May 2023 - petsc-users - mailman3.cels.anl.gov

Error during compile
by Joauma Marichal 31 May '23

31 May '23

Hello, I am writing to you as I am trying to compile petsc on my mac. I used: $ export PATH=/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/munki $ ./configure --download-fblaslapack --download-hypre --prefix=../marha/lib_petsc Which has worked previously but today, I get: **************************ERROR************************************* Error during compile, check arch-darwin-c-debug/lib/petsc/conf/make.log Send it and arch-darwin-c-debug/lib/petsc/conf/configure.log to petsc-maint(a)mcs.anl.gov<mailto:[email protected]> ******************************************************************** I attach the files. Thanks a lot for your help. Best regards, Joauma

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Re: [petsc-users] petsc-users Digest, Vol 173, Issue 131
by Waltz Jan 29 May '23

29 May '23

Thank you for your reply and help. I followed your advice to try it out, but found that the results were not quite right. It may be due to my misunderstanding. Could you please help me? The specific information is as follows: Codes: /* Solve J Y = F, where J is Jacobian matrix */ ierr = SNESComputeJacobian(snes, X, snes->jacobian, snes->jacobian_pre); CHKERRQ(ierr); PetscViewer viewer; /* View the matrix in a text file */ ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD, "/share/userfile/jianglei/Muti-layers-well-working/petsc/jacobianmatrix.m", &viewer);CHKERRQ(ierr); ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_MATLAB);CHKERRQ( ierr); /* Optional: use MATLAB format */ ierr = MatView(snes->jacobian, viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); MatAssemblyBegin(snes->jacobian,MAT_FINAL_ASSEMBLY); MatAssemblyEnd(snes->jacobian,MAT_FINAL_ASSEMBLY); PetscInt rstart, rend; MatGetOwnershipRange(snes->jacobian, &rstart, &rend); PetscInt row=1000, col=1000; PetscScalar v; if (row>=rstart && row<rend) { MatGetValues(snes->jacobian, 1, &row, 1, &col, &v); PetscPrintf(PETSC_COMM_WORLD, "rstart: %d, rend: %d, row: %d, col: %d, v: %e\n", rstart, rend, row, col, PetscRealPart(v)); } Results: [image: image.png] [image: image.png] [image: image.png] ====================== Step: 1, time: 0. days==================== 0 SNES Function norm 1.772062116708e-01 rstart: 0, rend: 4000, row: 1000, col: 1000, v: 7.443232e-06 That's all. Could you help me? On Tue, May 30, 2023 at 1:00 AM <petsc-users-request(a)mcs.anl.gov> wrote: > Send petsc-users mailing list submissions to > petsc-users(a)mcs.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mcs.anl.gov/mailman/listinfo/petsc-users > or, via email, send a message with subject or body 'help' to > petsc-users-request(a)mcs.anl.gov > > You can reach the person managing the list at > petsc-users-owner(a)mcs.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of petsc-users digest..." > > > Today's Topics: > > 1. MatGetValues() can't return the correct values (Waltz Jan) > 2. Re: MatGetValues() can't return the correct values (Barry Smith) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 29 May 2023 16:49:40 +0800 > From: Waltz Jan <jl2862237661(a)gmail.com> > To: petsc-users(a)mcs.anl.gov > Subject: [petsc-users] MatGetValues() can't return the correct values > Message-ID: > <CAEj=jGKvgY5ys=4_=YoEZrE5Xu4Pj6FVxSq8XgUH=N= > QF_C-vA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > /* Solve J Y = F, where J is Jacobian matrix */ > ierr = SNESComputeJacobian(snes, X, snes->jacobian, snes->jacobian_pre); > CHKERRQ(ierr); > > PetscInt rstart, rend; > MatGetOwnershipRange(snes->jacobian, &rstart, &rend); > PetscInt row=1000, col=1000; > PetscScalar v; > if (row>=rstart && row<rend) > { > MatGetValues(snes->jacobian, 1, &row, 1, &col, &v); > PetscPrintf(PETSC_COMM_WORLD, "rstart: %d, rend: %d, row: %d, col: %d, > v: %e\n", rstart, rend, row, col, v); > } > > It was supposed to return the value of the matrix at row 1001 and column > 1001, but it returned the value at row 2001 and column 2001 instead. There > is a two-fold relationship between these coordinates, and I'm not sure if > it's related to the fact that I set the number of processes to 2. >

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Get global offset in global vector for the points not owned by this processor.
by YuSh Lo 29 May '23

29 May '23

Hi, How to get the offset in global vector for the points not owned by this processor? I have a parallel DMPlex and a section assigned to it. GetSectionGetOffset with a global section returns -1 for the points not owned by this processor. Thanks, Josh

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MatGetValues() can't return the correct values
by Waltz Jan 29 May '23

29 May '23

/* Solve J Y = F, where J is Jacobian matrix */ ierr = SNESComputeJacobian(snes, X, snes->jacobian, snes->jacobian_pre); CHKERRQ(ierr); PetscInt rstart, rend; MatGetOwnershipRange(snes->jacobian, &rstart, &rend); PetscInt row=1000, col=1000; PetscScalar v; if (row>=rstart && row<rend) { MatGetValues(snes->jacobian, 1, &row, 1, &col, &v); PetscPrintf(PETSC_COMM_WORLD, "rstart: %d, rend: %d, row: %d, col: %d, v: %e\n", rstart, rend, row, col, v); } It was supposed to return the value of the matrix at row 1001 and column 1001, but it returned the value at row 2001 and column 2001 instead. There is a two-fold relationship between these coordinates, and I'm not sure if it's related to the fact that I set the number of processes to 2.

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Regarding Issue with Metis Double Precision
by s.pradeep kumar 28 May '23

28 May '23

Dear All, * I recently tried to install Metis along with PETSC 3.19.1, using following command,* ./configure --with-scalar-type=real --with-precision=double --download-metis --download-parmetis --with-cmake=1 --with-mpi-dir=/opt/cray/pe/mpich/8.1.9/ofi/gnu/9.1 --download-fblaslapack=1 --with-debugging=0 COPTFLAGS=-O2 FOPTFLAGS=-O2 *While compiling my code, I get this warning sign, * 34: warning: passing argument 10 of 'ParMETIS_V3_PartKway' from incompatible pointer type [-Wincompatible-pointer-types] 79 | nparts,tpwgts,ubvec,options, | ^~~~~~ | | | PetscScalar * {aka double *} In file included from /v2_petsc_check/ParmetisWrappers.c:5: NumericalLibraries/petsc-3.19.1/gnu-opt/include/parmetis.h:70:22: note: expected 'real_t *' {aka 'float *'} but argument is of type 'PetscScalar *' {aka 'double *'} 70 | real_t *tpwgts, real_t *ubvec, idx_t *options, idx_t *edgecut, idx_t *part, | ~~~~~~~~^~~~~~ /v2_petsc_check/ParmetisWrappers.c:79:41: warning: passing argument 11 of 'ParMETIS_V3_PartKway' from incompatible pointer type [-Wincompatible-pointer-types] 79 | nparts,tpwgts,ubvec,options, | ^~~~~ | | | PetscScalar * {aka double *} *Ignoring the warning sign leads to code crashing due to Parmetis Error,* parmetis error: the sum of tpwgts for constraint #0 is not 1.0 *How should I proceed further?* Regards, Pradeep

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Re: [petsc-users] Build Error
by Barry Smith 26 May '23

26 May '23

When PETSc is configured it creates a file configure.log in the PETSC_DIR directory; when make is run on it it creates a make.log file. The configure.log file is very useful for figuring anything that goes wrong. > On May 26, 2023, at 1:32 PM, SENECA, MICHAEL <mseneca(a)anl.gov> wrote: > > Where might I find the configure.log? Or do you mean the petsc build log information? > > > From: Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> > Date: Friday, May 26, 2023 at 9:40 AM > To: SENECA, MICHAEL <mseneca(a)anl.gov <mailto:[email protected]>> > Cc: petsc-users(a)mcs.anl.gov <mailto:[email protected]> <petsc-users(a)mcs.anl.gov <mailto:[email protected]>> > Subject: Re: [petsc-users] Build Error > > > PETSc configure is suppose to handle this cleanly. Please send configure.log to petsc-maint(a)mcs.anl.gov <mailto:[email protected]> as we need more context to understand why it is not working. > > PETSc configure looks for libgtoolize (which is what brew names it) and uses it for libtoolize > > You can use --with-libtoolize-exec=pathtolibtoolize (or --with-libtoolize=pathtolibtoolize for older versions of PETSc) to select the executable PETSc uses > > > > > > On May 25, 2023, at 1:35 PM, SENECA, MICHAEL via petsc-users <petsc-users(a)mcs.anl.gov <mailto:[email protected]>> wrote: > > Hi all, > > I have been attempting to install cardinal on my new MacBook M2 Pro chip but I have run into some errors when attempting to build petsc, the script attempts to access > /usr/bin/libtoolize > which does not exist on my MacBook. I have libtoolize installed via homebrew and have made a link from the homebrew installation to > usr/local/bin/libtoolize > But the script does not look in the local directory. From what I have gathered online, the /usr/bin/ should not be edited as it is managed by macOS and its system software which can lead to system instability. Do any of you know of a way around to get the petsc script to just look for libtoolize from my path and not /usr/bin/libtoolize? > > Best regards, > Michael Seneca

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Build Error
by SENECA, MICHAEL 26 May '23

26 May '23

Hi all, I have been attempting to install cardinal on my new MacBook M2 Pro chip but I have run into some errors when attempting to build petsc, the script attempts to access /usr/bin/libtoolize which does not exist on my MacBook. I have libtoolize installed via homebrew and have made a link from the homebrew installation to usr/local/bin/libtoolize But the script does not look in the local directory. From what I have gathered online, the /usr/bin/ should not be edited as it is managed by macOS and its system software which can lead to system instability. Do any of you know of a way around to get the petsc script to just look for libtoolize from my path and not /usr/bin/libtoolize? Best regards, Michael Seneca

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Questions about the DMDAGetElements command
by ziming xiong 26 May '23

26 May '23

Hello， I am using the command DMDAGetElements to get the number of elements in the grid and the index of the points within each element, but I found a problem that the accuracy of this command depends on the number of x, y, z direction cels I then create. Take \src\ksp\ksp\tutorials\71 as an example, when the values of cells are 4,3,2. using two processes to complete -dim 3 -cells 4,3,2 -pde_type Poisson -use_global, here the index of the points in the elements in each process will have problems, the given local index corresponds to the coordinates of the points in the local to see that the cell will have problems. Take my results as an example, process 1 gives the local indices of the first element's vertices (0 1 5 4 16 17 21 20). But the corresponding coordinates are 0 1 5 4 16 17 21 20 x 0 2 0 8 2 4 2 0 y 0 0 2 0 6 6 0 0 z 0 0 0 0 0 0 2 2 You can see that this is not a correct element Ziming

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reading and writing periodic DMPlex to file
by Berend van Wachem 24 May '23

24 May '23

Dear PETSc team and users, I have asked a few times about this before, but we haven't really gotten this to work yet. In our code, we use the DMPlex framework and are also interested in periodic geometries. As our simulations typically require many time-steps, we would like to be able to save the DM to file and to read it again to resume the simulation (a restart). Although this works for a non-periodic DM, we haven't been able to get this to work for a periodic one. To illustrate this, I have made a working example, consisting of 2 files, createandwrite.c and readandcreate.c. I have attached these 2 working examples. We are using Petsc-3.18.2. In the first file (createandwrite.c) a DMPlex is created and written to a file. Periodicity is activated on lines 52-55 of the code. In the second file (readandcreate.c) a DMPlex is read from the file. When a periodic DM is read, this does not work. Also, trying to 'enforce' periodicity, lines 55 - 66, does not work if the number of processes is larger than 1 - the code "hangs" without producing an error. Could you indicate what I am missing? I have really tried many different options, without finding a solution. Many thanks and kind regards, Berend.

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DMLabel to extract height-0 points by their DMPolytope value
by Ferrand, Jesus A. 24 May '23

24 May '23

Dear PETSc team: I am trying to use DMPlex and DMLabel to develop an API to write plexes to .cgns format in parallel. To that end, I need a way to extract the height-0 points and sort them by topological type (i.e., chunk of tetrahedra, followed by chunk of pyramids, etc.). I figured I could use the DMLabel produced by DMPlexComputeCellTypes() as follows: ** I get the "celltype" DMLabel ** PetscBool has_tetrahedra, has_hexahedra, has_pyramids, has_tri_prisms; PetscCall(DMLabelHasStratum(ctype_label, DM_POLYTOPE_TETRAHEDRON, &has_tetrahedra)); PetscCall(DMLabelHasStratum(ctype_label, DM_POLYTOPE_HEXAHEDRON, &has_hexahedra)); PetscCall(DMLabelHasStratum(ctype_label, DM_POLYTOPE_PYRAMID, &has_pyramids)); PetscCall(DMLabelHasStratum(ctype_label, DM_POLYTOPE_TRI_PRISM, &has_tri_prisms)); PetscInt nTopology = (PetscInt)has_tetrahedra + (PetscInt)has_hexahedra + (PetscInt)has_pyramids + (PetscInt)has_tri_prisms; PetscInt *pType, *vType, *nType; PetscMalloc3(nTopology, &pType, nTopology, &vType, nTopology, &nType); PetscInt counter = -1; if(has_tetrahedra){ counter++; pType[counter] = DM_POLYTOPE_TETRAHEDRON; vType[counter] = 4; PetscCall(DMLabelGetStratumSize(ctype_label, DM_POLYTOPE_TETRAHEDRON, &nType[counter])); } ** Repeat this pattern of if-statement for the rest. ** if(has_tri_prisms) { counter++; pType[counter] = DM_POLYTOPE_TRI_PRISM; vType[counter] = 6; PetscCall(DMLabelGetStratumSize(ctype_label, DM_POLYTOPE_TRI_PRISM, &nType[counter])); } IS pIS; PetscInt StratumIdx; const PetscInt* pPoints; for(PetscInt ii = 0; ii < nTopology; ii++){ PetscCall(DMLabelGetValueIndex(ctype_label, pType[ii], &StratumIdx)); PetscCall(DMLabelGetStratumIS(ctype_label, StratumIdx, &pIS)); PetscCall(ISGetIndices(pIS, &pPoints)); for(PetscInt jj = 0; jj < nType[ii]; jj++){ PetscCall(DMPlexGetTransitiveClosure(dm, pPoints[ii], PETSC_TRUE, &ClosureSize, &pClosure)); ** Assemble connectivity array for each chunk of height-0 topology ** PetscCall(DMPlexRestoreTransitiveClosure(dm, pPoints[ii], PETSC_TRUE, &ClosureSize, &pClosure)); } PetscCall(ISRestoreIndices(pS, &pPoints)); PetscCall(ISDestroy(&pIS)); } PetscFree3(pType, vType, nType); I think, that in principle, this is the correct approach for my immediate objective. However, my problem is that the DAG points returned by pIS through pPoints are outside the height-0 stratum. I can tell because I'm printing the contents of pPoints and comparing againts my DAG's height/depth strata. It is as if the DMLabel has a different numbering from the DAG. Also, for DMLabel's APIs, is the "stratum value" the same thing as the "label value"? My gutt feeling is that the former is 0 <= StratumValue < nStrata, and the latter could be potentially disjoint (e.g., LabelValue in [-1, 0, 3 , 6, 7, 8]). Is that what DMLabelGetValueIndex() is for? Sincerely: J.A. Ferrand Embry-Riddle Aeronautical University - Daytona Beach - FL Ph.D. Candidate, Aerospace Engineering M.Sc. Aerospace Engineering B.Sc. Aerospace Engineering B.Sc. Computational Mathematics Phone: (386)-843-1829 Email(s): ferranj2(a)my.erau.edu jesus.ferrand(a)gmail.com

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