24: mat_5200x24.txt ), although the number of entries was approximately the same in both cases.

Would you be so kind and check what is the problem? Thank you in advance!

Ondrej

dpuelz commented 5 years ago

Hey, I have a similar issue too, just noted on issue #6 .. hopefully we can get it figured out!

David

YupingLu commented 5 years ago

Hi all, I'll check the problem later this weekend.

dpuelz commented 5 years ago

Hi all, I'll check the problem later this weekend.

Hey Yuping, thanks for the help! Just curious, have you made any progress on a solution?

onmikula commented 5 years ago

Hello Yuping, do you thing the problem is going to be fixed any time soon? Ondrej

YupingLu commented 5 years ago

Hi Ondrej,

Sorry about the delay. I'm busy with multiple things recently. I'll look at it again at the end of this month. Hope the problem will be fixed soon.

Yuping

onmikula commented 5 years ago

Thank you for your reply. If the problem was fixed, I would appreciate it hugely. It would allow me to use the algorithm where it is possibly most useful (i.e. in graphs with large number of vertices of either type). Best wishes, Ondrej

onmikula commented 5 years ago

Hi Yuping, are there any news? I have found yet another nice application for the maximal biclique enumeration, so you can see your package is really needed. Best, Ondrej

dpuelz commented 5 years ago

Hey Yuping,

Agreed. Let us know if there’s a fix. Thanks!

— David

On Feb 15, 2019, at 12:07 PM, onmikula notifications@github.com<mailto:notifications@github.com> wrote:

Hi Yuping, are there any news? I have found yet another nice application for the maximal biclique enumeration, so you can see your package is really needed. Best, Ondrej

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/YupingLu/biclique/issues/7#issuecomment-464125400, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AJffJDTxk5-x-XnScn_1E9iuFmt9LyH8ks5vNulGgaJpZM4Zkyuk.

YupingLu commented 5 years ago

Hi Ondrej,

I finally got back to this. R doesn't allow C++ to ouput bicliques to screen. If the number of bicliques is big, R will not have enough memory to store all bicliques. That's why you get this error. I added a new parameter to only get the statistics without storing bicliques. You can get the top bicliques by setting lleast and rleast. If you still want to generate all the bicliques, we also have a C++ version available.

# Only get the statistics library(biclique) test=bi.clique('mat_5200x24.txt', getclique=0, filetype=1)

Number of left vertices : 5200 Number of right vertices : 24 Number of edges : 98874 Number of bicliques : 16731423 Maximum edge biclique : K2335,12 Maximum vertex biclique : K4898,1

# Get the maximum edge biclique test=bi.clique('mat_5200x24.txt', lleast = 2335, rleast = 12, filetype=1)

Yuping