Re: [petsc-users] DMPlexCreateExodusFromFile() does not work on macOS Sierra

Thanks, Blaise and Matt, I possibly mess up the brew installation somehow. I will clean up everything and start over, and report back. Fande, On Tue, Jan 24, 2017 at 9:26 AM, Matthew Knepley wrote: > Thanks! > >Matt > > On Tue, Jan 24, 2017 at 8:57 AM, Blaise A Bourdin

[petsc-users] consider an error message as a petscinfo??

Hi All, In MatSolve(), there is a piece of code: * if (mat->errortype) {ierr = PetscInfo1(mat,"MatFactorError %D\n",mat->errortype);CHKERRQ(ierr);ierr = VecSetInf(x);CHKERRQ(ierr); } else {ierr = (*mat->ops->solve)(mat,b,x);CHKERRQ(ierr); }* If a direct solver such as LU or

Re: [petsc-users] consider an error message as a petscinfo??

these > "exceptional cases" directly. > >Note that you can use options like -snes_error_if_not_converged or > -ksp_error_if_not_converged to force the error to be set as soon as any > problem with convergence or zero factorization is found (good for > debugging, but not usually for production

[petsc-users] lock matrices in EPS

Hi ALL, I am solving a generalized eigenvalue problem Ax=\lambda Bx. I want to retrieve matrices A and B from EPS, but got the following errors: [0]PETSC ERROR: No support for this operation for this object type [0]PETSC ERROR: Cannot retrieve original matrices (have been modified) [0]PETSC

Re: [petsc-users] SuperLU_dist issue in 3.7.4

On Fri, Oct 7, 2016 at 9:04 AM, Satish Balay wrote: > On Fri, 7 Oct 2016, Anton Popov wrote: > > > Hi guys, > > > > are there any news about fixing buggy behavior of SuperLU_DIST, exactly > what > > is described here: > > > >

Re: [petsc-users] How to solve the pressure possion equations with four neuman bc

Any references on this topic except the users manual? I am interested in mathematics theory on this topic. Fande Kong, On Fri, Sep 23, 2016 at 9:58 AM, Jed Brown wrote: > 丁老师 writes: > > > Dear friends: > > In the projection method for the solution

Re: [petsc-users] Matrix is missing diagonal entry

e, Oct 18, 2016 at 10:11 AM, Kong, Fande <fande.k...@inl.gov> wrote: > >> Hi Developers, >> >> Any reason to force users provide a matrix which does not miss any >> diagonal entries when using a LU-type solver? >> >> Sometime, it is impossible to have a

[petsc-users] Matrix is missing diagonal entry

Hi Developers, Any reason to force users provide a matrix which does not miss any diagonal entries when using a LU-type solver? Sometime, it is impossible to have all diagonal entries in a matrix, that is, the matrix has to miss some diagonal entries. For example, there is a saddle-point matrix

[petsc-users] matrix preallocation

Hi, For mechanics problems, the contact surface changes during each nonlinear iteration. Therefore, the sparsity of matrix also changes during each nonlinear iteration. We know the preallocaiton is important for performance. My question is: it is possible to re-allocate memory during each

Re: [petsc-users] SuperLU_dist issue in 3.7.4 failure of repeated calls to MatLoad() or MatMPIAIJSetPreallocation() with the same matrix

On Sun, Oct 23, 2016 at 3:56 PM, Barry Smith wrote: > >Thanks Satish, > > I have fixed this in barry/fix-matmpixxxsetpreallocation-reentrant > (in next for testing) > > Fande, > > This will also make MatMPIAIJSetPreallocation() work properly with >

Re: [petsc-users] SuperLU_dist issue in 3.7.4 failure of repeated calls to MatLoad() or MatMPIAIJSetPreallocation() with the same matrix

On Mon, Oct 24, 2016 at 8:07 AM, Kong, Fande <fande.k...@inl.gov> wrote: > > > On Sun, Oct 23, 2016 at 3:56 PM, Barry Smith <bsm...@mcs.anl.gov> wrote: > >> >>Thanks Satish, >> >> I have fixed this in barry/fix-matmpixxxsetpreallocation-re

Re: [petsc-users] question

If you are using the matrix-free method, the number of function evaluations is way more than the number of Newton iterations. Fande, On Mon, Oct 24, 2016 at 2:01 PM, Justin Chang wrote: > Sorry forgot to hit reply all > > On Monday, October 24, 2016, Justin Chang

Re: [petsc-users] question

Using -snes_linesearch_type basic to turn off the line search, you will see that the number of function evaluations is the same as the number of Newton iterations. Fande, On Mon, Oct 24, 2016 at 2:13 PM, Gideon Simpson wrote: > I just mean that if I were working

Re: [petsc-users] GAMG

On Mon, Oct 31, 2016 at 8:44 AM, Jed Brown wrote: > Jeremy Theler writes: > > > Hi again > > > > I have been wokring on these issues. Long story short: it is about the > > ordering of the unknown fields in the vector. > > > > Long story: > > The physics

Re: [petsc-users] Algorithms to remove null spaces in a singular system

Barry, Thanks so much for your explanation. It helps me a lot. On Mon, Oct 10, 2016 at 4:00 PM, Barry Smith <bsm...@mcs.anl.gov> wrote: > > > On Oct 10, 2016, at 4:01 PM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > Hi All, > > > > I know how to

Re: [petsc-users] Algorithms to remove null spaces in a singular system

On Tue, Oct 11, 2016 at 10:39 AM, Barry Smith <bsm...@mcs.anl.gov> wrote: > > > On Oct 11, 2016, at 9:33 AM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > Barry, Thanks so much for your explanation. It helps me a lot. > > > > On Mon, Oct 10, 201

Re: [petsc-users] Algorithms to remove null spaces in a singular system

> resulting file called binaryoutput. > >I need a test matrix to update the PETSc code for this case. > > > Barry > > > On Oct 11, 2016, at 3:04 PM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > > > > > On Tue, Oct 11, 2016 at 12:18 PM,

Re: [petsc-users] Algorithms to remove null spaces in a singular system

On Tue, Oct 11, 2016 at 12:18 PM, Barry Smith <bsm...@mcs.anl.gov> wrote: > > > On Oct 11, 2016, at 12:01 PM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > > > > > On Tue, Oct 11, 2016 at 10:39 AM, Barry Smith <bsm...@mcs.anl.gov> > wro

Re: [petsc-users] Algorithms to remove null spaces in a singular system

On Wed, Oct 12, 2016 at 10:21 PM, Jed Brown wrote: > Barry Smith writes: > > I would make that a separate routine that the users would call first. > > We have VecMDot and VecMAXPY. I would propose adding > > VecQR(PetscInt nvecs,Vec *vecs,PetscScalar

Re: [petsc-users] Algorithms to remove null spaces in a singular system

olutions to this issue? Fande Kong, On Thu, Oct 13, 2016 at 8:23 AM, Matthew Knepley <knep...@gmail.com> wrote: > On Thu, Oct 13, 2016 at 9:06 AM, Kong, Fande <fande.k...@inl.gov> wrote: > >> >> >> On Wed, Oct 12, 2016 at 10:21 PM, Jed Brown <j.

Re: [petsc-users] Algorithms to remove null spaces in a singular system

diagonal scaling we cannot apply the inverse of the > preconditioner to a vector and thus cannot compute the nullspace(AB). > -- > > Any feed back on the correctness or clarity of the material is > appreciated. The punch line is that right preconditioning cannot be trusted

Re: [petsc-users] Algorithms to remove null spaces in a singular system

to contribute something like this latter (of course, if you are ok with this algorithm), when we are moving to nonlinear problems in our applications. Fande Kong, > > Barry > > > > On Oct 13, 2016, at 5:20 PM, Kong, Fande <fande.k...@inl.gov> wrote: > >

[petsc-users] superlu_dist issue

Hi All, I think we have been discussing this topic for a while in other threads. But I still did not get yet. PETSc uses 'SamePattern' as the default FactPattern. Some test cases in MOOSE fail with this default option, but I can make these tests pass if I set the FactPattern as

Re: [petsc-users] PetscTableCreateHashSize

Thanks a lot Satish! Like Jed said, it would be better if we could come up an algorithm for automatically computing a hash size for a given n. Otherwise, we may need to add more entries to the lookup again in the future. Fande, On Mon, Jan 9, 2017 at 2:14 PM, Satish Balay

Re: [petsc-users] PetscTableCreateHashSize

BTW, one more question: There are some pieces of code in #if defined(PETSC_USE_CTABLE) #endif. How to disable ctable? That is, make PETSC_USE_CTABLE false during configuration. Fande, On Tue, Jan 10, 2017 at 12:33 AM, Jed Brown wrote: > Satish Balay

[petsc-users] PetscTableCreateHashSize

Hi All, Hash size is set manually according to the number of expected keys in the function PetscTableCreateHashSize(). Any reason to restrict the ``n"<3276800? One user here encountered an issue because of this restriction. The messages are as follows: [3]PETSC ERROR: -

Re: [petsc-users] PetscTableCreateHashSize

>else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"A really huge > hash is being requested.. cannot process: %D",sz); >PetscFunctionReturn(0); > } > > On Mon, 9 Jan 2017, Kong, Fande wrote: > > > Hi All, > > > > Hash size is set manually

Re: [petsc-users] coloring algorithms

, and it is from a grain-tracking thing. Distance 1 did magic work. We have 8 colors now using JP, power,.. Thanks. Fande, > > > > On Mar 23, 2017, at 4:57 PM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > Thanks, Hong, > > > > I did some tests with a matri

Re: [petsc-users] coloring algorithms

Thanks, Hong, I did some tests with a matrix (40x40): *row 0: (0, 1.) (2, 1.) (3, 1.) (11, 1.) (14, 1.) (15, 1.) (19, 1.) (22, 1.) (23, 1.) (24, 1.) (27, 1.) (28, 1.) row 1: (1, 1.) (2, 1.) (3, 1.) (6, 1.) (16, 1.) (17, 1.) (18, 1.) (21, 1.)

[petsc-users] coloring algorithms

Hi All, I was wondering if the coloring approaches listed online are working? Which ones are in parallel, and which ones are in sequential? http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatColoringType.html#MatColoringType If the coloring is in parallel, can it be used with

Re: [petsc-users] GAMG for the unsymmetrical matrix

You are also calling the AMG setup a lot, but not spending much time > in it. Try running with -info and grep on "GAMG". > > > On Fri, Apr 7, 2017 at 5:29 PM, Kong, Fande <fande.k...@inl.gov> wrote: > > Thanks, Barry. > > > > It works. > >

[petsc-users] GAMG for the unsymmetrical matrix

Hi All, I am using GAMG to solve a group of coupled diffusion equations, but the resulting matrix is not symmetrical. I got the following error messages: *[0]PETSC ERROR: Petsc has generated inconsistent data[0]PETSC ERROR: Have un-symmetric graph (apparently). Use

Re: [petsc-users] GAMG for the unsymmetrical matrix

I will try. > > Note, you should not see much degradation as you increase the number of > levels. 18145 eqs on a 3D problem will probably be noticeable. I generally > aim for about 3000. > It should be fine as long as the coarse problem is solved by a parallel solver. Fande, > >

Re: [petsc-users] GAMG for the unsymmetrical matrix

Thanks, Mark and Barry, It works pretty wells in terms of the number of linear iterations (using "-pc_gamg_sym_graph true"), but it is horrible in the compute time. I am using the two-level method via "-pc_mg_levels 2". The reason why the compute time is larger than other preconditioning options

[petsc-users] EPSViewer in SLEPc

Hi All, The EPSViewer in SLEPc looks weird. I do not understand the viewer logic. For example there is a piece of code in SLEPc (at line 225 of epsview.c): *if (!ispower) { if (!eps->ds) { ierr = EPSGetDS(eps,>ds);CHKERRQ(ierr); } ierr = DSView(eps->ds,viewer);CHKERRQ(ierr);

Re: [petsc-users] GAMG for the unsymmetrical matrix

4 4 1 4 1 4 4 1 4 51328 GAMG: createProl 40 1.0 8.3786e+01 1.0 4.56e+09 2.3 9.6e+06 2.5e+04 4.8e+03 21 42 12 32 10 21 42 12 32 10 14134 GAMG: partLevel 40 1.0 6.7755e+00 1.1 2.59e+08 2.3 2.9e+06 2.5e+03 1.5e+03 2 2 4 1 3 2 2 4 1 3 9431 > > >

Re: [petsc-users] GAMG for the unsymmetrical matrix

e: > > > On Wed, Apr 12, 2017 at 7:04 PM, Kong, Fande <fande.k...@inl.gov> wrote: > >> >> >> On Sun, Apr 9, 2017 at 6:04 AM, Mark Adams <mfad...@lbl.gov> wrote: >> >>> You seem to have two levels here and 3M eqs on the fine grid and 37 on &

[petsc-users] CG with right preconditioning supports NONE norm type only

Hi All, The NONE norm type is supported only when CG is used with a right preconditioner. Any reason for this? *0 Nonlinear |R| = 1.732051e+00 0 Linear |R| = 0.00e+00 1 Linear |R| = 0.00e+00

Re: [petsc-users] CG with right preconditioning supports NONE norm type only

ditioning. > > Barry > > > On Mar 8, 2017, at 10:26 AM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > Hi All, > > > > The NONE norm type is supported only when CG is used with a right > preconditioner. Any reason for this? > > > > > >

Re: [petsc-users] block ILU(K) is slower than the point-wise version?

> > On Mar 7, 2017, at 2:26 PM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > Uploaded to google drive, and sent you links in another email. Not sure > if it works or not. > > > > Fande, > > > > On Tue, Mar 7, 2017 at 12:29 PM, Barry Sm

Re: [petsc-users] block ILU(K) is slower than the point-wise version?

> Thanks. Even the symbolic is slower for BAIJ. I don't like that, it > definitely should not be since it is (at least should be) doing a symbolic > factorization on a symbolic matrix 1/11th the size! > > > >Keep us informed. > > > > > > > > > On Mar

Re: [petsc-users] CG with right preconditioning supports NONE norm type only

7, at 10:33 AM, Barry Smith <bsm...@mcs.anl.gov> wrote: > > > > > > Please tell us how you got this output. > > > > PETSc CG doesn't even implement right preconditioning. If you ask for > it it should error out. CG supports no norm computation with left

[petsc-users] KSPNormType natural

Hi All, What is the definition of KSPNormType natural? It is easy to understand none, preconditioned, and unpreconditioned, but not natural. Fande Kong,

[petsc-users] block ILU(K) is slower than the point-wise version?

Hi All, I am solving a nonlinear system whose Jacobian matrix has a block structure. More precisely, there is a mesh, and for each vertex there are 11 variables associated with it. I am using BAIJ. I thought block ILU(k) should be more efficient than the point-wise ILU(k). After some numerical

Re: [petsc-users] block ILU(K) is slower than the point-wise version?

On Mon, Mar 6, 2017 at 3:27 PM, Patrick Sanan <patrick.sa...@gmail.com> wrote: > On Mon, Mar 6, 2017 at 1:48 PM, Kong, Fande <fande.k...@inl.gov> wrote: > > Hi All, > > > > I am solving a nonlinear system whose Jacobian matrix has a block > structure.

Re: [petsc-users] block ILU(K) is slower than the point-wise version?

lve_SeqBAIJ_11_NaturalOrdering_ver1; > > } else { > >C->ops->solve = MatSolve_SeqBAIJ_N_NaturalOrdering; > > } > > > > Rerun and look at the new -log_view. Send all three -log_view to use > at this point. If this optimization helps and now > > Mat

Re: [petsc-users] block ILU(K) is slower than the point-wise version?

9:08 PM, Barry Smith <bsm...@mcs.anl.gov> wrote: > >> >> Thanks. Even the symbolic is slower for BAIJ. I don't like that, it >> definitely should not be since it is (at least should be) doing a symbolic >> factorization on a symbolic matrix 1/11th the size! >>

Re: [petsc-users] block ILU(K) is slower than the point-wise version?

I found one issue on my side. The preallocation is not right for the BAIJ matrix. Will this slow down MatLUFactor and MatSolve? How to converge AIJ to BAIJ using a command-line option? Fande, On Tue, Mar 7, 2017 at 3:26 PM, Jed Brown <j...@jedbrown.org> wrote: > "Kong, F

Re: [petsc-users] block ILU(K) is slower than the point-wise version?

t; MatLUFactorNum 1 1.0 6.0118e-02 1.0 2.55e+08 1.0 0.0e+00 0.0e+00 > > 0.0e+00 42 89 0 0 0 72 89 0 0 0 4241 > > MatILUFactorSym1 1.0 6.7251e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > > 0.0e+00 5 0 0 0 0 8 0 0 0 0 0 > > > &g

Re: [petsc-users] GAMG for the unsymmetrical matrix

gov> wrote: > > > On Apr 6, 2017, at 9:39 AM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > Thanks, Mark and Barry, > > > > It works pretty wells in terms of the number of linear iterations (using > "-pc_gamg_sym_graph true"), but it is horrible

Re: [petsc-users] EPSViewer in SLEPc

Thanks, Jose Fande, On Fri, Apr 7, 2017 at 4:41 AM, Jose E. Roman <jro...@dsic.upv.es> wrote: > I have pushed a commit that should avoid this problem. > Jose > > > El 6 abr 2017, a las 22:27, Kong, Fande <fande.k...@inl.gov> escribió: > > > > Hi All, >

Re: [petsc-users] GAMG for the unsymmetrical matrix

On Fri, Apr 7, 2017 at 3:52 PM, Barry Smith <bsm...@mcs.anl.gov> wrote: > > > On Apr 7, 2017, at 4:46 PM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > > > > > On Fri, Apr 7, 2017 at 3:39 PM, Barry Smith <bsm...@mcs.anl.gov> wrote: &

Re: [petsc-users] misleading "mpich" messages

Thanks, Barry and Satish, It makes sense. Fande, On Tue, Apr 25, 2017 at 4:33 PM, Barry Smith <bsm...@mcs.anl.gov> wrote: > > > On Apr 25, 2017, at 5:08 PM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > Thanks, Satish, > > > > One more que

Re: [petsc-users] misleading "mpich" messages

message. Looks possible for me. Fande, > > Barry > > > > On Apr 25, 2017, at 4:35 PM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > Hi, > > > > We configured PETSc with a version of MVAPICH, and complied with another > version of MVAPICH. Got th

Re: [petsc-users] misleading "mpich" messages

replaces it with MVAPICH2_NUMVERSION > > > > Satish > > > > On Tue, 25 Apr 2017, Kong, Fande wrote: > > > > > On Tue, Apr 25, 2017 at 3:42 PM, Barry Smith <bsm...@mcs.anl.gov> > wrote: > > > > > > > > > > >The error mes

[petsc-users] misleading "mpich" messages

Hi, We configured PETSc with a version of MVAPICH, and complied with another version of MVAPICH. Got the error messages: *error "PETSc was configured with one MPICH mpi.h version but now appears to be compiling using a different MPICH mpi.h version"* Why we could not say something about

[petsc-users] EPS monitor

Hi All, How to understand the following messages: 1 EPS nconv=0 first unconverged value (error) 2.06312 (3.29164033e-01) 2 EPS nconv=0 first unconverged value (error) 2.03951 (1.76223074e-01) 3 EPS nconv=0 first unconverged value (error) 2.01177 (5.71109559e-02) 4 EPS nconv=0 first

Re: [petsc-users] EPS monitor

wrote: > > > El 16 ago 2017, a las 21:36, Kong, Fande <fande.k...@inl.gov> escribió: > > > > Hi All, > > > > How to understand the following messages: > > > > 1 EPS nconv=0 first unconverged value (error) 2.06312 (3.29164033e-01) > > 2 E

[petsc-users] log_view for the master branch

Hi, I am using the current master branch. The log_view gives me the summary as follows, and the "WARNING" box repeats three times. Are we intending to do so? Thanks, Fande,

Re: [petsc-users] slepc trap for large matrix

On Wed, Jun 7, 2017 at 8:37 AM, Kannan, Ramakrishnan wrote: > Barry, > > Thanks for the kind response. I am building slepc 3.7.3 and when I > configure –with-64-bit-indices=1, I am getting the following error. > > ./configure --with-64-bit-indices=1 --prefix=/lustre/atlas/proj-

Re: [petsc-users] SNES ex12 visualization

On Thu, Sep 14, 2017 at 10:35 AM, Barry Smith <bsm...@mcs.anl.gov> wrote: > > > On Sep 14, 2017, at 11:10 AM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > > > > > On Thu, Sep 14, 2017 at 9:47 AM, Matthew Knepley <knep...@gmail.com> > wrote

Re: [petsc-users] SNES ex12 visualization

On Thu, Sep 14, 2017 at 9:47 AM, Matthew Knepley wrote: > On Thu, Sep 14, 2017 at 11:43 AM, Adriano Côrtes > wrote: > >> Dear Matthew, >> >> Thank you for your return. It worked, but this prompts another question. >> So why PetscViewer does not write

Re: [petsc-users] SNES ex12 visualization

On Thu, Sep 14, 2017 at 11:26 AM, Matthew Knepley <knep...@gmail.com> wrote: > On Thu, Sep 14, 2017 at 1:07 PM, Kong, Fande <fande.k...@inl.gov> wrote: > >> >> >> On Thu, Sep 14, 2017 at 10:35 AM, Barry Smith <bsm...@mcs.anl.gov> wrote: >> >

Re: [petsc-users] Can not configure PETSc-master with clang-3.9

lers do not. > > > > Basically xcode clang can pick up includes from the xcode specific > > location - but other tools look for includes in /usr/incldue > > > > And 'xcode-select --install' adds the /usr/include etc links. > > > > Satish > > > &

Re: [petsc-users] Can not configure PETSc-master with clang-3.9

hard > > On Mon, Oct 16, 2017 at 9:52 AM, Jed Brown <j...@jedbrown.org> wrote: > >> "Kong, Fande" <fande.k...@inl.gov> writes: >> >> > Hi All, >> > >> > I just upgraded MAC OS, and also updated all other related packages. >

Re: [petsc-users] Using higher order ILU preconditioner

Calling PCFactorSetMatOrderingType() (or command line option: -pc_factor_mat_ordering_type) to use RCM or 1WD usually helps me a lot. My application is based on highly-unstructured meshes. Fande, On Thu, Sep 28, 2017 at 2:53 PM, Rachit Prasad wrote: > Hi, > > I am trying to

[petsc-users] superlu_dist produces random results

Hi, There is a heat conduction problem. When superlu_dist is used as a preconditioner, we have random results from different runs. Is there a random algorithm in superlu_dist? If we use ASM or MUMPS as the preconditioner, we then don't have this issue. run 1: 0 Nonlinear |R| = 9.447423e+03

Re: [petsc-users] superlu_dist produces random results

= 9.447423e+03 1 Linear |R| = 1.360637e-11 1 Nonlinear |R| = 1.654334e-11 > > Barry > > > > On Nov 15, 2017, at 4:24 PM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > > > > > On Wed, Nov 15, 2017 at 2:52 PM, Smith, Barry F. <bsm...@m

Re: [petsc-users] superlu_dist produces random results

to superlu_dist. Fande, On Wed, Nov 15, 2017 at 1:59 PM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote: > > Meaningless differences > > > > On Nov 15, 2017, at 2:26 PM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > Hi, > > > > There i

Re: [petsc-users] superlu_dist produces random results

different "physical results"? > Let me update a little bit more. The simulation with SuperLU may fail at certain time step. Sometime we can also run the simulation successfully for the whole time range. It is totally random. We will try ASM and MUMPS. Fande, > > Barry &

Re: [petsc-users] superlu_dist produces random results

On Wed, Nov 15, 2017 at 2:52 PM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote: > > > > On Nov 15, 2017, at 3:36 PM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > Hi Barry, > > > > Thanks for your reply. I was wondering why this happens only when

Re: [petsc-users] segfault after recent scientific linux upgrade

On Thu, Dec 7, 2017 at 8:15 AM, Klaij, Christiaan wrote: > Satish, > > > > As a first try, I've kept petsc-3.7.5 and only replaced superlu > > by the new xsdk-0.2.0-rc1 version. Unfortunately, this doesn't > > fix the problem, see the backtrace below. > > > > Fande, > > > >

Re: [petsc-users] configuration error

We had exactly the same issue when upgraded compilers. I guess this is somehow related to gfortran. A simple way to work around for us is to change* if with_rpath*: to * if False *at line 54 of config/BuildSystem/config/libraries.py. Not sure if it works for you. Fande, On Mon, Oct 30,

[petsc-users] "Must select a target sorting criterion if using shift-and-invert"

Hi All, I am trying to solve a generalized eigenvalue problem (using SLEPc) with "-eps_type krylovschur -st_type sinvert". I got an error message: "Must select a target sorting criterion if using shift-and-invert". Not sure how to proceed. I do not quite understand this sentence. Fande,

[petsc-users] "snes_type test" is gone?

Hi PETSc Team, I was wondering if "snes_type test" has been gone? Quite a few MOOSE users use this option to test their Jacobian matrices. If it is gone, any reason? Fande,

Re: [petsc-users] "snes_type test" is gone?

snes_test_jacobian > instead. Note that the test is done every time the Jacobian is computed. > > It was meant to be "-snes_type test". > > > Hong (Mr.) > > > >> On Jun 4, 2018, at 3:27 PM, Kong, Fande wrote: > >> > >> Hi PETSc T

Re: [petsc-users] Could not determine how to create a shared library!

stions wrt theta builds. >> >> Satish >> >> On Thu, 3 May 2018, Satish Balay wrote: >> >> > Perhaps you should use MKL on theta? Again check >> config/examples/arch-cray-xc40-knl-opt.py >> > >> > Satish >> > >> > On Th

Re: [petsc-users] Context behind SNESComputeFunction call

On Fri, Jan 26, 2018 at 3:10 PM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote: > > > > On Jan 26, 2018, at 2:15 PM, Kong, Fande <fande.k...@inl.gov> wrote: > > > > > > > > On Mon, Jan 8, 2018 at 2:15 PM, Smith, Barry F. <bsm...@mcs.anl.gov

Re: [petsc-users] Context behind SNESComputeFunction call

Are you not just using -snes_mf > or -snes_mf_operator? Can you send me a sample code that has the extra > function evaluations? Because if you run through regular usage with the > debugger you will see there is no extra evaluation. > >Barry > > > > On Jan 26, 2018,

[petsc-users] How to generate manul.pdf from source files

Hi, I want to generate manul.pdf from source files on my own desktop. In directory: ./src/docs/tex/manual make ALL LOC=/Users/kongf/projects/petsc * make: *** No rule to make target `/Users/kongf/projects/petsc/docs/manualpages/htmlmap', needed by `listing_kspex1tmp.tex'. Stop.* What else

Re: [petsc-users] How to generate manul.pdf from source files

Jan 27, 2018 at 10:53 AM, Kong, Fande <fande.k...@inl.gov> wrote: > >> Hi, >> >> I want to generate manul.pdf from source files on my own desktop. >> >> In directory: ./src/docs/tex/manual >> >> make ALL LOC=/Users/kongf/projects/petsc >

Re: [petsc-users] with-openmp error with hypre

Curious about the comparison of 16x4 VS 64. Fande, On Tue, Feb 13, 2018 at 11:44 AM, Bakytzhan Kallemov wrote: > Hi, > > I am not sure about 64 flat run, > > unfortunately I did not save logs since it's easy to run, but for 16 - > here is the plot I got for different number

Re: [petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"

rkhome/projects/petsc-3.7.7/arch-linux2-c-opt- > 64bit/externalpackages/git.hypre > git rev-parse --git-dir > echo $? > git fsck > > If this works - you can rerun configure and see if the error persists > > Satish > > > On Wed, 7 Mar 2018, Kong, Fande wrote: > > > Hi PETSc team: > > > > What is the possible reason for this? > > > > The log file is attached. > > > > > > Fande, > > > >

Re: [petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"

On Wed, Mar 7, 2018 at 2:51 PM, Satish Balay <ba...@mcs.anl.gov> wrote: > On Wed, 7 Mar 2018, Kong, Fande wrote: > > > > If you need to workarround this - you can comment out that test > (3lines).. > > > > > > File "/home/kongf/workhome/projec

Re: [petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"

Command([self.sourceControl.git, > 'rev-parse','--git-dir'], cwd=self.packageDir, log = self.log) > > "#self.updateGitDir()" works. I still do not understand why. Fande, > > Satish > > On Wed, 7 Mar 2018, Kong, Fande wrote: > > > [kongf@falcon1 git.h

Re: [petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"

;ba...@mcs.anl.gov> wrote: > On Wed, 7 Mar 2018, Kong, Fande wrote: > > > > I meant just the 3 lines - not the whole function. > > > > I knew this. "3 lines" does not work at all. > > > > I forgot the error message. > > Then you are likely to

Re: [petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"

moose]$ uname -a Linux falcon1 3.0.101-108.13-default #1 SMP Wed Oct 11 12:30:40 UTC 2017 (294ccfe) x86_64 x86_64 x86_64 GNU/Linux moose]$ lsb_release -a LSB Version:

Re: [petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"

1 or falcon2 does it still fail? > > module load git/2.16.2-GCCcore-5.4.0 > > Thanks, > Cormac. > > > > On Wed, Apr 4, 2018 at 4:28 PM, Kong, Fande <fande.k...@inl.gov> wrote: > >> Hi Cormac, >> >> Do you know anything on "git"?

Re: [petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"

On Wed, Apr 4, 2018 at 3:55 PM, Jed Brown <j...@jedbrown.org> wrote: > "Kong, Fande" <fande.k...@inl.gov> writes: > > > Updated: > > > > If switch to a different version of git. The configuration is going to > > work. > > > > >

Re: [petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"

module load git/2.16.2-GCCcore-5.4.0" also works. Could you somehow make the default git work as well? Hence we do not need to have this extra "module load for git" Fande, On Wed, Apr 4, 2018 at 4:43 PM, Kong, Fande <fande.k...@inl.gov> wrote: > Thanks, Cormac, >

Re: [petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"

[i.e old glibc etc..] - and > this new git version [binary built locally or on a different OS and > installed locally ?]. > > Satish > > On Wed, 4 Apr 2018, Kong, Fande wrote: > > > moose]$ uname -a > > Linux falcon1 3.0.101-108.13-default #1 SMP Wed Oct 11 12:3

Re: [petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"

iguring PETSc. >> >> The manually loaded *gits* work just fine. >> >> >> Fande, >> >> >> On Wed, Apr 4, 2018 at 5:04 PM, Garvey, Cormac T <cormac.gar...@inl.gov> >> wrote: >> >>> I though it was fixed, yes I will look into it again.

Re: [petsc-users] A bad commit affects MOOSE

at ? MAT_REUSE_MATRIX : > MAT_INITIAL_MATRIX,>hpmat);CHKERRQ(ierr); > >} else { > > ierr = PetscObjectReference((PetscObject)pc->pmat);CHKERRQ(ierr); > > ierr = MatDestroy(>hpmat);CHKERRQ(ierr); > > > > 2018-04-02 23:46 GMT+02:00 Kong

Re: [petsc-users] A bad commit affects MOOSE

Why we can not use MPI_COMM_WORLD? Fande, > > Satish > > > On Mon, 2 Apr 2018, Kong, Fande wrote: > > > Hi All, > > > > I am trying to upgrade PETSc from 3.7.6 to 3.8.3 for MOOSE and its > > applications. I have a error message for a standard te

Re: [petsc-users] A bad commit affects MOOSE

FWMgkK9yEScbLA7pkrWydFuJnYflsU=_ > zpWRcyk3kHuEHoq02NDqYExnXIohXpNnjyabYnnDjU= > > Satish > > On Mon, 2 Apr 2018, Kong, Fande wrote: > > > On Mon, Apr 2, 2018 at 4:23 PM, Satish Balay <ba...@mcs.anl.gov> wrote: > > > > > Does this 'standard test' use MPI_COM

[petsc-users] A bad commit affects MOOSE

Hi All, I am trying to upgrade PETSc from 3.7.6 to 3.8.3 for MOOSE and its applications. I have a error message for a standard test: *preconditioners/pbp.lots_of_variables: MPI had an errorpreconditioners/pbp.lots_of_variables:

Re: [petsc-users] A bad commit affects MOOSE

Figured out: The reason is that in MatCreate_HYPRE(Mat B), we call MPI_Comm_dup instead of PetscCommDuplicate. The PetscCommDuplicate is better, and it does not actually create a communicator if the communicator is already known to PETSc. Furthermore, I do not think we should a comm in

Re: [petsc-users] A bad commit affects MOOSE

e hypre is needed to generate subcomms, perhaps it generates > too many? > >> > >> Barry > >> > >> > >>> On Apr 2, 2018, at 7:07 PM, Derek Gaston <fried...@gmail.com> wrote: > >>> > >>> I’m working with Fande on this an

Re: [petsc-users] A bad commit affects MOOSE

t; > > On Tue, Apr 3, 2018 at 9:12 AM, Stefano Zampini <stefano.zamp...@gmail.com > > wrote: > >> >> On Apr 3, 2018, at 4:58 PM, Satish Balay <ba...@mcs.anl.gov> wrote: >> >> On Tue, 3 Apr 2018, Kong, Fande wrote: >> >> On Tue, Apr 3, 2018 at

Re: [petsc-users] A bad commit affects MOOSE

On Tue, Apr 3, 2018 at 9:32 AM, Satish Balay <ba...@mcs.anl.gov> wrote: > On Tue, 3 Apr 2018, Stefano Zampini wrote: > > > > > > On Apr 3, 2018, at 4:58 PM, Satish Balay <ba...@mcs.anl.gov> wrote: > > > > > > On Tue, 3 Apr 2018, Kong, Fande

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