[petsc-users] Fwd: Fwd: same petsc problem

[Barry Smith]

  Version should not matter. Do other command line options work? You can also put 

   PetscOptionsSetValue("-ksp_view_mat","binary:filename"); 

in the code just before the call to KSPSolve().

   Or run in the debugger and put a break point in KSPSolve and then next/step through to see why the call to 
MatViewFromOptions() is not triggered.

  Barry


> On Jul 14, 2015, at 3:13 PM, Greg Miller <grgmiller at ucdavis.edu> wrote:
> 
> Thank you for the suggestion, Barry.  I've tried using these options, but the code generates no output.
> i.e., no saved binary files.  I'm using 3.5.3 - might that be the problem?  Do you recommend a 3.6 upgrade?
> Thank you,
> Greg
> 
> 
> On 07/13/2015 07:45 PM, Barry Smith wrote:
>> 
>>  You can save a (or multiple) linear system(s) with additional options
>> -ksp_view_mat  binary:filename -ksp_view_rhs binary:filename 
>> 
>> and then simply email the file named filename to petsc-maint at mcs.anl.gov with number of processes you are using and solver options and we can run the same problem and thus hopefully reproduce the troublesome behavior.
>> 
>> 
>>  Barry
>> 
>>> On Jul 13, 2015, at 3:23 PM, Mark Adams <mfadams at lbl.gov> wrote:
>>> 
>>> Please respond to all, to get the petsc mailing list.
>>> 
>>> The out file here looks fine.  It would help of you run in debug mode (and get -g) so that gdb can give line numbers.
>>> 
>>> If the error is in the dot product it looks like you are getting an Inf or Nan someplace.  If the first evaluation of the norm was the problem then run the bad code and add a VecView and MatView, and add a VecNorm and MatNorm so that the error happens in your code, just to check.  If you had 1e200 number in the vector then the 2 norm would give you this trap for overflow.  You could test with the inf norm and it works then it is an overflow problem.
>>> 
>>> 
>>> 
>>> 
>>> ---------- Forwarded message ----------
>>> From: Greg Miller <grgmiller at ucdavis.edu>
>>> Date: Mon, Jul 13, 2015 at 3:54 PM
>>> Subject: Re: Fwd: same petsc problem
>>> To: Mark Adams <mfadams at lbl.gov>
>>> Cc: "treb at lbl.gov" <treb at lbl.gov>
>>> 
>>> 
>>> thanks.  here it is.
>>> 
>>> I'm not getting the nan problem with this code - not sure why.  NaN  was showing up KSP_solve in the first evaluation of the vector norm.
>>> In going from my original example to the minimal code I mailed today the matrix coefficients got rounded through asci printing.
>>> That's the only difference I can think of.  The gdb stack from the old code is shown below.
>>> G
>>> 
>>> 
>>> 
>>> Program received signal SIGFPE, Arithmetic exception.
>>> 0x00007ffff6c4ed15 in ddot_ () from /usr/lib/libblas.so.3
>>> (gdb) where
>>> #0  0x00007ffff6c4ed15 in ddot_ () from /usr/lib/libblas.so.3
>>> #1  0x00000000008f87da in VecNorm_Seq (xin=0x22e7ca0, type=NORM_2, z=0x7fffffffba30)
>>>    at /home/usr/local/src/petsc-3.5.3/src/vec/vec/impls/seq/bvec2.c:614
>>> #2  0x00000000008c9eea in VecNorm (x=0x22e7ca0, type=NORM_2, val=0x7fffffffba30)
>>>    at /home/usr/local/src/petsc-3.5.3/src/vec/vec/interface/rvector.c:242
>>> #3  0x00000000008cab40 in VecNormalize (x=0x22e7ca0, val=0x7fffffffbaa0) at /home/usr/local/src/petsc-3.5.3/src/vec/vec/interface/rvector.c:337
>>> #4  0x0000000000d44a9d in KSPGMRESCycle (itcount=0x7fffffffbb08, ksp=0x2288ff0)
>>>    at /home/usr/local/src/petsc-3.5.3/src/ksp/ksp/impls/gmres/gmres.c:161
>>> #5  0x0000000000d453e3 in KSPSolve_GMRES (ksp=0x2288ff0) at /home/usr/local/src/petsc-3.5.3/src/ksp/ksp/impls/gmres/gmres.c:235
>>> 
>>> 
>>> On 07/13/2015 11:54 AM, Mark Adams wrote:
>>>> Greg, I am forwarding this to the PETSc mailing list.
>>>> 
>>>> Please send the entire output from this run.  As I recall you were getting a message that all values were not the same on all processors in GMRES.  I have seen this when I get NaNs in the system.
>>>> 
>>>> While you are doing this you should use a simple solver like change:
>>>> 
>>>> -pressure_pc_type gamg
>>>> 
>>>> to
>>>> 
>>>> -pressure_pc_type jacobi
>>>> 
>>>> 
>>>> And add:
>>>> 
>>>> *-*pressure_*ksp_monitor_true_residual*
>>>> 
>>>> Mark
>>>> 
>>>> 
>>>> ---------- Forwarded message ----------
>>>> From: *Greg Miller* <grgmiller at ucdavis.edu <mailto:grgmiller at ucdavis.edu>>
>>>> Date: Mon, Jul 13, 2015 at 2:08 PM
>>>> Subject: same petsc problem
>>>> To: Mark Adams <mfadams at lbl.gov <mailto:mfadams at lbl.gov>>
>>>> Cc: David Trebotich <treb at hpcrd.lbl.gov <mailto:treb at hpcrd.lbl.gov>>
>>>> 
>>>> 
>>>> Hi Mark.  I'm still stuck on the same petsc problem.   Would you please try the attached minimal example and advise me?
>>>> 
>>>> I'm running this without MPI:
>>>> make DIM=2 DEBUG=TRUE MPI=FALSE USE_PETSC=TRUE test
>>>> 
>>>> There is no input file.
>>>> 
>>>> Thank you,
>>>> Greg
>>>> 
>>>> --
>>>> Greg Miller
>>>> Department of Chemical Engineering and Materials Science
>>>> University of California, Davis
>>>> One Shields Avenue
>>>> Davis, CA 95616
>>>> grgmiller at ucdavis.edu <mailto:grgmiller at ucdavis.edu>
>>>> 
>>> 
>>> --
>>> Greg Miller
>>> Department of Chemical Engineering and Materials Science
>>> University of California, Davis
>>> One Shields Avenue
>>> Davis, CA 95616
>>> grgmiller at ucdavis.edu
>>> 
>>> <out.txt>
>> 
> 
> -- 
> Greg Miller
> Department of Chemical Engineering and Materials Science
> University of California, Davis
> One Shields Avenue
> Davis, CA 95616
> grgmiller at ucdavis.edu