September 2017 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] c++, float128 and complex patch
by Michael Gegg 06 Sep '17

06 Sep '17

Hello everyone, a while ago I wrote about a patch for petsc with complex number c++ and float128 using c99 complex numbers and you suggested to just use petsc with a c build and then just call it from c++ (see below). I thought that this worked, but I only tried it for my patched version. Now I tried to do this for the normal v3.7.6 and I get a lot of errors that PetscCompex is not defined when I call it from c++. The installation works fine and also the tutorial examples. (which are all c) It seems that if I call petsc from c++ it tries to switch to c++ complex numbers even though I build petsc with c, which are obviously not defined. So, could you give me a hint on how I should configure petsc so that this works? Is there a way to enforce the c99 complex numbers even when calling petsc from c++? I always used ./configure ... --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --with-clanguage=c --with-scalar-type=complex --with-precision=__float128 --download-f2cblaslapack As I said, with my patch this works fine. Thanks in advance. Also I realized that parmetis does only support double and not float128 and so building petsc with float128 and parmetis crashes. I also made a patch for that, that just declares all parmetis relevant parameters as real_t instead of PetscReal. Would you be interested in including this patch? (its only 2 lines) Thank you. Michael Am 03.05.2017 um 18:08 schrieb Michael Gegg: > > > > Am 03.05.2017 um 16:27 schrieb Matthew Knepley: >> On Wed, May 3, 2017 at 9:22 AM, Michael Gegg >> <michael.gegg(a)tu-berlin.de <mailto:[email protected]>> wrote: >> >> Hello Petsc developers, >> >> thank you for providing such a marvellous numerics package, we >> had/have a lot of fun using it. For our purposes it was necessary >> to use Petsc with c++, float128 and complex. Since this is not >> possible with the standard build we made a patch. It uses c style >> complex numbers as a workaround. >> It can be used with the Parmetis package (there is a little fix >> in the interface there) and we have made a Slepc patch that then >> also allows to use c++, float128 and complex. >> It would be great if you could include it in the petsc software. >> We checked the patch for v3.7.6 and v3.7.3 (latest Slepc release) >> >> >> One question. Why would you compile PETSc with C++ if you wanted to >> use C99 complex? You can do that with the C build, and call >> PETSc the same way from C++. >> > No specific reason. Thanks for the hint, I tried it and it works. I > could have saved some effort there, but I also learned a thing or two > ;) I just didn't know that this was possible. > Thanks, > Michael >> Thanks, >> >> Matt >> >> With best regards, >> >> Michael Gegg >> >> >> >> >> -- >> What most experimenters take for granted before they begin their >> experiments is infinitely more interesting than any results to which >> their experiments lead. >> -- Norbert Wiener >

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Re: [petsc-dev] Random123
by Jed Brown 05 Sep '17

05 Sep '17

Karl Rupp <rupp(a)iue.tuwien.ac.at> writes: > Hi Toby, > > FYI: the Random123 license is just what is commonly referred to as the > 2-clause BSD license: It is 3-clause, just formatted without a bullet for the third clause. > https://opensource.org/licenses/BSD-2-Clause > I don't see any problem with making a repo for it and using it for a > PetscRandom implementation (IANAL). > > Best regards, > Karli > > > > On 09/05/2017 06:26 PM, Tobin Isaac wrote: >> I just came across Random123 [1]: portable, parallel, high-quality pseudorandom number generators. It's developed by DE Shaw, but the license [2] looks to me like we should be able to make a repo for it and use it as a PetscRandom implementation. Does anyone savvier than me want to look at the license and see if I'm missing something? >> >> Cheers, >> Toby >> >> [1]: https://doi.org/10.1145/2063384.2063405 >> [2]: http://www.deshawresearch.com/downloads/download_random123.cgi/Random123_Li… >>

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Re: [petsc-dev] Random123
by Jed Brown 05 Sep '17

05 Sep '17

It is the 3-clause BSD license, with the third clause formatted in a funny way. https://en.wikipedia.org/wiki/BSD_licenses#3-clause_license_.28.22BSD_Licen… Tobin Isaac <tisaac(a)cc.gatech.edu> writes: > Thanks. I'm just a simple caveman academic: your private sector > research frightens and confuses me! > > > On Tue, Sep 05, 2017 at 09:32:29PM -0500, Barry Smith wrote: >> >> Heck we have repos of things with far more stringent silly licenses :-) >> >> Barry >> >> > On Sep 5, 2017, at 7:45 PM, Karl Rupp <rupp(a)iue.tuwien.ac.at> wrote: >> > >> > Hi Toby, >> > >> > FYI: the Random123 license is just what is commonly referred to as the 2-clause BSD license: >> > https://opensource.org/licenses/BSD-2-Clause >> > I don't see any problem with making a repo for it and using it for a PetscRandom implementation (IANAL). >> > >> > Best regards, >> > Karli >> > >> > >> > >> > On 09/05/2017 06:26 PM, Tobin Isaac wrote: >> >> I just came across Random123 [1]: portable, parallel, high-quality pseudorandom number generators. It's developed by DE Shaw, but the license [2] looks to me like we should be able to make a repo for it and use it as a PetscRandom implementation. Does anyone savvier than me want to look at the license and see if I'm missing something? >> >> Cheers, >> >> Toby >> >> [1]: https://doi.org/10.1145/2063384.2063405 >> >> [2]: http://www.deshawresearch.com/downloads/download_random123.cgi/Random123_Li… >>

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Re: [petsc-dev] Random123
by Tobin Isaac 05 Sep '17

05 Sep '17

Thanks. I'm just a simple caveman academic: your private sector research frightens and confuses me! On Tue, Sep 05, 2017 at 09:32:29PM -0500, Barry Smith wrote: > > Heck we have repos of things with far more stringent silly licenses :-) > > Barry > > > On Sep 5, 2017, at 7:45 PM, Karl Rupp <rupp(a)iue.tuwien.ac.at> wrote: > > > > Hi Toby, > > > > FYI: the Random123 license is just what is commonly referred to as the 2-clause BSD license: > > https://opensource.org/licenses/BSD-2-Clause > > I don't see any problem with making a repo for it and using it for a PetscRandom implementation (IANAL). > > > > Best regards, > > Karli > > > > > > > > On 09/05/2017 06:26 PM, Tobin Isaac wrote: > >> I just came across Random123 [1]: portable, parallel, high-quality pseudorandom number generators. It's developed by DE Shaw, but the license [2] looks to me like we should be able to make a repo for it and use it as a PetscRandom implementation. Does anyone savvier than me want to look at the license and see if I'm missing something? > >> Cheers, > >> Toby > >> [1]: https://doi.org/10.1145/2063384.2063405 > >> [2]: http://www.deshawresearch.com/downloads/download_random123.cgi/Random123_Li… >

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Re: [petsc-dev] Random123
by Barry Smith 05 Sep '17

05 Sep '17

Heck we have repos of things with far more stringent silly licenses :-) Barry > On Sep 5, 2017, at 7:45 PM, Karl Rupp <rupp(a)iue.tuwien.ac.at> wrote: > > Hi Toby, > > FYI: the Random123 license is just what is commonly referred to as the 2-clause BSD license: > https://opensource.org/licenses/BSD-2-Clause > I don't see any problem with making a repo for it and using it for a PetscRandom implementation (IANAL). > > Best regards, > Karli > > > > On 09/05/2017 06:26 PM, Tobin Isaac wrote: >> I just came across Random123 [1]: portable, parallel, high-quality pseudorandom number generators. It's developed by DE Shaw, but the license [2] looks to me like we should be able to make a repo for it and use it as a PetscRandom implementation. Does anyone savvier than me want to look at the license and see if I'm missing something? >> Cheers, >> Toby >> [1]: https://doi.org/10.1145/2063384.2063405 >> [2]: http://www.deshawresearch.com/downloads/download_random123.cgi/Random123_Li…

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Re: [petsc-dev] Random123
by Karl Rupp 05 Sep '17

05 Sep '17

Hi Toby, FYI: the Random123 license is just what is commonly referred to as the 2-clause BSD license: https://opensource.org/licenses/BSD-2-Clause I don't see any problem with making a repo for it and using it for a PetscRandom implementation (IANAL). Best regards, Karli On 09/05/2017 06:26 PM, Tobin Isaac wrote: > I just came across Random123 [1]: portable, parallel, high-quality pseudorandom number generators. It's developed by DE Shaw, but the license [2] looks to me like we should be able to make a repo for it and use it as a PetscRandom implementation. Does anyone savvier than me want to look at the license and see if I'm missing something? > > Cheers, > Toby > > [1]: https://doi.org/10.1145/2063384.2063405 > [2]: http://www.deshawresearch.com/downloads/download_random123.cgi/Random123_Li… >

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Re: [petsc-dev] Random123
by Matthew Knepley 05 Sep '17

05 Sep '17

To me, it looks fine. Matt On Tue, Sep 5, 2017 at 7:26 PM, Tobin Isaac <tisaac(a)cc.gatech.edu> wrote: > I just came across Random123 [1]: portable, parallel, high-quality > pseudorandom number generators. It's developed by DE Shaw, but the license > [2] looks to me like we should be able to make a repo for it and use it as > a PetscRandom implementation. Does anyone savvier than me want to look at > the license and see if I'm missing something? > > Cheers, > Toby > > [1]: https://doi.org/10.1145/2063384.2063405 > [2]: http://www.deshawresearch.com/downloads/download_random123. > cgi/Random123_License.txt > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener http://www.caam.rice.edu/~mk51/

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Random123
by Tobin Isaac 05 Sep '17

05 Sep '17

I just came across Random123 [1]: portable, parallel, high-quality pseudorandom number generators. It's developed by DE Shaw, but the license [2] looks to me like we should be able to make a repo for it and use it as a PetscRandom implementation. Does anyone savvier than me want to look at the license and see if I'm missing something? Cheers, Toby [1]: https://doi.org/10.1145/2063384.2063405 [2]: http://www.deshawresearch.com/downloads/download_random123.cgi/Random123_Li…

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Re: [petsc-dev] How are we deciding the memory alignment that BuildSystem should choose?
by Jed Brown 05 Sep '17

05 Sep '17

Richard Tran Mills <rtmills(a)anl.gov> writes: > Folks, > > I am wondering how PETSc's BuildSystem currently chooses the memory > alignment to use. In the example file I provide in the repo for the Cori > KNL nodes, I specify '--with-memalign=64' to match the cache line width. If > I don't do this, then configure chooses a 16 byte alignment. Do people > think that we should try to make a better effort to choose a more > appropriate alignment? > > I believe that all modern x86 CPUs use a 64 byte cache width, so should we > be defaulting to that? I don't know how much this matters on a Xeon > processor, but it can be important on Xeon Phi. The preference for 16 was for SSE2, prior to AVX and AVX512. With AVX, I believe there is no particular reason to prefer more than 32-byte alignment -- it just ensures that objects cannot share cache lines. Harmless with large arrays, but not ideal for smaller allocations like nodes in a linked list. (PETSc doesn't use these very often, but it would be nice if control structures don't soak up more cache than they need.)

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How are we deciding the memory alignment that BuildSystem should choose?
by Richard Tran Mills 05 Sep '17

05 Sep '17

Folks, I am wondering how PETSc's BuildSystem currently chooses the memory alignment to use. In the example file I provide in the repo for the Cori KNL nodes, I specify '--with-memalign=64' to match the cache line width. If I don't do this, then configure chooses a 16 byte alignment. Do people think that we should try to make a better effort to choose a more appropriate alignment? I believe that all modern x86 CPUs use a 64 byte cache width, so should we be defaulting to that? I don't know how much this matters on a Xeon processor, but it can be important on Xeon Phi. --Richard

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