[Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

Hi all, I recently developed a Cython-based, OpenMP-accelerated quartic (and cubic, quadratic) polynomial solver to address a personal research need for quickly solving a very large number of independent low-degree polynomial equations for both real and complex coefficients. For example, on

[Numpy-discussion] Cython-based OpenMP-accelerated quartic, polynomial solver

The algorithms for cubics and quadratics come from Numerical Recipes (3rd ed.), and the quartic problem is internally reduced to a cubic and two quadratics, using well-known standard tricks.Nice, wll documented code. Just to be sure you are on safe ground, you took the *algorithms* but

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic, polynomial solver

Hi, On 29.09.2015 19:16, Matti Picus wrote: The algorithms for cubics and quadratics come from Numerical Recipes (3rd ed.), and the quartic problem is internally reduced to a cubic and two quadratics, using well-known standard tricks. Nice, wll documented code. Just to be sure you are on safe g

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

This sounds pretty cool -- and I've had a use case. So it would be nice to get into Numpy. But: I doubt we'd want OpenMP dependence in Numpy itself. But maybe a pure Cython non-MP version? Are we putting Cuthon in Numpy now? I lost track. -CHB Sent from my iPhone > On Sep 29, 2015, at 7:35 AM

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On Tue, Sep 29, 2015 at 6:48 PM, Chris Barker - NOAA Federal < chris.bar...@noaa.gov> wrote: > This sounds pretty cool -- and I've had a use case. So it would be > nice to get into Numpy. > > But: I doubt we'd want OpenMP dependence in Numpy itself. > > But maybe a pure Cython non-MP version? > >

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

Hi, On 30.09.2015 03:48, Chris Barker - NOAA Federal wrote: This sounds pretty cool -- and I've had a use case. So it would be nice to get into Numpy. But: I doubt we'd want OpenMP dependence in Numpy itself. It is indeed a good point not to add new dependencies for a small feature such as t

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

Hi, On 30.09.2015 04:37, Charles R Harris wrote: On Tue, Sep 29, 2015 at 6:48 PM, Chris Barker - NOAA Federal mailto:chris.bar...@noaa.gov>> wrote: This sounds pretty cool -- and I've had a use case. So it would be nice to get into Numpy. But: I doubt we'd want OpenMP dependenc

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 30 September 2015 at 10:20, Juha Jeronen wrote: > > Are we putting Cuthon in Numpy now? I lost track. >> > > I thought so? But then again, I'm just a user :) As of this moment, there are three Cython modules in Numpy, so yes. Releases ship the C generated modules, so it is not a dependency.

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

Yes, obviously, the code has NR parts, so it can't be licensed as BSD as it is... Matthieu 2015-09-30 2:37 GMT+01:00 Charles R Harris : > > > On Tue, Sep 29, 2015 at 6:48 PM, Chris Barker - NOAA Federal > wrote: >> >> This sounds pretty cool -- and I've had a use case. So it would be >> nice to

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

Hi, What qualifies as an NR part? (See my previous message concerning the references; NR is not the only source which has these algorithms. Again, the code itself is original to this solver, I haven't even looked at the code provided with NR.) -J --

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

Juha Jeronen jyu.fi> writes: > I recently developed a Cython-based, OpenMP-accelerated quartic (and > cubic, quadratic) polynomial solver to address a personal research need > for quickly solving a very large number of independent low-degree > polynomial equations for both real and complex coef

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On Wed, Sep 30, 2015 at 3:20 AM, Juha Jeronen wrote: > Hi, > > On 30.09.2015 03:48, Chris Barker - NOAA Federal wrote: > >> This sounds pretty cool -- and I've had a use case. So it would be >> nice to get into Numpy. >> >> But: I doubt we'd want OpenMP dependence in Numpy itself. >> > > It is in

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On Wed, Sep 30, 2015 at 6:57 AM, Nathan Goldbaum wrote: > Note however that with the current version of the code, not having OpenMP >> will severely limit the performance, especially on quad-core machines, >> since an important factor in the speed comes from the parallel processing >> of the inde

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On Sep 30, 2015 2:28 AM, "Daπid" wrote: [...] > Is there a nice way to ship both versions? After all, most implementations of BLAS and friends do spawn OpenMP threads, so I don't think it would be outrageous to take advantage of it in more places; provided there is a nice way to fallback to a seri

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On Wed, Sep 30, 2015 at 10:35 AM, Matthieu Brucher < matthieu.bruc...@gmail.com> wrote: > > Yes, obviously, the code has NR parts, so it can't be licensed as BSD > as it is... It's not obvious to me, especially after Juha's further clarifications. -- Robert Kern __

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

After, I agree with you. 2015-09-30 18:14 GMT+01:00 Robert Kern : > On Wed, Sep 30, 2015 at 10:35 AM, Matthieu Brucher > wrote: >> >> Yes, obviously, the code has NR parts, so it can't be licensed as BSD >> as it is... > > It's not obvious to me, especially after Juha's further clarifications. >

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 30/09/15 11:27, Daπid wrote: Is there a nice way to ship both versions? After all, most implementations of BLAS and friends do spawn OpenMP threads, so I don't think it would be outrageous to take advantage of it in more places; Some do, others don't. ACML uses OpenMP. GotoBLAS uses OpenM

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 30/09/15 18:20, Nathaniel Smith wrote: This is incorrect -- the only common implementation of BLAS that uses *OpenMP* threads is OpenBLAS, MKL and ACML also use OpenMP. Sturla ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org https

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 30/09/15 18:20, Chris Barker wrote: We'd need a run-time check. We need to amend the compiler classes in numpy.distutils with OpenMP relevant information (compiler flags and libraries). The OpenMP support libraries must be statically linked. Sturla

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 30/09/15 15:57, Nathan Goldbaum wrote: Basically, just try to compile a simple OpenMP test program in a subprocess. If that succeeds, then great, we can add -fopenmp as a compilation flag. If not, don't do that. Unless you use GCC on Linux, it will be more complex than that. I.e. do you ne

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 30/09/15 18:20, Chris Barker wrote: python threads with nogil? This is often the easiest, particularly if we construct a fork-safe threadpool. Sturla ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org https://mail.scipy.org/mailman

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 30.09.2015 19:20, Chris Barker wrote: On Wed, Sep 30, 2015 at 6:57 AM, Nathan Goldbaum mailto:nathan12...@gmail.com>> wrote: Note however that with the current version of the code, not having OpenMP will severely limit the performance, especially on quad-core machines

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 30.09.2015 13:21, Pauli Virtanen wrote: Juha Jeronen jyu.fi> writes: I recently developed a Cython-based, OpenMP-accelerated quartic (and cubic, quadratic) polynomial solver to address a personal research need for quickly solving a very large number of independent low-degree polynomial equat

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 30.09.2015 19:20, Nathaniel Smith wrote: The challenges to providing transparent multithreading in numpy generally are: - gcc + OpenMP on linux still breaks multiprocessing. There's a patch to fix this but they still haven't applied it; alternatively there's a workaround you can use in mul

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 01.10.2015 01:04, Sturla Molden wrote: There are two principal problems with using OpenMP in NumPy: One is that the GNU OpenMP threadpool is not fork-safe, and can break multiprocessing on some platforms (e.g. when using Python 2.7 on Linux). Anything that uses GCD has this nasty effect on

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 01/10/15 02:20, Juha Jeronen wrote: Then again, the matter is further complicated by considering codes that run on a single machine, versus codes that run on a cluster.Threads being local to each node in a cluster, You can run MPI programs on a single machine and you get OpenMP implementat

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 01/10/15 02:32, Juha Jeronen wrote: Sounds good. Out of curiosity, are there any standard fork-safe threadpools, or would this imply rolling our own? You have to roll your own. Basically use pthreads_atfork to register a callback that shuts down the threadpool before a fork and another c

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 30 September 2015 at 18:20, Nathaniel Smith wrote: > On Sep 30, 2015 2:28 AM, "Daπid" wrote: > [...] > > Is there a nice way to ship both versions? After all, most > implementations of BLAS and friends do spawn OpenMP threads, so I don't > think it would be outrageous to take advantage of it

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On Wed, Sep 30, 2015 at 11:54 PM, Daπid wrote: > > > On 30 September 2015 at 18:20, Nathaniel Smith wrote: >> >> On Sep 30, 2015 2:28 AM, "Daπid" wrote: >> [...] >> > Is there a nice way to ship both versions? After all, most >> > implementations of BLAS and friends do spawn OpenMP threads, so I

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 01.10.2015 03:32, Sturla Molden wrote: On 01/10/15 02:20, Juha Jeronen wrote: Then again, the matter is further complicated by considering codes that run on a single machine, versus codes that run on a cluster.Threads being local to each node in a cluster, You can run MPI programs on a sin

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 01.10.2015 03:52, Sturla Molden wrote: On 01/10/15 02:32, Juha Jeronen wrote: Sounds good. Out of curiosity, are there any standard fork-safe threadpools, or would this imply rolling our own? You have to roll your own. Basically use pthreads_atfork to register a callback that shuts down

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 2 October 2015 at 11:58, Juha Jeronen wrote: > >> > First version done and uploaded: > > > https://yousource.it.jyu.fi/jjrandom2/miniprojects/trees/master/misc/polysolve_for_numpy > Small comment: now you are checking if the input is a scalar or a ndarray, but it should also accept any array-

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 02.10.2015 13:07, Daπid wrote: On 2 October 2015 at 11:58, Juha Jeronen > wrote: First version done and uploaded: https://yousource.it.jyu.fi/jjrandom2/miniprojects/trees/master/misc/polysolve_for_numpy Small comment: now you are checking if the inp

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 1 October 2015 at 09:05, Nathaniel Smith wrote: > > >> - gcc + OpenMP on linux still breaks multiprocessing. There's a patch to > >> fix this but they still haven't applied it; alternatively there's a > >> workaround you can use in multiprocessing (not using fork mode), but > this > >> require

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

Discussion of Numerical Python > Cc: > Date: Fri, 2 Oct 2015 13:31:47 +0300 > Subject: Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic > polynomial solver > On 02.10.2015 13:07, Daπid wrote: > > > On 2 October 2015 at 11:58, Juha Jeronen wrote: > >

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

; To: Discussion of Numerical Python >> Cc: >> Date: Fri, 2 Oct 2015 13:31:47 +0300 >> Subject: Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic >> polynomial solver >> >> On 02.10.2015 13:07, Daπid wrote: >> >> >> On 2 Octo

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

Juha Jeronen wrote: > Mm. I've quite often run MPI locally (it's nice for multicore scientific > computing on Python), but I had no idea that OpenMP had cluster > implementations. Thanks for the tip. Intel has been selling one, I think there are others too. OpenMP has a flush pragma for sync

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

Sturla Molden wrote: > OpenMP has a flush pragma for synchronizing shared variables. This means > that OpenMP is not restricted to shared memory hardware. A "pragma omp > flush" can just as well invoke some IPC mechanism, even network > communication. By the way, while this is the case for C an

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

Sturla Molden wrote: > Cython actually requires that there is a shared address space, and it > invokes something that strictly speaking has undefined behavior under the > OpenMP standard. So thus, a prange block in Cython is expected to work > correctly on a laptop with a multicore processor, but

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 02/10/15 13:05, Daπid wrote: Have you tried asking Python-dev for help with this? Hopefully they would have some weight there. It seems both GCC dev and Apple (for GCD and Accelerate) has taken a similar stance on this. There is tiny set of functions the POSIX standard demands should work

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On Mon, Oct 5, 2015 at 2:52 PM, Sturla Molden wrote: > On 02/10/15 13:05, Daπid wrote: > >> Have you tried asking Python-dev for help with this? Hopefully they >> would have some weight there. > > It seems both GCC dev and Apple (for GCD and Accelerate) has taken a similar > stance on this. There

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On Mon, Oct 5, 2015 at 3:05 PM, Nathaniel Smith wrote: > On Mon, Oct 5, 2015 at 2:52 PM, Sturla Molden wrote: >> On 02/10/15 13:05, Daπid wrote: >> >>> Have you tried asking Python-dev for help with this? Hopefully they >>> would have some weight there. >> >> It seems both GCC dev and Apple (for

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On 30 September 2015 at 18:20, Nathaniel Smith wrote: > - parallel code in general is not very composable. If someone is calling a > numpy operation from one thread, great, transparently using multiple > threads internally is a win. If they're exploiting some higher-level > structure in their pro

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

On Tue, Oct 6, 2015 at 1:14 AM, Daπid wrote: > One idea: what about creating a "parallel numpy"? There are a few > algorithms that can benefit from parallelisation. This library would mimic > Numpy's signature, and the user would be responsible for choosing the > single threaded or the parallel o

Re: [Numpy-discussion] Cython-based OpenMP-accelerated quartic polynomial solver

t 7:05 AM, mailto:numpy-discussion-requ...@scipy.org>> wrote: From: Juha Jeronen mailto:juha.jero...@jyu.fi>> To: Discussion of Numerical Python mailto:numpy-discussion@scipy.org>> Cc: Date: Fri, 2 Oct 2015 13:31:47 +0300 Subje