Re: [Numpy-discussion] MKL and OpenBLAS

2014-02-02 Thread Sturla Molden
Sturla Molden wrote: > > Yes, it seems to be a GNU problem: > > http://bisqwit.iki.fi/story/howto/openmp/#OpenmpAndFork > > This Howto also claims Intel compilers is not affected. It seems another patch has been proposed to the libgomp team today: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=

Re: [Numpy-discussion] MKL and OpenBLAS

2014-02-02 Thread Sturla Molden
Carl Kleffner wrote: > If you work in an academia world it can be relevant once third parties > are involved in a bigger project. A situation may be reached, where you > just have to prove the license situation of all of your software components. If you involve third parties outside academia, y

Re: [Numpy-discussion] Fast decrementation of indices

2014-02-02 Thread Jaime Fernández del Río
Cannot test right now, but np.unique(b, return_inverse=True)[1].reshape(2, -1) should do what you are after, I think. On Feb 2, 2014 11:58 AM, "Mads Ipsen" wrote: > Hi, > > I have run into a potential 'for loop' bottleneck. Let me outline: > > The following array describes bonds (connections) in

Re: [Numpy-discussion] Fast decrementation of indices

2014-02-02 Thread Alexander Belopolsky
On Sun, Feb 2, 2014 at 2:58 PM, Mads Ipsen wrote: > Since atoms [1,2,3,7,8] have been > deleted, the remaining atoms with indices larger than the deleted atoms > must be decremented. > Let >>> x array([[ 0, 1, 2, 3], [ 4, 5, 6, 7], [ 8, 9, 10, 11]]) and >>> i = [1, 0, 2]

[Numpy-discussion] Fast decrementation of indices

2014-02-02 Thread Mads Ipsen
Hi, I have run into a potential 'for loop' bottleneck. Let me outline: The following array describes bonds (connections) in a benzene molecule b = [[0, 0, 0, 1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 6, 7, 8, 9, 10, 11], [5, 6, 1, 0, 2, 7, 3, 8, 1, 4, 9, 2, 10, 5, 3, 4, 11, 0,

Re: [Numpy-discussion] Indexing changes in 1.9

2014-02-02 Thread Travis Oliphant
This sounds like a great and welcome work and improvements. Does it make sense to also do something about the behavior of advanced indexing when slices are interleaved between lists and integers. I know that jay borque has some preliminary work to fix this. There are a some straightforward fixe

Re: [Numpy-discussion] MKL and OpenBLAS

2014-02-02 Thread Carl Kleffner
If you work in an academia world it can be relevant once third parties are involved in a bigger project. A situation may be reached, where you just have to prove the license situation of all of your software components. Numpy and scipy is 'selled' as BSD or MIT based foundation for scientific softw

Re: [Numpy-discussion] Indexing changes in 1.9

2014-02-02 Thread Charles R Harris
On Sun, Feb 2, 2014 at 10:06 AM, Charles R Harris wrote: > Sebastian has done a lot of work to refactor/rationalize numpy indexing. > The changes are extensive enough that it would be good to have more public > review, so here is the release note. > > The NumPy indexing has seen a complete rewrit

[Numpy-discussion] Indexing changes in 1.9

2014-02-02 Thread Charles R Harris
Sebastian has done a lot of work to refactor/rationalize numpy indexing. The changes are extensive enough that it would be good to have more public review, so here is the release note. The NumPy indexing has seen a complete rewrite in this version. This makes > most advanced integer indexing opera

Re: [Numpy-discussion] MKL and OpenBLAS

2014-02-02 Thread Sturla Molden
Carl Kleffner wrote: > In the case of numpy-MKL the MKL binaries are statically linked to the > pyd-files. Given the usefulness, performance and robustness of the > MKL-based binaries a definite answer to this question would be desirable. > Say: "Can I use and re-redistribute a product with a pre

Re: [Numpy-discussion] MKL and OpenBLAS

2014-02-02 Thread Carl Kleffner
Concerning numpy-MKL licence I refer to this question on the Intel Forum: http://software.intel.com/en-us/forums/topic/328344 "Question on Redistribution related to numpy/scipy" In the case of numpy-MKL the MKL binaries are statically linked to the pyd-files. Given the usefulness, performance an