August 2020 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] TAOPDIPM
by Pierre Jolivet 04 Aug '20

04 Aug '20

Thanks to you both, I’ll forward this to my user. Pierre > On 4 Aug 2020, at 7:30 PM, Dener, Alp <adener(a)anl.gov> wrote: > > Hi Pierre, > > This is indeed an issue with TAO default tolerances. > > Specifically it has to do with constraint tolerances. The default value is an exact zero. > > The problem should still work with line 89 commented out. Our default gradient tolerance is 1e-8. In your case, commenting out line 90 is causing the solver to try to converge constraints to exact zero and it cannot. > > I will get a patch out for this within the week but in the meantime please ensure that the constraint tolerances are set for any constrained problem. > > Thank you! > — > Alp > >> On Aug 4, 2020, at 12:24 PM, Munson, Todd via petsc-dev <petsc-dev(a)mcs.anl.gov> wrote: >> >> >> Hi Pierre, >> >> I would say the answer to that question is "no, its not expected". >> >> We will look into fixing it. It seems like the default tolerances are being set to zero and the result is an inability to satisfy the constraints or gradient of the Lagrangian to that small of a tolerance. >> >> Thanks for point this out to us! We will get it resolved. >> >> Thanks, Todd. >> >> On 8/4/20, 12:12 PM, "petsc-dev on behalf of Pierre Jolivet" <petsc-dev-bounces(a)mcs.anl.gov on behalf of pierre.jolivet(a)enseeiht.fr> wrote: >> >> Hello, >> If I comment line 89 and 90 of src/tao/constrained/tutorials/ex1.c from master, the example deadlocks with a single process. >> Is this expected? >> >> Thanks, >> Pierre >> >> $ ./ex1 -tao_monitor >> ---- Constrained Problem ----- >> Solution should be f(1,1)=-2 >> 0 TAO, Function value: 8., Residual: 8.48528 >> 1 TAO, Function value: 1.28532, Residual: 10.7411 >> 2 TAO, Function value: -2.56703, Residual: 1.87847 >> 3 TAO, Function value: -2.03161, Residual: 0.12881 >> 4 TAO, Function value: -1.99961, Residual: 0.0450855 >> 5 TAO, Function value: -1.99993, Residual: 0.000916939 >> 6 TAO, Function value: -1.99999, Residual: 6.69184e-05 >> 7 TAO, Function value: -2., Residual: 7.15427e-06 >> 8 TAO, Function value: -2., Residual: 7.15779e-07 >> 9 TAO, Function value: -2., Residual: 7.15777e-08 >> 10 TAO, Function value: -2., Residual: 7.15777e-09 >> 11 TAO, Function value: -2., Residual: 7.15779e-10 >> 12 TAO, Function value: -2., Residual: 7.15775e-11 >> 13 TAO, Function value: -2., Residual: 7.1599e-12 >> 14 TAO, Function value: -2., Residual: 7.1599e-13 >> 15 TAO, Function value: -2., Residual: 7.22085e-14 >> 16 TAO, Function value: -2., Residual: 6.44626e-15 >> 17 TAO, Function value: -2., Residual: 1.00751e-15 >> 18 TAO, Function value: -2., Residual: 1.70295e-17 >> 19 TAO, Function value: -2., Residual: 1.70295e-18 >> 20 TAO, Function value: -2., Residual: 1.70295e-19 >> 21 TAO, Function value: -2., Residual: 1.70295e-20 >> 22 TAO, Function value: -2., Residual: 1.70295e-21 >> 23 TAO, Function value: -2., Residual: 1.70295e-22 >> 24 TAO, Function value: -2., Residual: 1.70295e-23 >> 25 TAO, Function value: -2., Residual: 1.70295e-24 >> 26 TAO, Function value: -2., Residual: 1.70295e-25 >> 27 TAO, Function value: -2., Residual: 1.70295e-26 >> 28 TAO, Function value: -2., Residual: 1.70295e-27 >> 29 TAO, Function value: -2., Residual: 1.70295e-28 >> 30 TAO, Function value: -2., Residual: 1.70295e-29 >> 31 TAO, Function value: -2., Residual: 1.70295e-30 >> 32 TAO, Function value: -2., Residual: 1.70295e-31 >> 33 TAO, Function value: -2., Residual: 1.70295e-32 >> 34 TAO, Function value: -2., Residual: 1.70295e-33 >> 35 TAO, Function value: -2., Residual: 1.70295e-34 >> 36 TAO, Function value: -2., Residual: 1.70295e-35 >> 37 TAO, Function value: -2., Residual: 1.70295e-36 >> 38 TAO, Function value: -2., Residual: 1.70295e-37 >> 39 TAO, Function value: -2., Residual: 1.70295e-38 >> 40 TAO, Function value: -2., Residual: 1.70295e-39 >> 41 TAO, Function value: -2., Residual: 1.70295e-40 >> 42 TAO, Function value: -2., Residual: 1.70295e-41 >> 43 TAO, Function value: -2., Residual: 1.70295e-42 >> 44 TAO, Function value: -2., Residual: 1.70295e-43 >> 45 TAO, Function value: -2., Residual: 1.70295e-44 >> 46 TAO, Function value: -2., Residual: 1.70295e-45 >> 47 TAO, Function value: -2., Residual: 1.70295e-46 >> 48 TAO, Function value: -2., Residual: 1.70295e-47 >> 49 TAO, Function value: -2., Residual: 1.70295e-48 >> 50 TAO, Function value: -2., Residual: 1.70295e-49 >> 51 TAO, Function value: -2., Residual: 1.70295e-50 >> 52 TAO, Function value: -2., Residual: 1.70295e-51 >> ^C >> >

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Re: [petsc-dev] How far should internal error checking go?
by Jed Brown 04 Aug '20

04 Aug '20

I don't know what the question is. You can `git grep PETSC_ERR_PLIB` for places where we are checking for corruption in something that PETSc has produced. When those checks are expensive (like checking if indices are sorted), they use `if (PetscUnlikelyDebug(cond)) { ... }` or `if (PetscDefined(HAVE_DEBUG)) { ... }`. Jacob Faibussowitsch <jacob.fai(a)gmail.com> writes: > Hello All, > > How far should one go in error checking when using #if defined(PETSC_USE_DEBUG)? So far I have gone with the mantra that internal petsc routines (including ones authored by myself) should be considered infallible and that I should only be checking for garbage *input* from the user. But there is not a person in existence that doesn’t write buggy code, as evidenced by the somewhat routine “fixing bug in XYZ” merge requests one sees. > > On the other hand it is also not reasonable to check every single output with a fine-tooth comb because for the majority of cases code written by petsc developers is working as intended. Take for example writing an array sorting algorithm. Since every operation is "performance critical” these are often written in less logical or less readable formats leading to some subtle bugs that the writer doesn’t immediately catch. If these remain uncaught through CI/CD and then bleeds into a user code I see absolutely no chance of the user (or even other devs) ever being able to identify that the sorting algorithm deep in some function stack is the one producing the bug without significant effort. One could include a “dumb” version of the same algorithm that checks a copy of the initial array for missing/misplaced elements but as mentioned above this is a pointless slowdown 99% of the time. > > CI/CD -- while excellent at catching a lot of machine-specific bugs -- isn’t bulletproof either. It relies on the assumption that the writer knows all possible sources of bugs in their code and provides a test case for each, but to quote Isaac Newton “what we know is a drop, what we don’t know is an ocean”. I have been mulling over this problem for a while now, and have looked through the user manual/developers manual but have not found a definitive answer. > > Best regards, > > Jacob Faibussowitsch > (Jacob Fai - booss - oh - vitch) > Cell: (312) 694-3391

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Re: [petsc-dev] TAOPDIPM
by Dener, Alp 04 Aug '20

04 Aug '20

Hi Pierre, This is indeed an issue with TAO default tolerances. Specifically it has to do with constraint tolerances. The default value is an exact zero. The problem should still work with line 89 commented out. Our default gradient tolerance is 1e-8. In your case, commenting out line 90 is causing the solver to try to converge constraints to exact zero and it cannot. I will get a patch out for this within the week but in the meantime please ensure that the constraint tolerances are set for any constrained problem. Thank you! — Alp > On Aug 4, 2020, at 12:24 PM, Munson, Todd via petsc-dev <petsc-dev(a)mcs.anl.gov> wrote: > > > Hi Pierre, > > I would say the answer to that question is "no, its not expected". > > We will look into fixing it. It seems like the default tolerances are being set to zero and the result is an inability to satisfy the constraints or gradient of the Lagrangian to that small of a tolerance. > > Thanks for point this out to us! We will get it resolved. > > Thanks, Todd. > > On 8/4/20, 12:12 PM, "petsc-dev on behalf of Pierre Jolivet" <petsc-dev-bounces(a)mcs.anl.gov on behalf of pierre.jolivet(a)enseeiht.fr> wrote: > > Hello, > If I comment line 89 and 90 of src/tao/constrained/tutorials/ex1.c from master, the example deadlocks with a single process. > Is this expected? > > Thanks, > Pierre > > $ ./ex1 -tao_monitor > ---- Constrained Problem ----- > Solution should be f(1,1)=-2 > 0 TAO, Function value: 8., Residual: 8.48528 > 1 TAO, Function value: 1.28532, Residual: 10.7411 > 2 TAO, Function value: -2.56703, Residual: 1.87847 > 3 TAO, Function value: -2.03161, Residual: 0.12881 > 4 TAO, Function value: -1.99961, Residual: 0.0450855 > 5 TAO, Function value: -1.99993, Residual: 0.000916939 > 6 TAO, Function value: -1.99999, Residual: 6.69184e-05 > 7 TAO, Function value: -2., Residual: 7.15427e-06 > 8 TAO, Function value: -2., Residual: 7.15779e-07 > 9 TAO, Function value: -2., Residual: 7.15777e-08 > 10 TAO, Function value: -2., Residual: 7.15777e-09 > 11 TAO, Function value: -2., Residual: 7.15779e-10 > 12 TAO, Function value: -2., Residual: 7.15775e-11 > 13 TAO, Function value: -2., Residual: 7.1599e-12 > 14 TAO, Function value: -2., Residual: 7.1599e-13 > 15 TAO, Function value: -2., Residual: 7.22085e-14 > 16 TAO, Function value: -2., Residual: 6.44626e-15 > 17 TAO, Function value: -2., Residual: 1.00751e-15 > 18 TAO, Function value: -2., Residual: 1.70295e-17 > 19 TAO, Function value: -2., Residual: 1.70295e-18 > 20 TAO, Function value: -2., Residual: 1.70295e-19 > 21 TAO, Function value: -2., Residual: 1.70295e-20 > 22 TAO, Function value: -2., Residual: 1.70295e-21 > 23 TAO, Function value: -2., Residual: 1.70295e-22 > 24 TAO, Function value: -2., Residual: 1.70295e-23 > 25 TAO, Function value: -2., Residual: 1.70295e-24 > 26 TAO, Function value: -2., Residual: 1.70295e-25 > 27 TAO, Function value: -2., Residual: 1.70295e-26 > 28 TAO, Function value: -2., Residual: 1.70295e-27 > 29 TAO, Function value: -2., Residual: 1.70295e-28 > 30 TAO, Function value: -2., Residual: 1.70295e-29 > 31 TAO, Function value: -2., Residual: 1.70295e-30 > 32 TAO, Function value: -2., Residual: 1.70295e-31 > 33 TAO, Function value: -2., Residual: 1.70295e-32 > 34 TAO, Function value: -2., Residual: 1.70295e-33 > 35 TAO, Function value: -2., Residual: 1.70295e-34 > 36 TAO, Function value: -2., Residual: 1.70295e-35 > 37 TAO, Function value: -2., Residual: 1.70295e-36 > 38 TAO, Function value: -2., Residual: 1.70295e-37 > 39 TAO, Function value: -2., Residual: 1.70295e-38 > 40 TAO, Function value: -2., Residual: 1.70295e-39 > 41 TAO, Function value: -2., Residual: 1.70295e-40 > 42 TAO, Function value: -2., Residual: 1.70295e-41 > 43 TAO, Function value: -2., Residual: 1.70295e-42 > 44 TAO, Function value: -2., Residual: 1.70295e-43 > 45 TAO, Function value: -2., Residual: 1.70295e-44 > 46 TAO, Function value: -2., Residual: 1.70295e-45 > 47 TAO, Function value: -2., Residual: 1.70295e-46 > 48 TAO, Function value: -2., Residual: 1.70295e-47 > 49 TAO, Function value: -2., Residual: 1.70295e-48 > 50 TAO, Function value: -2., Residual: 1.70295e-49 > 51 TAO, Function value: -2., Residual: 1.70295e-50 > 52 TAO, Function value: -2., Residual: 1.70295e-51 > ^C >

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How far should internal error checking go?
by Jacob Faibussowitsch 04 Aug '20

04 Aug '20

Hello All, How far should one go in error checking when using #if defined(PETSC_USE_DEBUG)? So far I have gone with the mantra that internal petsc routines (including ones authored by myself) should be considered infallible and that I should only be checking for garbage *input* from the user. But there is not a person in existence that doesn’t write buggy code, as evidenced by the somewhat routine “fixing bug in XYZ” merge requests one sees. On the other hand it is also not reasonable to check every single output with a fine-tooth comb because for the majority of cases code written by petsc developers is working as intended. Take for example writing an array sorting algorithm. Since every operation is "performance critical” these are often written in less logical or less readable formats leading to some subtle bugs that the writer doesn’t immediately catch. If these remain uncaught through CI/CD and then bleeds into a user code I see absolutely no chance of the user (or even other devs) ever being able to identify that the sorting algorithm deep in some function stack is the one producing the bug without significant effort. One could include a “dumb” version of the same algorithm that checks a copy of the initial array for missing/misplaced elements but as mentioned above this is a pointless slowdown 99% of the time. CI/CD -- while excellent at catching a lot of machine-specific bugs -- isn’t bulletproof either. It relies on the assumption that the writer knows all possible sources of bugs in their code and provides a test case for each, but to quote Isaac Newton “what we know is a drop, what we don’t know is an ocean”. I have been mulling over this problem for a while now, and have looked through the user manual/developers manual but have not found a definitive answer. Best regards, Jacob Faibussowitsch (Jacob Fai - booss - oh - vitch) Cell: (312) 694-3391

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Re: [petsc-dev] TAOPDIPM
by Munson, Todd 04 Aug '20

04 Aug '20

Hi Pierre, I would say the answer to that question is "no, its not expected". We will look into fixing it. It seems like the default tolerances are being set to zero and the result is an inability to satisfy the constraints or gradient of the Lagrangian to that small of a tolerance. Thanks for point this out to us! We will get it resolved. Thanks, Todd. On 8/4/20, 12:12 PM, "petsc-dev on behalf of Pierre Jolivet" <petsc-dev-bounces(a)mcs.anl.gov on behalf of pierre.jolivet(a)enseeiht.fr> wrote: Hello, If I comment line 89 and 90 of src/tao/constrained/tutorials/ex1.c from master, the example deadlocks with a single process. Is this expected? Thanks, Pierre $ ./ex1 -tao_monitor ---- Constrained Problem ----- Solution should be f(1,1)=-2 0 TAO, Function value: 8., Residual: 8.48528 1 TAO, Function value: 1.28532, Residual: 10.7411 2 TAO, Function value: -2.56703, Residual: 1.87847 3 TAO, Function value: -2.03161, Residual: 0.12881 4 TAO, Function value: -1.99961, Residual: 0.0450855 5 TAO, Function value: -1.99993, Residual: 0.000916939 6 TAO, Function value: -1.99999, Residual: 6.69184e-05 7 TAO, Function value: -2., Residual: 7.15427e-06 8 TAO, Function value: -2., Residual: 7.15779e-07 9 TAO, Function value: -2., Residual: 7.15777e-08 10 TAO, Function value: -2., Residual: 7.15777e-09 11 TAO, Function value: -2., Residual: 7.15779e-10 12 TAO, Function value: -2., Residual: 7.15775e-11 13 TAO, Function value: -2., Residual: 7.1599e-12 14 TAO, Function value: -2., Residual: 7.1599e-13 15 TAO, Function value: -2., Residual: 7.22085e-14 16 TAO, Function value: -2., Residual: 6.44626e-15 17 TAO, Function value: -2., Residual: 1.00751e-15 18 TAO, Function value: -2., Residual: 1.70295e-17 19 TAO, Function value: -2., Residual: 1.70295e-18 20 TAO, Function value: -2., Residual: 1.70295e-19 21 TAO, Function value: -2., Residual: 1.70295e-20 22 TAO, Function value: -2., Residual: 1.70295e-21 23 TAO, Function value: -2., Residual: 1.70295e-22 24 TAO, Function value: -2., Residual: 1.70295e-23 25 TAO, Function value: -2., Residual: 1.70295e-24 26 TAO, Function value: -2., Residual: 1.70295e-25 27 TAO, Function value: -2., Residual: 1.70295e-26 28 TAO, Function value: -2., Residual: 1.70295e-27 29 TAO, Function value: -2., Residual: 1.70295e-28 30 TAO, Function value: -2., Residual: 1.70295e-29 31 TAO, Function value: -2., Residual: 1.70295e-30 32 TAO, Function value: -2., Residual: 1.70295e-31 33 TAO, Function value: -2., Residual: 1.70295e-32 34 TAO, Function value: -2., Residual: 1.70295e-33 35 TAO, Function value: -2., Residual: 1.70295e-34 36 TAO, Function value: -2., Residual: 1.70295e-35 37 TAO, Function value: -2., Residual: 1.70295e-36 38 TAO, Function value: -2., Residual: 1.70295e-37 39 TAO, Function value: -2., Residual: 1.70295e-38 40 TAO, Function value: -2., Residual: 1.70295e-39 41 TAO, Function value: -2., Residual: 1.70295e-40 42 TAO, Function value: -2., Residual: 1.70295e-41 43 TAO, Function value: -2., Residual: 1.70295e-42 44 TAO, Function value: -2., Residual: 1.70295e-43 45 TAO, Function value: -2., Residual: 1.70295e-44 46 TAO, Function value: -2., Residual: 1.70295e-45 47 TAO, Function value: -2., Residual: 1.70295e-46 48 TAO, Function value: -2., Residual: 1.70295e-47 49 TAO, Function value: -2., Residual: 1.70295e-48 50 TAO, Function value: -2., Residual: 1.70295e-49 51 TAO, Function value: -2., Residual: 1.70295e-50 52 TAO, Function value: -2., Residual: 1.70295e-51 ^C

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Re: [petsc-dev] TAOPDIPM
by Barry Smith 04 Aug '20

04 Aug '20

> On Aug 4, 2020, at 12:12 PM, Pierre Jolivet <pierre.jolivet(a)enseeiht.fr> wrote: > > Hello, > If I comment line 89 and 90 of src/tao/constrained/tutorials/ex1.c from master, the example deadlocks with a single process. > Is this expected? > > Thanks, > Pierre > > $ ./ex1 -tao_monitor > ---- Constrained Problem ----- > Solution should be f(1,1)=-2 > 0 TAO, Function value: 8., Residual: 8.48528 > 1 TAO, Function value: 1.28532, Residual: 10.7411 > 2 TAO, Function value: -2.56703, Residual: 1.87847 > 3 TAO, Function value: -2.03161, Residual: 0.12881 > 4 TAO, Function value: -1.99961, Residual: 0.0450855 > 5 TAO, Function value: -1.99993, Residual: 0.000916939 > 6 TAO, Function value: -1.99999, Residual: 6.69184e-05 > 7 TAO, Function value: -2., Residual: 7.15427e-06 > 8 TAO, Function value: -2., Residual: 7.15779e-07 > 9 TAO, Function value: -2., Residual: 7.15777e-08 > 10 TAO, Function value: -2., Residual: 7.15777e-09 > 11 TAO, Function value: -2., Residual: 7.15779e-10 > 12 TAO, Function value: -2., Residual: 7.15775e-11 > 13 TAO, Function value: -2., Residual: 7.1599e-12 > 14 TAO, Function value: -2., Residual: 7.1599e-13 > 15 TAO, Function value: -2., Residual: 7.22085e-14 > 16 TAO, Function value: -2., Residual: 6.44626e-15 > 17 TAO, Function value: -2., Residual: 1.00751e-15 > 18 TAO, Function value: -2., Residual: 1.70295e-17 > 19 TAO, Function value: -2., Residual: 1.70295e-18 > 20 TAO, Function value: -2., Residual: 1.70295e-19 > 21 TAO, Function value: -2., Residual: 1.70295e-20 > 22 TAO, Function value: -2., Residual: 1.70295e-21 > 23 TAO, Function value: -2., Residual: 1.70295e-22 > 24 TAO, Function value: -2., Residual: 1.70295e-23 > 25 TAO, Function value: -2., Residual: 1.70295e-24 > 26 TAO, Function value: -2., Residual: 1.70295e-25 > 27 TAO, Function value: -2., Residual: 1.70295e-26 > 28 TAO, Function value: -2., Residual: 1.70295e-27 > 29 TAO, Function value: -2., Residual: 1.70295e-28 > 30 TAO, Function value: -2., Residual: 1.70295e-29 > 31 TAO, Function value: -2., Residual: 1.70295e-30 > 32 TAO, Function value: -2., Residual: 1.70295e-31 > 33 TAO, Function value: -2., Residual: 1.70295e-32 > 34 TAO, Function value: -2., Residual: 1.70295e-33 > 35 TAO, Function value: -2., Residual: 1.70295e-34 > 36 TAO, Function value: -2., Residual: 1.70295e-35 > 37 TAO, Function value: -2., Residual: 1.70295e-36 > 38 TAO, Function value: -2., Residual: 1.70295e-37 > 39 TAO, Function value: -2., Residual: 1.70295e-38 > 40 TAO, Function value: -2., Residual: 1.70295e-39 > 41 TAO, Function value: -2., Residual: 1.70295e-40 > 42 TAO, Function value: -2., Residual: 1.70295e-41 > 43 TAO, Function value: -2., Residual: 1.70295e-42 > 44 TAO, Function value: -2., Residual: 1.70295e-43 > 45 TAO, Function value: -2., Residual: 1.70295e-44 > 46 TAO, Function value: -2., Residual: 1.70295e-45 > 47 TAO, Function value: -2., Residual: 1.70295e-46 > 48 TAO, Function value: -2., Residual: 1.70295e-47 > 49 TAO, Function value: -2., Residual: 1.70295e-48 > 50 TAO, Function value: -2., Residual: 1.70295e-49 > 51 TAO, Function value: -2., Residual: 1.70295e-50 > 52 TAO, Function value: -2., Residual: 1.70295e-51 > ^C

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TAOPDIPM
by Pierre Jolivet 04 Aug '20

04 Aug '20

Hello, If I comment line 89 and 90 of src/tao/constrained/tutorials/ex1.c from master, the example deadlocks with a single process. Is this expected? Thanks, Pierre $ ./ex1 -tao_monitor ---- Constrained Problem ----- Solution should be f(1,1)=-2 0 TAO, Function value: 8., Residual: 8.48528 1 TAO, Function value: 1.28532, Residual: 10.7411 2 TAO, Function value: -2.56703, Residual: 1.87847 3 TAO, Function value: -2.03161, Residual: 0.12881 4 TAO, Function value: -1.99961, Residual: 0.0450855 5 TAO, Function value: -1.99993, Residual: 0.000916939 6 TAO, Function value: -1.99999, Residual: 6.69184e-05 7 TAO, Function value: -2., Residual: 7.15427e-06 8 TAO, Function value: -2., Residual: 7.15779e-07 9 TAO, Function value: -2., Residual: 7.15777e-08 10 TAO, Function value: -2., Residual: 7.15777e-09 11 TAO, Function value: -2., Residual: 7.15779e-10 12 TAO, Function value: -2., Residual: 7.15775e-11 13 TAO, Function value: -2., Residual: 7.1599e-12 14 TAO, Function value: -2., Residual: 7.1599e-13 15 TAO, Function value: -2., Residual: 7.22085e-14 16 TAO, Function value: -2., Residual: 6.44626e-15 17 TAO, Function value: -2., Residual: 1.00751e-15 18 TAO, Function value: -2., Residual: 1.70295e-17 19 TAO, Function value: -2., Residual: 1.70295e-18 20 TAO, Function value: -2., Residual: 1.70295e-19 21 TAO, Function value: -2., Residual: 1.70295e-20 22 TAO, Function value: -2., Residual: 1.70295e-21 23 TAO, Function value: -2., Residual: 1.70295e-22 24 TAO, Function value: -2., Residual: 1.70295e-23 25 TAO, Function value: -2., Residual: 1.70295e-24 26 TAO, Function value: -2., Residual: 1.70295e-25 27 TAO, Function value: -2., Residual: 1.70295e-26 28 TAO, Function value: -2., Residual: 1.70295e-27 29 TAO, Function value: -2., Residual: 1.70295e-28 30 TAO, Function value: -2., Residual: 1.70295e-29 31 TAO, Function value: -2., Residual: 1.70295e-30 32 TAO, Function value: -2., Residual: 1.70295e-31 33 TAO, Function value: -2., Residual: 1.70295e-32 34 TAO, Function value: -2., Residual: 1.70295e-33 35 TAO, Function value: -2., Residual: 1.70295e-34 36 TAO, Function value: -2., Residual: 1.70295e-35 37 TAO, Function value: -2., Residual: 1.70295e-36 38 TAO, Function value: -2., Residual: 1.70295e-37 39 TAO, Function value: -2., Residual: 1.70295e-38 40 TAO, Function value: -2., Residual: 1.70295e-39 41 TAO, Function value: -2., Residual: 1.70295e-40 42 TAO, Function value: -2., Residual: 1.70295e-41 43 TAO, Function value: -2., Residual: 1.70295e-42 44 TAO, Function value: -2., Residual: 1.70295e-43 45 TAO, Function value: -2., Residual: 1.70295e-44 46 TAO, Function value: -2., Residual: 1.70295e-45 47 TAO, Function value: -2., Residual: 1.70295e-46 48 TAO, Function value: -2., Residual: 1.70295e-47 49 TAO, Function value: -2., Residual: 1.70295e-48 50 TAO, Function value: -2., Residual: 1.70295e-49 51 TAO, Function value: -2., Residual: 1.70295e-50 52 TAO, Function value: -2., Residual: 1.70295e-51 ^C

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Re: [petsc-dev] Configure --with-X-dir= Using Relative Path
by Satish Balay 02 Aug '20

02 Aug '20

If you need to reuse reusing previously installed packages - its best to install packages at a prefix location - and not list packages from a different PETSC_ARCH [as there are other stuff here that can conflict with the build] 1. Install all the packages. ./configure --prefix=$HOME/soft/packages --download-zlib --download-metis 2. Now use these preinstalled packages. ./configure --with-zlib-dir=$HOME/soft/packages -with-metis-dir=$HOME/soft/packages Note: you can avoid --download-zlib by using distro package in the VM. And --with-mpich-dir= should be --with-mpi-dir= Satish On Sun, 2 Aug 2020, Barry Smith wrote: > > Jacob, > > Since the reconfigure scripts are python you'll need to use python variables to access environmental variables like os.environ['PETSC_DIR'] > > Barry > > > > On Aug 2, 2020, at 1:57 PM, Jacob Faibussowitsch <jacob.fai(a)gmail.com> wrote: > > > > Hello All, > > > > I am reconfiguring an arch within a docker using the attached reconfigure script. My petsc dir is mounted via the following commands to docker -v ${PETSC_DIR}:/petsc:delegated. I am trying to use the existing arches on my native machine as the install directories for packages compiled within the docker images because SSH keys aren’t persistent in the images and hence git pull’s won’t work. I encountered this odd bug when trying —with-zlib-dir where it prepends the existing $PETSC_DIR to the directory name automatically, but this problem persists for any package. > > > > There is no configure.log generated since this I guess is early enough in the configure process, so unfortunately the only error output is the wall of error text from terminal. The error indicates that configure is passing ./[COMMAND LINE DIRECTORY] instead of [COMMAND LINE DIRECTORY] to configure. > > > > $ ls ${PETSC_DIR}/master-arch-darwin-c-debug/externalpackages/ > > Permissions Size User Date Modified Name > > drwxrwxr-x - root 8 Jul 16:07 petsc-pkg-mumps-d1a5c931b762 > > drwxr-xr-x - root 3 Jul 21:39 hdf5-1.12.0 > > drwxrwxr-x - root 1 Aug 21:34 netcdf-c-4.5.0 > > drwxr-xr-x - root 3 Jul 21:38 zlib-1.2.11 > > drwxr-xr-x - root 29 Jul 17:43 mpich-3.3.2 > > drwxr-xr-x - root 6 Jul 17:06 Chaco-2.2-p2 > > drwxr-xr-x - root 1 Aug 21:36 git.ctetgen > > drwxr-xr-x - root 1 Aug 21:34 git.exodusii > > drwxr-xr-x - root 1 Aug 21:31 git.med > > drwxr-xr-x - root 1 Aug 21:31 git.metis > > drwxr-xr-x - root 1 Aug 21:31 git.parmetis > > drwxr-xr-x - root 1 Aug 21:32 git.pnetcdf > > drwxr-xr-x - root 1 Aug 21:35 git.scalapack > > drwxr-xr-x - root 1 Aug 21:31 git.sowing > > drwxr-xr-x - root 1 Aug 21:34 git.triangle > > > > $ echo $PETSC_DIR > > /petsc > > > > $./reconfigure-arch-linux-c-debug > > =============================================================================== > > Configuring PETSc to compile on your system > > =============================================================================== > > ******************************************************************************* > > TypeError or ValueError possibly related to ERROR in COMMAND LINE ARGUMENT while running ./configure > > ------------------------------------------------------------------------------- > > Nonexistent directory: /petsc/${PETSC_DIR}/master-arch-darwin-c-debug/externalpackages/zlib-1.2.11 for key with-zlib-dir > > ******************************************************************************* > > > > > > File "/petsc/config/configure.py", line 449, in petsc_configure > > framework = config.framework.Framework(['--configModules=PETSc.Configure','--optionsModule=config.compilerOptions']+sys.argv[1:], loadArgDB = 0) > > File "/petsc/config/BuildSystem/config/framework.py", line 107, in __init__ > > self.createChildren() > > File "/petsc/config/BuildSystem/config/framework.py", line 324, in createChildren > > self.getChild(moduleName) > > File "/petsc/config/BuildSystem/config/framework.py", line 309, in getChild > > config.setupDependencies(self) > > File "/petsc/config/PETSc/Configure.py", line 91, in setupDependencies > > obj = self.registerPythonFile(package,'config.packages') > > File "/petsc/config/PETSc/Configure.py", line 49, in registerPythonFile > > utilityObj = self.framework.require(directory+utilityName, self) > > File "/petsc/config/BuildSystem/config/framework.py", line 329, in require > > config = self.getChild(moduleName, keywordArgs) > > File "/petsc/config/BuildSystem/config/framework.py", line 309, in getChild > > config.setupDependencies(self) > > File "/petsc/config/BuildSystem/config/packages/ADIOS.py", line 17, in setupDependencies > > self.zlib = framework.require('config.packages.zlib',self) > > File "/petsc/config/BuildSystem/config/framework.py", line 329, in require > > config = self.getChild(moduleName, keywordArgs) > > File "/petsc/config/BuildSystem/config/framework.py", line 307, in getChild > > config.setup() > > File "/petsc/config/BuildSystem/config/base.py", line 94, in setup > > script.Script.setup(self) > > File "/petsc/config/BuildSystem/script.py", line 108, in setup > > logger.Logger.setup(self) > > File "/petsc/config/BuildSystem/logger.py", line 75, in setup > > args.ArgumentProcessor.setup(self) > > File "/petsc/config/BuildSystem/args.py", line 76, in setup > > self.setupArguments(self.argDB) > > File "/petsc/config/BuildSystem/script.py", line 92, in setupArguments > > self.setupHelp(self.help) > > File "/petsc/config/BuildSystem/config/packages/zlib.py", line 16, in setupHelp > > config.package.Package.setupHelp(self, help) > > File "/petsc/config/BuildSystem/config/package.py", line 156, in setupHelp > > help.addArgument(self.PACKAGE,'-with-'+self.package+'-dir=<dir>',nargs.ArgDir(None,None,'Indicate the root directory of the '+self.name+' installation',mustExist = 1)) > > File "/petsc/config/BuildSystem/help.py", line 108, in addArgument > > self.argDB.setType(self.getArgName(name), argType, forceLocal = 1) > > File "/petsc/config/BuildSystem/RDict.py", line 222, in setType > > value.setValue(v.getValue()) > > File "/petsc/config/BuildSystem/nargs.py", line 325, in setValue > > raise ValueError('Nonexistent directory: '+str(value)+' for key '+str(self.key)) > > > > > > <reconfigure-arch-linux-c-debug.py> > > > > Best regards, > > > > Jacob Faibussowitsch > > (Jacob Fai - booss - oh - vitch) > > Cell: (312) 694-3391 > > > >

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Re: [petsc-dev] Configure --with-X-dir= Using Relative Path
by Barry Smith 02 Aug '20

02 Aug '20

Jacob, Since the reconfigure scripts are python you'll need to use python variables to access environmental variables like os.environ['PETSC_DIR'] Barry > On Aug 2, 2020, at 1:57 PM, Jacob Faibussowitsch <jacob.fai(a)gmail.com> wrote: > > Hello All, > > I am reconfiguring an arch within a docker using the attached reconfigure script. My petsc dir is mounted via the following commands to docker -v ${PETSC_DIR}:/petsc:delegated. I am trying to use the existing arches on my native machine as the install directories for packages compiled within the docker images because SSH keys aren’t persistent in the images and hence git pull’s won’t work. I encountered this odd bug when trying —with-zlib-dir where it prepends the existing $PETSC_DIR to the directory name automatically, but this problem persists for any package. > > There is no configure.log generated since this I guess is early enough in the configure process, so unfortunately the only error output is the wall of error text from terminal. The error indicates that configure is passing ./[COMMAND LINE DIRECTORY] instead of [COMMAND LINE DIRECTORY] to configure. > > $ ls ${PETSC_DIR}/master-arch-darwin-c-debug/externalpackages/ > Permissions Size User Date Modified Name > drwxrwxr-x - root 8 Jul 16:07 petsc-pkg-mumps-d1a5c931b762 > drwxr-xr-x - root 3 Jul 21:39 hdf5-1.12.0 > drwxrwxr-x - root 1 Aug 21:34 netcdf-c-4.5.0 > drwxr-xr-x - root 3 Jul 21:38 zlib-1.2.11 > drwxr-xr-x - root 29 Jul 17:43 mpich-3.3.2 > drwxr-xr-x - root 6 Jul 17:06 Chaco-2.2-p2 > drwxr-xr-x - root 1 Aug 21:36 git.ctetgen > drwxr-xr-x - root 1 Aug 21:34 git.exodusii > drwxr-xr-x - root 1 Aug 21:31 git.med > drwxr-xr-x - root 1 Aug 21:31 git.metis > drwxr-xr-x - root 1 Aug 21:31 git.parmetis > drwxr-xr-x - root 1 Aug 21:32 git.pnetcdf > drwxr-xr-x - root 1 Aug 21:35 git.scalapack > drwxr-xr-x - root 1 Aug 21:31 git.sowing > drwxr-xr-x - root 1 Aug 21:34 git.triangle > > $ echo $PETSC_DIR > /petsc > > $./reconfigure-arch-linux-c-debug > =============================================================================== > Configuring PETSc to compile on your system > =============================================================================== > ******************************************************************************* > TypeError or ValueError possibly related to ERROR in COMMAND LINE ARGUMENT while running ./configure > ------------------------------------------------------------------------------- > Nonexistent directory: /petsc/${PETSC_DIR}/master-arch-darwin-c-debug/externalpackages/zlib-1.2.11 for key with-zlib-dir > ******************************************************************************* > > > File "/petsc/config/configure.py", line 449, in petsc_configure > framework = config.framework.Framework(['--configModules=PETSc.Configure','--optionsModule=config.compilerOptions']+sys.argv[1:], loadArgDB = 0) > File "/petsc/config/BuildSystem/config/framework.py", line 107, in __init__ > self.createChildren() > File "/petsc/config/BuildSystem/config/framework.py", line 324, in createChildren > self.getChild(moduleName) > File "/petsc/config/BuildSystem/config/framework.py", line 309, in getChild > config.setupDependencies(self) > File "/petsc/config/PETSc/Configure.py", line 91, in setupDependencies > obj = self.registerPythonFile(package,'config.packages') > File "/petsc/config/PETSc/Configure.py", line 49, in registerPythonFile > utilityObj = self.framework.require(directory+utilityName, self) > File "/petsc/config/BuildSystem/config/framework.py", line 329, in require > config = self.getChild(moduleName, keywordArgs) > File "/petsc/config/BuildSystem/config/framework.py", line 309, in getChild > config.setupDependencies(self) > File "/petsc/config/BuildSystem/config/packages/ADIOS.py", line 17, in setupDependencies > self.zlib = framework.require('config.packages.zlib',self) > File "/petsc/config/BuildSystem/config/framework.py", line 329, in require > config = self.getChild(moduleName, keywordArgs) > File "/petsc/config/BuildSystem/config/framework.py", line 307, in getChild > config.setup() > File "/petsc/config/BuildSystem/config/base.py", line 94, in setup > script.Script.setup(self) > File "/petsc/config/BuildSystem/script.py", line 108, in setup > logger.Logger.setup(self) > File "/petsc/config/BuildSystem/logger.py", line 75, in setup > args.ArgumentProcessor.setup(self) > File "/petsc/config/BuildSystem/args.py", line 76, in setup > self.setupArguments(self.argDB) > File "/petsc/config/BuildSystem/script.py", line 92, in setupArguments > self.setupHelp(self.help) > File "/petsc/config/BuildSystem/config/packages/zlib.py", line 16, in setupHelp > config.package.Package.setupHelp(self, help) > File "/petsc/config/BuildSystem/config/package.py", line 156, in setupHelp > help.addArgument(self.PACKAGE,'-with-'+self.package+'-dir=<dir>',nargs.ArgDir(None,None,'Indicate the root directory of the '+self.name+' installation',mustExist = 1)) > File "/petsc/config/BuildSystem/help.py", line 108, in addArgument > self.argDB.setType(self.getArgName(name), argType, forceLocal = 1) > File "/petsc/config/BuildSystem/RDict.py", line 222, in setType > value.setValue(v.getValue()) > File "/petsc/config/BuildSystem/nargs.py", line 325, in setValue > raise ValueError('Nonexistent directory: '+str(value)+' for key '+str(self.key)) > > > <reconfigure-arch-linux-c-debug.py> > > Best regards, > > Jacob Faibussowitsch > (Jacob Fai - booss - oh - vitch) > Cell: (312) 694-3391 >

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Configure --with-X-dir= Using Relative Path
by Jacob Faibussowitsch 02 Aug '20

02 Aug '20

Hello All, I am reconfiguring an arch within a docker using the attached reconfigure script. My petsc dir is mounted via the following commands to docker -v ${PETSC_DIR}:/petsc:delegated. I am trying to use the existing arches on my native machine as the install directories for packages compiled within the docker images because SSH keys aren’t persistent in the images and hence git pull’s won’t work. I encountered this odd bug when trying —with-zlib-dir where it prepends the existing $PETSC_DIR to the directory name automatically, but this problem persists for any package. There is no configure.log generated since this I guess is early enough in the configure process, so unfortunately the only error output is the wall of error text from terminal. The error indicates that configure is passing ./[COMMAND LINE DIRECTORY] instead of [COMMAND LINE DIRECTORY] to configure. $ ls ${PETSC_DIR}/master-arch-darwin-c-debug/externalpackages/ Permissions Size User Date Modified Name drwxrwxr-x - root 8 Jul 16:07 petsc-pkg-mumps-d1a5c931b762 drwxr-xr-x - root 3 Jul 21:39 hdf5-1.12.0 drwxrwxr-x - root 1 Aug 21:34 netcdf-c-4.5.0 drwxr-xr-x - root 3 Jul 21:38 zlib-1.2.11 drwxr-xr-x - root 29 Jul 17:43 mpich-3.3.2 drwxr-xr-x - root 6 Jul 17:06 Chaco-2.2-p2 drwxr-xr-x - root 1 Aug 21:36 git.ctetgen drwxr-xr-x - root 1 Aug 21:34 git.exodusii drwxr-xr-x - root 1 Aug 21:31 git.med drwxr-xr-x - root 1 Aug 21:31 git.metis drwxr-xr-x - root 1 Aug 21:31 git.parmetis drwxr-xr-x - root 1 Aug 21:32 git.pnetcdf drwxr-xr-x - root 1 Aug 21:35 git.scalapack drwxr-xr-x - root 1 Aug 21:31 git.sowing drwxr-xr-x - root 1 Aug 21:34 git.triangle $ echo $PETSC_DIR /petsc $./reconfigure-arch-linux-c-debug =============================================================================== Configuring PETSc to compile on your system =============================================================================== ******************************************************************************* TypeError or ValueError possibly related to ERROR in COMMAND LINE ARGUMENT while running ./configure ------------------------------------------------------------------------------- Nonexistent directory: /petsc/${PETSC_DIR}/master-arch-darwin-c-debug/externalpackages/zlib-1.2.11 for key with-zlib-dir ******************************************************************************* File "/petsc/config/configure.py", line 449, in petsc_configure framework = config.framework.Framework(['--configModules=PETSc.Configure','--optionsModule=config.compilerOptions']+sys.argv[1:], loadArgDB = 0) File "/petsc/config/BuildSystem/config/framework.py", line 107, in __init__ self.createChildren() File "/petsc/config/BuildSystem/config/framework.py", line 324, in createChildren self.getChild(moduleName) File "/petsc/config/BuildSystem/config/framework.py", line 309, in getChild config.setupDependencies(self) File "/petsc/config/PETSc/Configure.py", line 91, in setupDependencies obj = self.registerPythonFile(package,'config.packages') File "/petsc/config/PETSc/Configure.py", line 49, in registerPythonFile utilityObj = self.framework.require(directory+utilityName, self) File "/petsc/config/BuildSystem/config/framework.py", line 329, in require config = self.getChild(moduleName, keywordArgs) File "/petsc/config/BuildSystem/config/framework.py", line 309, in getChild config.setupDependencies(self) File "/petsc/config/BuildSystem/config/packages/ADIOS.py", line 17, in setupDependencies self.zlib = framework.require('config.packages.zlib',self) File "/petsc/config/BuildSystem/config/framework.py", line 329, in require config = self.getChild(moduleName, keywordArgs) File "/petsc/config/BuildSystem/config/framework.py", line 307, in getChild config.setup() File "/petsc/config/BuildSystem/config/base.py", line 94, in setup script.Script.setup(self) File "/petsc/config/BuildSystem/script.py", line 108, in setup logger.Logger.setup(self) File "/petsc/config/BuildSystem/logger.py", line 75, in setup args.ArgumentProcessor.setup(self) File "/petsc/config/BuildSystem/args.py", line 76, in setup self.setupArguments(self.argDB) File "/petsc/config/BuildSystem/script.py", line 92, in setupArguments self.setupHelp(self.help) File "/petsc/config/BuildSystem/config/packages/zlib.py", line 16, in setupHelp config.package.Package.setupHelp(self, help) File "/petsc/config/BuildSystem/config/package.py", line 156, in setupHelp help.addArgument(self.PACKAGE,'-with-'+self.package+'-dir=<dir>',nargs.ArgDir(None,None,'Indicate the root directory of the '+self.name+' installation',mustExist = 1)) File "/petsc/config/BuildSystem/help.py", line 108, in addArgument self.argDB.setType(self.getArgName(name), argType, forceLocal = 1) File "/petsc/config/BuildSystem/RDict.py", line 222, in setType value.setValue(v.getValue()) File "/petsc/config/BuildSystem/nargs.py", line 325, in setValue raise ValueError('Nonexistent directory: '+str(value)+' for key '+str(self.key)) Best regards, Jacob Faibussowitsch (Jacob Fai - booss - oh - vitch) Cell: (312) 694-3391

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