Re: [petsc-dev] (no subject)

2017-09-21 Thread Richard Tran Mills
Thanks for sharing this, Barry. I haven't had time to read their paper, but it looks worth a read. Hong, since many machine-learning or data-mining problems can be cast as linear algebra problems (several examples involving eigenproblems come to mind), I'm guessing that there must be several

Re: [petsc-dev] MatTransposeMatMult

2017-09-21 Thread Jed Brown
Hong writes: > It was implemented a decade ago for small to medium matrices. > Your matrix structure reveals the worst part of outer product. > > After discussing it with Barry, we decided to replace the algorithm (not > API) using At=A^T and C=At*B for sequential

Re: [petsc-dev] MatTransposeMatMult

2017-09-21 Thread Hong
Jed: > Hong writes: > > > Jed, > > I reproduced what you observed. > > 30x time is spent on numerical C = At*B. > > We compute A^T*B using outer product C=(A^T)[:,i]*B[i,:]. > > For your large matrix A: rows=574902, cols=184446, > > outer product takes long long time to

Re: [petsc-dev] MatTransposeMatMult

2017-09-21 Thread Jed Brown
Hong writes: > Jed, > I reproduced what you observed. > 30x time is spent on numerical C = At*B. > We compute A^T*B using outer product C=(A^T)[:,i]*B[i,:]. > For your large matrix A: rows=574902, cols=184446, > outer product takes long long time to insert values to C. > > We

Re: [petsc-dev] (no subject)

2017-09-21 Thread Zhang, Hong
Great news! According to their papers, MLSVM works only in serial. I am not sure what is stopping them using PETSc in parallel. Btw, are there any other cases that use PETSc for machine learning? Hong (Mr.) > On Sep 21, 2017, at 1:02 PM, Barry Smith wrote: > > > From:

Re: [petsc-dev] HDF5 error from GAMG

2017-09-21 Thread Barry Smith
Mark, It doesn't look like this a PETSc example (in a PETSc branch). If you can send me full instructions for building/compiling a code that has this behavior please send me all info so I can run it and debug it. Barry Otherwise it is just speculation city. > On Sep 18, 2017, at

Re: [petsc-dev] HDF5 error from GAMG

2017-09-21 Thread Barry Smith
> On Sep 18, 2017, at 7:59 PM, Mark Adams wrote: > > Also, I tested this on my Mac (this output) and on Cori at NERSC and the > behavior looked identical. > > On Mon, Sep 18, 2017 at 8:44 PM, Mark Adams wrote: > I get this strange error when I use GAMG, in

[petsc-dev] (no subject)

2017-09-21 Thread Barry Smith
From: Ilya Safro isa...@g.clemson.edu Date: September 17, 2017 Subject: MLSVM 1.0, Multilevel Support Vector Machines We are pleased to announce the release of MLSVM 1.0, a library of fast multilevel algorithms for training nonlinear support vector machine models on large-scale datasets. The

Re: [petsc-dev] MatTransposeMatMult

2017-09-21 Thread Hong
Jed, I reproduced what you observed. 30x time is spent on numerical C = At*B. We compute A^T*B using outer product C=(A^T)[:,i]*B[i,:]. For your large matrix A: rows=574902, cols=184446, outer product takes long long time to insert values to C. We may use At=A^T and C=At*B instead. Hong On Thu,

Re: [petsc-dev] MatTransposeMatMult

2017-09-21 Thread Hong
Jed : > ~jedbrown/ceres_solver_iteration_001_A.petsc on mcs.anl.gov. > I got this file. How many matrices in this file? How to load them? It seems the first matrix is rectangular. Hong > > The issue is that MatTransposeMatMult is implemented using sparse outer > products which is quite