Re: [petsc-users] Question about memory usage in Multigrid preconditioner

2016-07-11 Thread Dave May
Hi Frank, On 11 July 2016 at 19:14, frank wrote: > Hi Dave, > > I re-run the test using bjacobi as the preconditioner on the coarse mesh > of telescope. The Grid is 3072*256*768 and process mesh is 96*8*24. The > petsc option file is attached. > I still got the "Out Of Memory" error. The error

Re: [petsc-users] [Slepc 3.7.1][macOS] install name is set to build folder instead of prefix

2016-07-11 Thread Denis Davydov
> On 11 Jul 2016, at 21:06, Jose E. Roman wrote: > > I don't understand why I don't get this warning. > Still I don't see where the problem is. Please tell me exactly what you want > me to change, or better make a pull request. The problem has to do with the assumptions in python scripts. See

Re: [petsc-users] [Slepc 3.7.1][macOS] install name is set to build folder instead of prefix

2016-07-11 Thread Jose E. Roman
I don't understand why I don't get this warning. Still I don't see where the problem is. Please tell me exactly what you want me to change, or better make a pull request. Thanks. Jose > El 11 jul 2016, a las 17:06, Denis Davydov escribió: > > Here is the warning: > > Your SLEPC_DIR may not m

Re: [petsc-users] Diagonalization of a 3D dense matrix

2016-07-11 Thread Matthew Knepley
On Mon, Jul 11, 2016 at 1:22 PM, Ketan Maheshwari < ketancmaheshw...@gmail.com> wrote: > Matthew, > > I am probably not using the right language but I meant that each element > has three indices associated with it: x, y, z. > > Here is a snapshot: > > 1 10 555.7113635929515209e-03 > 1 10 56

Re: [petsc-users] Diagonalization of a 3D dense matrix

2016-07-11 Thread Ketan Maheshwari
Matthew, I am probably not using the right language but I meant that each element has three indices associated with it: x, y, z. Here is a snapshot: 1 10 555.7113635929515209e-03 1 10 564.2977490038287334e-03 1 10 572.8719519782193204e-03 1 10 581.4380140927001712e-03 1 10 59

Re: [petsc-users] Question about memory usage in Multigrid preconditioner

2016-07-11 Thread frank
Hi Dave, I re-run the test using bjacobi as the preconditioner on the coarse mesh of telescope. The Grid is 3072*256*768 and process mesh is 96*8*24. The petsc option file is attached. I still got the "Out Of Memory" error. The error occurred before the linear solver finished one step. So I do

Re: [petsc-users] Diagonalization of a 3D dense matrix

2016-07-11 Thread Matthew Knepley
On Mon, Jul 11, 2016 at 12:05 PM, Ketan Maheshwari < ketancmaheshw...@gmail.com> wrote: > Hello PETSC-ers, > > I am a research faculty at Univ of Pittsburgh trying to use PETSC/SLEPC to > obtain the diagonalization of a large matrix using Lanczos or Davidson > method. > > The matrix is a 3 dimensi

[petsc-users] Diagonalization of a 3D dense matrix

2016-07-11 Thread Ketan Maheshwari
Hello PETSC-ers, I am a research faculty at Univ of Pittsburgh trying to use PETSC/SLEPC to obtain the diagonalization of a large matrix using Lanczos or Davidson method. The matrix is a 3 dimensional dense matrix with a total of 216000 elements. After looking into some of the examples in PETSC

Re: [petsc-users] [Slepc 3.7.1][macOS] install name is set to build folder instead of prefix

2016-07-11 Thread Denis Davydov
Here is the warning: Your SLEPC_DIR may not match the directory you are in SLEPC_DIR /Users/davydden/spack/var/spack/stage/slepc-3.7.1-p7hqqclwqvbvra6j44lka3xuc4eycvdg/slepc-3.7.1 Current directory /private/var/folders/5k/sqpp24tx3ylds4fgm13pfht0gn/T/davydden/spack-stage/spack-stage-m7Xg8I

Re: [petsc-users] HDF5 and PETSc

2016-07-11 Thread Matthew Knepley
On Mon, Jul 11, 2016 at 3:13 AM, Marco Zocca wrote: > Sorry for the previous mail, I hadn't fully read ./configure --help : > all external package options are listed there, including HDF5 > > As far as I can see in > https://www.mcs.anl.gov/petsc/miscellaneous/external.html and on the > PDF manu

Re: [petsc-users] [Slepc 3.7.1][macOS] install name is set to build folder instead of prefix

2016-07-11 Thread Jose E. Roman
I cannot reproduce this behaviour. If I do for instance this (on OS X El Capitan): $ cd ~/tmp $ ln -s $SLEPC_DIR . $ cd slepc-3.7.1 $ ./configure $ make $ otool -lv $PETSC_ARCH/lib/libslepc.dylib | grep slepc I don't get a warning, and the output of otool is the same that would result if done o

Re: [petsc-users] HDF5 and PETSc

2016-07-11 Thread Marco Zocca
Sorry for the previous mail, I hadn't fully read ./configure --help : all external package options are listed there, including HDF5 As far as I can see in https://www.mcs.anl.gov/petsc/miscellaneous/external.html and on the PDF manual, not all external packages are mentioned, and this tripped me

[petsc-users] HDF5 and PETSc

2016-07-11 Thread Marco Zocca
Good morning, Does the HDF5 functionality need to be explicitly requested at configure time? I just noticed that my default configuration on a single-node machine does not compile any relevant symbol. I do not have HDF5 installed on my system yet, but I assumed PETSc includes it by default, or