[petsc-users] Code speedup after upgrading

Hi, I am using a code which is based on petsc (and also parmetis). Recently I made the following changes and now the code is running about two times faster than before: - Upgraded Ubuntu 18.04 to 20.04 - Upgraded petsc 3.13.4 to 3.14.5 - This time I installed parmetis and metis directly

Re: [petsc-users] MUMPS failure

Barry, I am curious about your statement "does not work generically".  If I compile with -fdefault-integer-8, I would assume that this produces objects/libraries that will use 64bit integers.  As long as I have not declared explicit kind=4 integers, what else could go wrong. -sanjay PS: I am n

Re: [petsc-users] MUMPS failure

> On Mar 22, 2021, at 3:24 PM, Junchao Zhang wrote: > > > > > On Mon, Mar 22, 2021 at 1:39 PM Barry Smith > wrote: > >Version of PETSc and MUMPS? We fixed a bug in MUMPs a couple years ago > that produced error messages as below. Please confirm you are using t

Re: [petsc-users] Local Discontinuous Galerkin with PETSc TS

u_t = G(u) I don't see why you won't just compute any needed u_x from the given u and then you can use any explicit or implicit TS solver trivially. For implicit methods it can automatically compute the Jacobian of G for you or you can provide it directly. Explicit methods will just use

Re: [petsc-users] Local Discontinuous Galerkin with PETSc TS

On Mon, Mar 22, 2021 at 7:53 PM Salazar De Troya, Miguel via petsc-users < petsc-users@mcs.anl.gov> wrote: > Hello > > > > I am interested in implementing the LDG method in “A local discontinuous > Galerkin method for directly solving Hamilton–Jacobi equations” > https://www.sciencedirect.com/scie

[petsc-users] Question about periodic conditions

Hi, I implemented a PETSc code to solve Maxwell's equations for the magnetic and electric fields (B and E) in a cylinder: 0 < r_min <= r <= r_max;with r_max > r_min phi_min = 0 <= r <= phi_max = 2 π z_min <= z =< z_max;with z_max > z_min. I am using a PE

[petsc-users] Local Discontinuous Galerkin with PETSc TS

Hello I am interested in implementing the LDG method in “A local discontinuous Galerkin method for directly solving Hamilton–Jacobi equations” https://www.sciencedirect.com/science/article/pii/S0021999110005255. The equation is more or less of the form (for 1D case): p1 = f(u_x)

Re: [petsc-users] Re-ordering in DMPlexCreateFromCellListParallelPetsc

@+ -- Nicolas On 22/03/2021 17:53, Matthew Knepley wrote: On Mon, Mar 22, 2021 at 12:20 PM Nicolas Barral > wrote: Thanks for your answers Matt. On 22/03/2021 13:45, Matthew Knepley wrote: > On Mon, Mar 22, 2021 at 6:22 AM Nicolas Bar

Re: [petsc-users] MUMPS failure

On Mon, Mar 22, 2021 at 1:39 PM Barry Smith wrote: > >Version of PETSc and MUMPS? We fixed a bug in MUMPs a couple years ago > that produced error messages as below. Please confirm you are using the > latest PETSc and MUMPS. > >You can run your production version with the option -malloc_d

Re: [petsc-users] PF+Navier stokes

Singular systems come up in solving PDEs almost always due to issues related to boundary conditions. For example all Neumann (natural) boundary conditions can produce singular systems. Direct factorizations generically will eventually hit a zero pivot in such cases and there is no universall

Re: [petsc-users] funny link error

> On Mar 22, 2021, at 12:19 PM, Matthew Knepley wrote: > > On Mon, Mar 22, 2021 at 12:16 PM Scott Kruger > wrote: > > The short answer is $PETSC_INSTALL_DIR/lib/pkgconfig/PETSc.pc > > Attached is a PETSc CMake snippet that should show you how to use > pkg-config. >

Re: [petsc-users] MUMPS failure

Version of PETSc and MUMPS? We fixed a bug in MUMPs a couple years ago that produced error messages as below. Please confirm you are using the latest PETSc and MUMPS. You can run your production version with the option -malloc_debug ; this will slow it down a bit but if there is memory

Re: [petsc-users] MUMPS failure

Also, maybe run with -info dump and grep for MUMPS errors in dump.%p, because some failures are silent otherwise. Thanks, Pierre > On 22 Mar 2021, at 7:09 PM, Matthew Knepley wrote: > > On Mon, Mar 22, 2021 at 2:07 PM Chris Hewson > wrote: > Hi Matt, > > No, we are

Re: [petsc-users] MUMPS failure

On Mon, Mar 22, 2021 at 2:07 PM Chris Hewson wrote: > Hi Matt, > > No, we are running it without debugging in prod and then running debug I > can't reproduce the error, from stderr we get: > > [1]PETSC ERROR: > > [1]PETSC ER

Re: [petsc-users] MUMPS failure

Hi Matt, No, we are running it without debugging in prod and then running debug I can't reproduce the error, from stderr we get: [1]PETSC ERROR: [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably

Re: [petsc-users] MUMPS failure

On Mon, Mar 22, 2021 at 1:56 PM Chris Hewson wrote: > Hi All, > > I have been having a problem with MUMPS randomly crashing in our program > and causing the entire program to crash. I am compiling in -O2 optimization > mode and using --download-mumps etc. to compile PETSc. If I rerun the > progra

Re: [petsc-users] PF+Navier stokes

On Mon, Mar 22, 2021 at 2:00 PM Sepideh Kavousi wrote: > I found some discussions in the following link and > https://lists.mcs.anl.gov/pipermail/petsc-users/2010-May/006422.html and > the following paper: > https://www.sciencedirect.com/science/article/pii/S0021999107004330 > But I am engineer a

Re: [petsc-users] PF+Navier stokes

I found some discussions in the following link and https://lists.mcs.anl.gov/pipermail/petsc-users/2010-May/006422.html and the following paper: https://www.sciencedirect.com/science/article/pii/S0021999107004330 But I am engineer and the discussions are confusing for me. Would you please tell

[petsc-users] MUMPS failure

Hi All, I have been having a problem with MUMPS randomly crashing in our program and causing the entire program to crash. I am compiling in -O2 optimization mode and using --download-mumps etc. to compile PETSc. If I rerun the program, 95%+ of the time I can't reproduce the error. It seems to be a

Re: [petsc-users] funny link error

On Mon, Mar 22, 2021 at 12:16 PM Scott Kruger wrote: > > The short answer is $PETSC_INSTALL_DIR/lib/pkgconfig/PETSc.pc > > Attached is a PETSc CMake snippet that should show you how to use > pkg-config. > > It also shows how to set the compilers to the same as PETSc's for build > consistency, but

Re: [petsc-users] Re-ordering in DMPlexCreateFromCellListParallelPetsc

On Mon, Mar 22, 2021 at 12:20 PM Nicolas Barral < nicolas.bar...@math.u-bordeaux.fr> wrote: > Thanks for your answers Matt. > > On 22/03/2021 13:45, Matthew Knepley wrote: > > On Mon, Mar 22, 2021 at 6:22 AM Nicolas Barral > > > > wrote: > > > > On 21

Re: [petsc-users] Re-ordering in DMPlexCreateFromCellListParallelPetsc

Thanks for your answers Matt. On 22/03/2021 13:45, Matthew Knepley wrote: On Mon, Mar 22, 2021 at 6:22 AM Nicolas Barral > wrote: On 21/03/2021 21:29, Matthew Knepley wrote: > On Sat, Mar 20, 2021 at 10:07 AM Nicolas Barral > mailto:nicol

Re: [petsc-users] funny link error

The short answer is $PETSC_INSTALL_DIR/lib/pkgconfig/PETSc.pc Attached is a PETSc CMake snippet that should show you how to use pkg-config. It also shows how to set the compilers to the same as PETSc's for build consistency, but this part is not strictly necessary (but perhaps a good idea). FYI

Re: [petsc-users] funny link error

On Mon, Mar 22, 2021 at 11:04 AM Mark Adams wrote: > Thanks Scott, > > Can you please tell us where this pkg-config file is? > Looks like ${PETSC_ARCH}/lib/pkgconfig Matt > Thank again, > Mark > > On Mon, Mar 22, 2021 at 10:45 AM Scott Kruger wrote: > >> >> From you make.log, it looks lik

Re: [petsc-users] funny link error

Thanks Scott, Can you please tell us where this pkg-config file is? Thank again, Mark On Mon, Mar 22, 2021 at 10:45 AM Scott Kruger wrote: > > From you make.log, it looks like petsc found it here: > /opt/cray/wlm_detect/1.3.3-7.0.1.1_4.19__g7109084.ari/lib64 > > PETSc has it and found it beca

Re: [petsc-users] funny link error

>From you make.log, it looks like petsc found it here: /opt/cray/wlm_detect/1.3.3-7.0.1.1_4.19__g7109084.ari/lib64 PETSc has it and found it because BuildSystem did the query of what it takes to get C/C++/Fortran to work together. Why is it needed? That's up to Cray. But the question is: H

Re: [petsc-users] PF+Navier stokes

On Mon, Mar 22, 2021 at 10:04 AM Sepideh Kavousi wrote: > Hello, > I want to solve PF solidification+Navier stokes using Finite different > method, and I have a strange problem. My code runs fine for some system > sizes and fails for some of the system sizes. When I run with the following > optio

[petsc-users] PF+Navier stokes

Hello, I want to solve PF solidification+Navier stokes using Finite different method, and I have a strange problem. My code runs fine for some system sizes and fails for some of the system sizes. When I run with the following options: mpirun -np 2 ./one.out -ts_monitor -snes_fd_color -ts_max_snes

Re: [petsc-users] Re-ordering in DMPlexCreateFromCellListParallelPetsc

On Mon, Mar 22, 2021 at 6:22 AM Nicolas Barral < nicolas.bar...@math.u-bordeaux.fr> wrote: > On 21/03/2021 21:29, Matthew Knepley wrote: > > On Sat, Mar 20, 2021 at 10:07 AM Nicolas Barral > > > > wrote: > > > > Hi all, > > > > I'm building a plex

Re: [petsc-users] Re-ordering in DMPlexCreateFromCellListParallelPetsc

On 21/03/2021 21:29, Matthew Knepley wrote: On Sat, Mar 20, 2021 at 10:07 AM Nicolas Barral > wrote: Hi all, I'm building a plex from elements arrays using DMPlexCreateFromCellListParallelPetsc. Once the plex is built, I need to set