Re: [petsc-users] Confusing Schur preconditioner behaviour

Hi Dave, >If you are doing that, then you need to tell fieldsplit to use the Amat to >define the splits otherwise it will define the Schur compliment as >S = B22 - B21 inv(B11) B12 >preconditiones with B22, where as what you want is >S = A22 - A21 inv(A11) A12 >preconditioned with B22. >If your

[petsc-users] SLEPc Build Error

Hello, I am trying to install PETSc with following configure options: ./configure --download-openmpi --download-openblas --download-slepc --download-cmake --download-metis --download-parmetis Compilation is done but after the following command, I got an error: make PETSC_DIR=/home/slurm_local/e

Re: [petsc-users] SLEPc Build Error

This is slepc.log: Checking environment... done Checking PETSc installation... ERROR: Unable to link with PETSc ERROR: See "arch-linux2-c-debug/lib/slepc/conf/configure.log" file for details Matthew Knepley , 19 Mar 2019 Sal, 13:36 tarihinde şunu yazdı: > On Tue, Mar 19, 2019 at 6:31 AM Eda Ok

Re: [petsc-users] SLEPc Build Error

And what is in $SLEPC_DIR/arch-linux2-c-debug/lib/slepc/conf/configure.log ? Jose > El 19 mar 2019, a las 11:41, Eda Oktay via petsc-users > escribió: > > This is slepc.log: > > Checking environment... done > Checking PETSc installation... > ERROR: Unable to link with PETSc > ERROR: See "arch

Re: [petsc-users] SLEPc Build Error

Correction: the correct path is $PETSC_DIR/$PETSC_ARCH/externalpackages/git.slepc/$PETSC_ARCH/lib/slepc/conf/configure.log > El 19 mar 2019, a las 11:46, Jose E. Roman via petsc-users > escribió: > > And what is in $SLEPC_DIR/arch-linux2-c-debug/lib/slepc/conf/configure.log ? > Jose > >> El

Re: [petsc-users] SLEPc Build Error

Starting Configure Run at Tue Mar 19 11:53:05 2019 Configure Options: --prefix=/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug Working directory: /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/ex

Re: [petsc-users] PCFieldSplit gives different results for direct and iterative solver

Hello Barry, Thank you for your reply. I reduced the tolerances and get desired solution. I am solving a multiphase incompressible n-s problems and currently we are using augmented lagrangina technique with uzawa iteration. Because the problems are getting larger, we are also looking for some o

Re: [petsc-users] SLEPc Build Error

There seems to be a link problem with PETSc. Suggest re-configuring without the option --download-slepc Then, after building PETSc, try 'make check' to make sure that PETSc is built correctly. Then install SLEPc afterwards. Jose > El 19 mar 2019, a las 11:58, Eda Oktay escribió: > > ==

Re: [petsc-users] Confusing Schur preconditioner behaviour

Hi Colin, On Tue, 19 Mar 2019 at 09:33, Cotter, Colin J wrote: > Hi Dave, > > >If you are doing that, then you need to tell fieldsplit to use the Amat > to define the splits otherwise it will define the Schur compliment as > >S = B22 - B21 inv(B11) B12 > >preconditiones with B22, where as what y

Re: [petsc-users] PCFieldSplit gives different results for direct and iterative solver

Perhaps you need a better preconditioner for it. Hello Matt, Thank you for your help. Yes, I think I need a better preconditioner; it requires about 600 iterations for Schur complement. Is there any tutorials for this? Or shall I just try different combinations and find the most suitable one? K

Re: [petsc-users] SLEPc Build Error

Without slepc, I configured petsc succesfully. Then I installed slepc with following steps: export PETSC_ARCH=arch-linux2-c-debug export PETSC_DIR=/home/slurm_local/e200781/petsc-3.10.4 export SLEPC_DIR=/home/slurm_local/e200781/slepc-3.10.2 cd slepc-3.10.2 ./configure However, I still get the er

Re: [petsc-users] SLEPc Build Error

What is the output of 'make check' in $PETSC_DIR ? > El 19 mar 2019, a las 13:02, Eda Oktay escribió: > > Without slepc, I configured petsc succesfully. Then I installed slepc with > following steps: > > export PETSC_ARCH=arch-linux2-c-debug > export PETSC_DIR=/home/slurm_local/e200781/petsc-3

Re: [petsc-users] [petsc4py] DMPlexCreateFromDAG and other missing functions

Thanks Matt, I tried your suggestions to implement DMPlexCreateFromDAG in petsc4py: 1. In petsc4py/src/PETSc/petscdmplex.pxi I uncommented: int DMMPlexCreateFromDAG(PetscDM,PetscInt,const_PetscInt[],const_PetscInt[], const_PetscInt[],const_PetscInt[],const_PetscS

Re: [petsc-users] [petsc4py] DMPlexCreateFromDAG and other missing functions

I am sorry for the bad formatting of my createFromDAG function. I attach this function, and I hope it will be easier to read. Mar 19, 2019, 12:46 PM by finnkochin...@keemail.me: > Thanks Matt, > I tried your suggestions to implement DMPlexCreateFromDAG in petsc4py: > > > 1. In > petsc4py/src/PET

Re: [petsc-users] PCFieldSplit gives different results for direct and iterative solver

> > > > -fieldsplit_velocity_ksp_type preonly -fieldsplit_velocity_pc_type gamg > -fieldsplit_pressure_ksp_type minres -fieldsplit_pressure_pc_type none > You should use cg for the ksp_type with gamg if you are symmetric and gmres if not (you can try cg even if it is mildly asymmetric). minr

[petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab

Hello team, Currently we're using the PETSc binary file format to save Vecs and Mats and visualize them in Matlab. It looks like HDF5 works more efficiently with large data sets (faster I/O), and we're wondering if PETSc Vecs/Mats saved in HDF5 viewer can be visualized in Matlab as well? Thank

Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab

Got it, thanks! From: Matthew Knepley Sent: Tuesday, March 19, 2019 10:10 AM To: Yuyun Yang Cc: petsc-users@mcs.anl.gov Subject: Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab On Tue, Mar 19, 2019 at 11:58 AM Yuyun Yang via petsc-users mailto:petsc-users@mcs.anl.gov>> wro

Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab

It's simply for visualization purposes. I wasn't sure if HDF5 would perform better than binary, and what specific functions are needed to load the PETSc vectors/matrices, so wanted to ask for some advice here. Since Matt mentioned it's not likely to be much faster than binary, I guess there is n

Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab

Yuyun Yang via petsc-users writes: > It's simply for visualization purposes. I wasn't sure if HDF5 would perform > better than binary, and what specific functions are needed to load the PETSc > vectors/matrices, so wanted to ask for some advice here. Since Matt mentioned > it's not likely to b

Re: [petsc-users] MatCompositeMerge + MatCreateRedundantMatrix

If it is not too complicated it would be nice if MPICreateSubMatricesMPI  would be avaible for other matrices than MPIAIJ.       On Mon, Mar 18, 2019 at 10:30 PM Marius Buerkle wrote: I have another question regarding MatCreateRedundantMatrix and MPICreateSubMatricesMPI.

Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab

Sounds good, thanks for the advice! -Original Message- From: Jed Brown Sent: Tuesday, March 19, 2019 1:23 PM To: Yuyun Yang ; zakaryah ; petsc-users@mcs.anl.gov Subject: Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab Yuyun Yang via petsc-users writes: > It's sim