May 2017 - petsc-users - mailman3.cels.anl.gov

When using MatIS, do I need to call MatAssemblyBegin/End between MatISSetLocalMat (local set) and MatISGetMPIXAIJ (get global assembly) ?
by Franck Houssen 31 May '17

31 May '17

When using MatIS, do I need to call MatAssemblyBegin/End between MatISSetLocalMat (local set) and MatISGetMPIXAIJ (get global assembly) ? Franck

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If I use MatISSetLocalMat with a MatCreateSeqAIJ local matrix, do I need to use MatISSetPreallocation for the global matrix ?
by Franck Houssen 31 May '17

31 May '17

If I use MatISSetLocalMat with a preallocated MatCreateSeqAIJ local matrix, do I need to use MatISSetPreallocation for the global matrix ? Here is the pseudo-code: MatCreateIS(PETSC_COMM_WORLD, ..., &globalMat) MatISSetPreallocation(globalMatrix, ...) // Is this necessary ? MatCreateSeqAIJ(PETSC_COMM_SELF, ..., &localMatrix) // Prealloc done on the fly MatSetValues(localMatrix, ...) MatISSetLocalMat(globalMatrix, localMatrix) Is it necessary to call MatISSetPreallocation for globalMatrix ? (prealloc should have been done locally for each local matrix, no ?) Franck

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Installation Error
by 李瑞 31 May '17

31 May '17

Dear professor or engineer: I meet a problem about installation to petsc. When I type the code "./configure --with-cc=gcc --with-cxx=0 --with-fc=0 --download-f2cblaslapack --download-mpich" on my terminal,the answer reveals the following results. >>>ERROR:root:code for hash md5 was not found. Traceback (most recent call last): File "/home/zhuizhuluori/lirui/software/vapor-2.5.0-Linux_x86_64/vapor/vapor-2.5.0/lib/python2.7/hashlib.py", line 139, in <module globals()[__func_name] = __get_hash(__func_name) File "/home/zhuizhuluori/lirui/software/vapor-2.5.0-Linux_x86_64/vapor/vapor-2.5.0/lib/python2.7/hashlib.py", line 91, in __get_builtin_constructor raise ValueError('unsupported hash type ' + name) ValueError: unsupported hash type md5 ERROR:root:code for hash sha1 was not found ..... I have used petsc for a long time,and never see the this problem.my laptop is installed an old version of petsc and I wanna change it to a new version.How can I fix it?Thanks for your heartful suggestion!

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How to VecView with a formatted precision (%10.8f) ?
by Franck Houssen 30 May '17

30 May '17

How to VecView with a formatted precision (%10.8f) ? Not possible ? Franck

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Must I destroy the local matrix I have (created and) set with MatISSetLocalMat ?
by Franck Houssen 30 May '17

30 May '17

Must I destroy the local matrix I have (created and) set with MatISSetLocalMat ? Franck

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Re: [petsc-users] DMPlex export to hdf5/vtk for triangle/prism mesh
by Adrian Croucher 29 May '17

29 May '17

hi, I was asking about support for exactly these 6-node wedge elements in DMPlex back in January. At the time, there was no support for them. Has there been some progress since then? We are going to need them before we can release our software, which we're aiming to do by the end of the year. Cheers, Adrian > Message: 4 > Date: Fri, 26 May 2017 22:40:40 -0500 > From: Matthew Knepley <knepley(a)gmail.com> > To: "Fabian.Jakub" <Fabian.Jakub(a)physik.uni-muenchen.de> > Cc: PETSc <petsc-users(a)mcs.anl.gov> > Subject: Re: [petsc-users] DMPlex export to hdf5/vtk for > triangle/prism mesh > Message-ID: > <CAMYG4GkVOTtFL_OBpUBPGEcBTikMbLOb5ruz=VU7tVTO6JQHTQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Fri, May 26, 2017 at 12:27 PM, Fabian.Jakub < > Fabian.Jakub(a)physik.uni-muenchen.de> wrote: > > > Dear Petsc Team, > > > > I am playing around with DMPlex, using it to generate the Mesh for the > > ICON weather model(http://doi.org/10.1002/2015MS000431), which employs a > > triangle mesh horizontally and columns, vertically. > > > > This results in a grid, looking like prisms, where top and bottom faces > > are triangles and side faces are rectangles. > > > > I was delighted to see that I could export the triangle DMPlex (2d Mesh) > > to hdf5 and use petsc_gen_xdmf.py to then visualize the mesh in > > visit/paraview. > > This is especially nice when exporting petscsections/vectors directly to > > VTK. > > > > Great. > > > > I then tried the same approach for the prism grid in 3D. > > I attached the code for one single cell, as well as the output in hdf5. > > > > However, trying to convert the hdf5 output, it fails with: > > > > make prism.xmf > > > > $PETSC_DIR/bin/petsc_gen_xdmf.py prism.h5 > > Traceback (most recent call last): > > File > > "/software/meteo/xenial/x86_64/petsc/master/debug_gcc/..// > > bin/petsc_gen_xdmf.py", > > line 241, in <module> > > generateXdmf(f) > > File > > "/software/meteo/xenial/x86_64/petsc/master/debug_gcc/..// > > bin/petsc_gen_xdmf.py", > > line 235, in generateXdmf > > Xdmf(xdmfFilename).write(hdfFilename, topoPath, numCells, > > numCorners, cellDim, geomPath, numVertices, spaceDim, time, vfields, > > cfields) > > File > > "/software/meteo/xenial/x86_64/petsc/master/debug_gcc/..// > > bin/petsc_gen_xdmf.py", > > line 193, in write > > self.writeSpaceGridHeader(fp, numCells, numCorners, cellDim, spaceDim) > > File > > "/software/meteo/xenial/x86_64/petsc/master/debug_gcc/..// > > bin/petsc_gen_xdmf.py", > > line 75, in writeSpaceGridHeader > > ''' % (self.cellMap[cellDim][numCorners], numCells, "XYZ" if > > spaceDim > 2 else "XY")) > > KeyError: 6 > > > > > > Also, if I try to export a vector directly to vtk, visit and paraview > > fail to open it. > > > > My question is: > > Is this a general limitation of these output formats, that I can not mix > > faces with 3 and 4 vertices or is it a limitation of the > > petsc_gen_xdmf.py or the VTK Viewer. > > > > petsc_gen_xdmf. Take a look here > > > https://bitbucket.org/petsc/petsc/src/1731673c3fe570066779d46b51a4aee7a4577… > > This is what fails. You need to add something like > > 6: "Wedge" > > in the dictionary. See http://www.xdmf.org/index.php/XDMF_Model_and_Format > > > > I'd also welcome any thoughts on the prism mesh in general. > > Is it that uncommon to use and do you foresee other complications with it? > > > > You need an element that works with prisms, but it seems you already have > one. I know > there is good work from here: https://arxiv.org/abs/1411.2940 > > > > I fear I cannot change the discretization of the host model but maybe it > > makes sense to use a different grid for my radiative transfer code? > > > > I do not really do RT, but would be happy to try and think about it. > > Thanks, > > Matt > > > > Many thanks, > > > > > > Fabian > > > -- Dr Adrian Croucher Senior Research Fellow Department of Engineering Science University of Auckland, New Zealand email: a.croucher(a)auckland.ac.nz tel: +64 (0)9 923 4611

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a question about PetscSectionCreate
by leejearl 29 May '17

29 May '17

Hi, Dave: I want to store a PetscInt tag for every cell of the dmplex with the struct. Thanks, leejearl >>/Hi, Dave: />/ > Thank you for your kind reply. If I want to store a mixture of />/PetscReal and PetscInt, how can I do it? / >What operations do you need to perform with your struct? >>//>/ > Thanks, />/ > leejearl />>//>>

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Can't retrieve inner KSP from Schur complement
by Lucas Clemente Vella 29 May '17

29 May '17

I want to set a custom convergence test for the inner KSPs of Schur complement method, so I am using PCFieldSplitGetSubKSP() to get the inner KSPs: int n_subksp; KSP *subksp = NULL; PCFieldSplitGetSubKSP(s->pc, &n_subksp, &subksp); assert(n_subksp == 2); But I get a segmentation fault on MatSchurComplementGetKSP(). From file src/ksp/ksp/utils/schurm.c (line 320): PetscErrorCode MatSchurComplementGetKSP(Mat S, KSP *ksp) { Mat_SchurComplement *Na; PetscFunctionBegin; PetscValidHeaderSpecific(S,MAT_CLASSID,1); PetscValidPointer(ksp,2); Na = (Mat_SchurComplement*) S->data; *ksp = Na->ksp; // <<<<< segfaults on this line, 'Na' is an invalid pointer... PetscFunctionReturn(0); } This is the stack trace given by valgrind: ==13559== Invalid read of size 8 ==13559== at 0x56B8780: MatSchurComplementGetKSP (schurm.c:320) ==13559== by 0x55F5B08: PCFieldSplitGetSubKSP_FieldSplit_Schur(_p_PC*, int*, _p_KSP***) (fieldsplit.c:1367) ==13559== by 0x5605187: PCFieldSplitGetSubKSP (fieldsplit.c:1869) ==13559== by 0x166305: set_singular_convergence_test (solver-petsc.c:293) ### irrelevant calls, from inside my program ==13559== Address 0x6c0 is not stack'd, malloc'd or (recently) free'd ==13559== I tried doing this operation both before and after MatAssembly*() calls, and with both I get the same result. Petsc version is 3.7.5, installed from Ubuntu repository. Is this a bug? Or I am doing it wrong? -- Lucas Clemente Vella lvella(a)gmail.com

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petsc4py and python's logging module
by David Nolte 29 May '17

29 May '17

Dear all, is it possible to use python's logging module (https://docs.python.org/2/howto/logging.html) to handle PETSc output in python, such as the residuals during a KSP/SNES solve? I log my solver's activity to a file using the logging module, it would be great to include the PETSc output aswell. Regards, David

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Errors about PETSc MPI+GPU
by Xinzhe Wu 29 May '17

29 May '17

Dear all, We have developed the codes with PETSc + SLEPc which works well on CPU version. Now we want to try these codes with GPU + MPI, but get some weird errors shown as below. I have found someone talked about this problem here http://lists.mcs.anl.gov/pipermail/petsc-dev/2016-March/018836.html , but I can hardly understand it. Can anyone help me with these issues? Thank you in advance! [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Error in external library [0]PETSC ERROR: CUBLAS error 1 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: [2]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [2]PETSC ERROR: Error in external library [2]PETSC ERROR: CUBLAS error 1 [2]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [2]PETSC ERROR: Petsc Development GIT revision: v3.7.6-3965-gf375733 GIT Date: 2017-05-28 10:32:02 -0500 [2]PETSC ERROR: ./hyperh on a arch-linux2-c-debug named romeo44 by xinzhewu Mon May 29 18:03:58 2017 [2]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-fblaslapack --with-visibility=0 --with-shared-libraries=0 --with-cuda=1 --with-thrust=1 --with-precision=double --with-clanguage=c --with-pestc-arch=linux-c-no-debug-complex --with-scalar-type=complex [2]PETSC ERROR: #1 PetscInitialize() line 906 in /home/xinzhewu/Petsc-GPUs/petsc/src/sys/objects/pinit.c [2]PETSC ERROR: #2 SlepcInitialize() line 259 in /home/xinzhewu/Petsc-GPUs/slepc/src/sys/slepcinit.c -- Xinzhe WU Ph.D Student of Computer Science Maison de la Simulation, CNRS USR3441 Building 565, CEA Saclay 91191, Gif-sur-Yvette, France Tel: +33 (0) 1 69 08 59 93

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