November 2015 - petsc-users - mailman3.cels.anl.gov

master branch option "-snes_monitor_solution"
by Ed Bueler 22 Nov '15

22 Nov '15

Dear PETSc -- When I use option -snes_monitor_solution in master branch I get the error below. I have a sense that this is related to the change listed at http://www.mcs.anl.gov/petsc/documentation/changes/dev.html, namely "SNESSetMonitor(SNESMonitorXXX, calls now require passing a viewer as the final argument, you can no longer pass a NULL)" but the error message below is not informative enough to tell me what to do at the command line. Note that my X11 windows do work, as other options successfully give line graphs etc. Do I need -snes_monitor_solution Z with some value for Z? If so, where are the possibilities documented? Thanks! Ed $ ./ex5 -snes_monitor_solution [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Null argument, when expecting valid pointer [0]PETSC ERROR: Null Object: Parameter # 4 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Development GIT revision: v3.6.2-1635-g5e95a8a GIT Date: 2015-11-21 16:14:08 -0600 [0]PETSC ERROR: ./ex5 on a linux-c-dbg named bueler-leopard by ed Sun Nov 22 10:31:33 2015 [0]PETSC ERROR: Configure options --download-mpich --download-triangle --with-debugging=1 [0]PETSC ERROR: #1 SNESMonitorSolution() line 33 in /home/ed/petsc/src/snes/interface/snesut.c [0]PETSC ERROR: #2 SNESMonitor() line 3383 in /home/ed/petsc/src/snes/interface/snes.c [0]PETSC ERROR: #3 SNESSolve_NEWTONLS() line 191 in /home/ed/petsc/src/snes/impls/ls/ls.c [0]PETSC ERROR: #4 SNESSolve() line 3984 in /home/ed/petsc/src/snes/interface/snes.c [0]PETSC ERROR: #5 main() line 171 in /home/ed/petsc/src/snes/examples/tutorials/ex5.c [0]PETSC ERROR: PETSc Option Table entries: [0]PETSC ERROR: -snes_monitor_solution [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint(a)mcs.anl.gov---------- application called MPI_Abort(MPI_COMM_WORLD, 85) - process 0 [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 85) - process 0 -- Ed Bueler Dept of Math and Stat and Geophysical Institute University of Alaska Fairbanks Fairbanks, AK 99775-6660 301C Chapman and 410D Elvey 907 474-7693 and 907 474-7199 (fax 907 474-5394)

2 1

petsc master build error
by Ce Qin 22 Nov '15

22 Nov '15

Dear all, I got this error when compile petsc master branch. Best regards, Ce Qin

2 2

Use of DMDAVecGetArrayF90 and DMDAVecRestoreArrayF90
by TAY wee-beng 21 Nov '15

21 Nov '15

Hi, Inside my subroutine, I need to access the DA variable cu_types_array frequently. So I need to call DMDAVecGetArrayF90 and DMDAVecRestoreArrayF90 before and after frequently. Is this necessary? Can I call DMDAVecGetArrayF90 at the start and only call DMDAVecRestoreArrayF90 towards the end, where I don't need to modify the values of cu_types_array anymore? Will this cause memory corruption? Also, must the array be restored using DMDAVecRestoreArrayF90 before calling DMLocalToLocalBegin,DMLocalToLocalEnd? -- Thank you. Yours sincerely, TAY wee-beng

3 7

Compiling PETSc on Windows with Cygwin: errors with `win32fe cl`; okay to use `gcc`, `g++`, `gfortran` as compilers instead of `win32cf cl`?
by Brian Merchant 21 Nov '15

21 Nov '15

Hi all, I'd like to try and install PETSc on Windows (even though I have been forewarned that it is better to simply install it on a unix system). Some information about my system: * Windows 10 Pro, 64 bit * latest Cygwin with make, gcc, g++, gfortran installed The PETSc installation instructions suggest that I run the following command: ./configure --with-cc="win32fe cl" --with-fc="win32fe ifort" --with-cxx="win32fe\ cl" --download-fblaslapack\ However, that results in the following error: C compiler you provided with -with-cc=win32fe cl does not work. Cannot compile C with /cygdrive/a/petsc/bin/win32fe/win32fe cl. The answer to this stackexchange question: http://stackoverflow.com/questions/30229620/petsc-build-error-c-compiler-do… recommends the following command instead (with escaped whitespace): ./configure --with-cc="win32fe\ cl" --with-fc="win32fe\ ifort" --with-cxx="win32fe\ cl" --download-fblaslapack Running that command results in the following error (note no second line in error): C compiler you provided with -with-cc=win32fe\ cl does not work. In both cases, the configure.log output only contains (I do not use Chinese characters, these were in the file): > 㰡祳汭湩㹫arch-mswin-c-debug/lib/petsc/conf/configure.log What should I do? Also, do `gcc`/`g++` compiled programs not work on Windows? I ask because if I simply run the suggested command in the "Quick Installation" guide, using `gcc` and `g++`; then I don't get compilation errors. Would it be okay to simply use those compilers then? Kind regards, Brian

3 7

adding mat rows
by Carles Bona 20 Nov '15

20 Nov '15

Dear all, I would like to add some of my equations before I modify them. I haven't found any high level function that would allow me to add rows of a matrix (I am working with a parallel BAIJ). Is there any nice way of doing this? I have tried with MatGetRow/MatRestoreRow, but I am struggling a bit to retain the cols and vals, as only one processor can call MatGetRow but if only that processor tries to allocate memory then one gets a segmentation fault. I guess I should allocate enough memory on all processors... If I refrain from storing the cols and vals I need to call MatSetValues before returning the pointer, with a subsequent call to assemblybegin/end for each row, which slows down the code. The other option would be to forget about these row additions after the matrix has been filled and try to fill it while taking into account these row additions at the same time. I guess I need to be constantly checking for indices then. So, which option (not necessarily mentioned here) would you reccomend? Thanks a lot, Carles

3 8

Citation for hypre BoomerAMG
by Young, Matthew, Adam 19 Nov '15

19 Nov '15

When I run my code with -citations, it produces @manual{hypre-web-page, title = {{\sl hypre}: High Performance Preconditioners}, organization = {Lawrence Livermore National Laboratory}, note = {\url{http://www.llnl.gov/CASC/hypre/}} } for BoomerAMG. However, the result of \citep{hypre-web-page} is "[hyp]" in the text and a bibliography entry with only "()" for the author. This seems incorrect. If this is the intended output, can you tell me what I'm doing wrong in LaTeX? The other references (two for PETSc and one for GMRES) are fine. --Matt -------------------------------------------------------------- Matthew Young Graduate Student Boston University Dept. of Astronomy --------------------------------------------------------------

3 4

Understanding PETSC: boundary layer flow with SNES
by Pavel Schor 19 Nov '15

19 Nov '15

Dear PETSC users, I am a newbie to PETSC and I try to understand it. My first attempt is to solve 2D laminar boundary layer equations: u*du/dx +v*du/dy = Ue*(dUe/dx). -nu*d2u/dy2 dudx + dvdy = 0 B.C.: y=0: u=0, v=0 y=H: u(x)=Ue(x) Where H is height of the domain, Ue(x) is edge velocity given by a potential flow solver. I assume Ue(x)=10.0 I have several questions regarding the workflow in PETSC, I took SNES example29 (2D cavity flow) and I tried to modify it: 1) There are vectors x and f. I suppose vector x to represent the values of velocity and vector f to represent velocity residuals. Please is this correct? Based on example29 and my assumption, I calculated the velocity: dhx = (PetscReal)(info->mx-1); dhy = (PetscReal)(info->my-1); dx = 1.0/dhx; dy = 1./dhy; u = x[j][i].u; v = x[j][i].v; dudx = (x[j][i+1].u - x[j][i-1].u)/2.0/dx; dudy = (x[j+1][i].u - x[j-1][i].u)/2.0/dy; dvdy = (x[j+1][i].v - x[j-1][i].v)/2.0/dy; d2udy2 = (-2.0*u + x[j-1][i].u + x[j+1][i].u)/dy/dy; /* U velocity */ f[j][i].u = u*dudx +v*dudy -Ue*dUedx -nu*d2udy2; /* V velocity */ f[j][i].v = dudx + dvdy; The code does not work. With initial conditions x[j][i].u=Ue; and x[0][i].u=0.0; the result is the same as the initial conditions. 2) In SNES example29, there are boundary conditions specified on vector f? For example: /* Test whether we are on the top edge of the global array */ if (yinte == info->my) { j = info->my - 1; yinte = yinte - 1; /* top edge */ for (i=info->xs; i<info->xs+info->xm; i++) { f[j][i].u = x[j][i].u - lid; f[j][i].v = x[j][i].v; I don't understand the last two lines. I just deleted the conditions for left and right edges and replaced f[j][i].u = x[j][i].u - lid; with f[j][i].u = x[j][i].u - Ue; 3) Please could someone explain the normalization on following lines? (Taken from example 29) /* Define mesh intervals ratios for uniform grid. Note: FD formulae below are normalized by multiplying through by local volume element (i.e. hx*hy) to obtain coefficients O(1) in two dimensions. */ dhx = (PetscReal)(info->mx-1); dhy = (PetscReal) (info->my-1); hx = 1.0/dhx; hy = 1.0/dhy; hxdhy = hx*dhy; hydhx = hy*dhx; Thanks in advance & Kind regards Pavel Schor PhD. student, Institute of aerospace engineering, Brno University of technology

2 1

set limits for a nonlinear step
by Michael Povolotskyi 18 Nov '15

18 Nov '15

Dear Petsc developers, in the old days there was a function SNESLineSearchSetParams How to set a maximum value for the nonlinear step now? Thank you, Michael. -- Michael Povolotskyi, PhD Research Assistant Professor Network for Computational Nanotechnology Hall for Discover and Learning Research, Room 441 West Lafayette, IN 47907 Phone (765) 4949396

2 1

DMPlex for high order elements
by Alejandro D Otero 18 Nov '15

18 Nov '15

Hi, I am trying to define a spectral element mesh in the frame of DMPlex structure. To begin with I am thinking of quadrilateral 2d elements. Lets say I have a 16 node element with 2 nodes on each edge besides the 2 corners and 4 nodes inside the element. I'd like to treat all nodes as vertex in the DMPlex structure. I am wondering whether I can make internal edge nodes (those not in the extremes of the edge) depend on the corresponding edge and internal nodes (those not on the element edges) depend on the corresponding element? If this is not the right way of doing this from DMPlex philosophical point of view, could you please give me an example? Thanks in advance, best regards, Alejandro

2 2

problem using 64-bit-indices
by Randall Mackie 17 Nov '15

17 Nov '15

I ran into a problem yesterday where a call to DMDACreate3d gave an error message about the size being too big and that I should use —with-64-bit-indices. So I recompiled PETSc (latest version, 3.6.2) with that option, but when I recompiled my code, I found the following errors: call VecGetArrayF90(vSeqZero,ptr_a,ierr) 1 Error: Type mismatch in argument 'ierr' at (1); passed INTEGER(8) to INTEGER(4) call VecRestoreArrayF90(vSeqZero,ptr_a,ierr) 1 Error: Type mismatch in argument 'ierr' at (1); passed INTEGER(8) to INTEGER(4) call DMDAVecGetArrayF90(da,J,ptr_j,ierr) 1 Error: There is no specific subroutine for the generic 'dmdavecgetarrayf90' at (1) So strangely, even though all my variables are defined like PetscInt, PetscReal, etc, VecGetArrayF90 is still expecting a 4 byte integer, which is easy enough for me to do, but there seems to be a problem with DMDAVecGetArrayF90. In the meantime, I’ll switch to VecGetArrayF90, and retry my code, but I thought I’d pass along these error messages. Randy M.

2 2