[petsc-users] Floating point exception
Barry Smith
bsmith at mcs.anl.gov
Fri Apr 24 15:16:53 CDT 2015
It is probably stopping here on a harmless underflow. You need to edit the PETSc code to not worry about underflow.
Edit the file /home/dsu/Soft/PETSc/petsc-3.5.2/src/sys/error/fp.c and locate
#elif defined PETSC_HAVE_XMMINTRIN_H
_MM_SET_EXCEPTION_MASK(_MM_MASK_INEXACT);
#else
change it to
#elif defined PETSC_HAVE_XMMINTRIN_H
_MM_SET_EXCEPTION_MASK(_MM_MASK_INEXACT | _MM_MASK_UNDERFLOW);
#else
Then run make gnumake in the PETSc directory to compile the new version. Now link and run the program again with -fp_trap and see where it gets stuck this time.
Barry
> On Apr 24, 2015, at 3:01 PM, Danyang Su <danyang.su at gmail.com> wrote:
>
>
>
> On 15-04-24 11:12 AM, Barry Smith wrote:
>>> On Apr 24, 2015, at 1:05 PM, Danyang Su <danyang.su at gmail.com> wrote:
>>>
>>> Hi All,
>>>
>>> One of my case crashes because of floating point exception when using 4 processors, as shown below. But if I run this case with 1 processor, it works fine. I have tested the codes with around 100 cases up to 768 processors, all other cases work fine. I just wonder if this kind of error is caused because of NaN in jacobi matrix, RHS or preconditioner?
>> Yes, almost for sure it is one of these places.
>>
>> First run the bad case with -fp_trap if all goes well you'll see the function where the FPE is generated. Then run also with -start_in_debugger and
>> type cont in all four debugger windows. When the FPE happens the debugger should stop showing exactly where the FPE happens.
>>
>> Barry
> Hi Barry,
>
> If run with -fp_trap -start_in_debugger, I got the following error
>
> [0]PETSC ERROR: *** unknown floating point error occurred ***
> [0]PETSC ERROR: The specific exception can be determined by running in a debugger. When the
> [0]PETSC ERROR: debugger traps the signal, the exception can be found with fetestexcept(0x3d)
> [0]PETSC ERROR: where the result is a bitwise OR of the following flags:
> [0]PETSC ERROR: FE_INVALID=0x1 FE_DIVBYZERO=0x4 FE_OVERFLOW=0x8 FE_UNDERFLOW=0x10 FE_INEXACT=0x20
> [0]PETSC ERROR: Try option -start_in_debugger
> [0]PETSC ERROR: likely location of problem given in stack below
> [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> [0]PETSC ERROR: INSTEAD the line number of the start of the function
> [0]PETSC ERROR: is given.
> [0]PETSC ERROR: [0] PetscDefaultFPTrap line 379 /home/dsu/Soft/PETSc/petsc-3.5.2/src/sys/error/fp.c
> [0]PETSC ERROR: User provided function() line 0 in Unknown file trapped floating point error
>
> Program received signal SIGABRT: Process abort signal.
>
> Backtrace for this error:
> #0 0x7F4FEAB1C7D7
> #1 0x7F4FEAB1CDDE
> #2 0x7F4FE9E1AD3F
> #3 0x7F4FE9E1ACC9
> #4 0x7F4FE9E1E0D7
> #5 0x7F4FEB0B6DCB
> #6 0x7F4FEB0B1825
> #7 0x7F4FEB0B817F
> #8 0x7F4FE9E1AD3F
> #9 0x6972C8 in tprfrtlc_ at tprfrtlc.F90:2393 (discriminator 3)
> #10 0x4C6C87 in gcreact_ at gcreact.F90:678
> #11 0x707E19 in initicrt_ at initicrt.F90:589
> #12 0x4F42D0 in initprob_ at initprob.F90:430
> #13 0x5AAF72 in driver_pc at driver_pc.F90:438
>
> I checked the code at tprfrtlc.F90:2393,
>
> realbuffer_gb(1:nvars) = (/time,(c(ic),ic=1,nc-1), &
> (cx(ix),ix=1,nxout)/)
>
> All the values (time, c, cx) are reasonable, as shown below. The only possibility is that realbuffer_gb is in declared as real*4 if using sing precision output while time, c, cx are declared in real*8. I have a lot of similar data conversion from real*8 to real*4 output, other code does not return error.
>
> time 0.0000000000000000
> c 1 9.9999999999999995E-008
> c 2 3.1555251077549618E-003
> c 3 7.1657814842179362E-008
> c 4 1.0976214263087059E-067
> c 5 5.2879822292305797E-004
> c 6 9.9999999999999964E-005
> c 7 6.4055731968811337E-005
> c 8 3.4607572892578404E-020
> cx 1 3.4376650636008101E-005
> cx 2 7.3989678854017763E-012
> cx 3 9.5317170613607207E-012
> cx 4 2.2344525794718353E-015
> cx 5 3.0624685689695889E-008
> cx 6 1.0046157902783967E-007
> cx 7 1.5320169154914984E-004
> cx 8 8.6930292776346176E-014
> cx 9 3.5944267559348721E-005
> cx 10 3.0072645866951157E-018
> cx 11 2.3592486321095017E-013
>
> Thanks,
>
> Danyang
>
>>
>>> I can check all the entries of jacobi matrix to see if the value is valid, but this seems not a good idea as it takes a long time to reach this point. If I restart the simulation from a specified time (e.g., 7.685 in this case), then the error does not occur.
>>>
>>> Would you please give me any suggestion on debugging this case?
>>>
>>> Thanks and Regards,
>>>
>>> Danyang
>>>
>>>
>>> timestep: 2730 time: 7.665E+00 years delt: 1.000E-02 years iter: 1 max.sia: 0.000E+00 tol.sia: 0.000E+00
>>> timestep: 2731 time: 7.675E+00 years delt: 1.000E-02 years iter: 1 max.sia: 0.000E+00 tol.sia: 0.000E+00
>>> timestep: 2732 time: 7.685E+00 years delt: 1.000E-02 years iter: 1 max.sia: 0.000E+00 tol.sia: 0.000E+00
>>> timestep: 2733 time: 7.695E+00 years delt: 1.000E-02 years iter: 1 max.sia: 0.000E+00 tol.sia: 0.000E+00
>>> timestep: 2734 time: 7.705E+00 years delt: 1.000E-02 years iter: 1 max.sia: 0.000E+00 tol.sia: 0.000E+00
>>> Reduce time step for reactive transport
>>> timestep: 2734 time: 7.700E+00 years delt: 5.000E-03 years iter: 1 max.sia: 0.000E+00 tol.sia: 0.000E+00
>>> Reduce time step for reactive transport
>>> timestep: 2734 time: 7.697E+00 years delt: 2.500E-03 years iter: 1 max.sia: 0.000E+00 tol.sia: 0.000E+00
>>> [1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
>>> [1]PETSC ERROR: Floating point exception
>>> [2]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
>>> [2]PETSC ERROR: Floating point exception
>>> [2]PETSC ERROR: Vec entry at local location 0 is not-a-number or infinite at end of function: Parameter number 3
>>> [2]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>>> [2]PETSC ERROR: Petsc Release Version 3.5.2, Sep, 08, 2014
>>> [2]PETSC ERROR: [1]PETSC ERROR: Vec entry at local location 0 is not-a-number or infinite at end of function: Parameter number 3
>>> [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>>> [1]PETSC ERROR: Petsc Release Version 3.5.2, Sep, 08, 2014
>>> [1]PETSC ERROR: ../min3p_thcm_petsc_dbg on a linux-gnu-dbg named nwmop by dsu Thu Apr 23 15:38:52 2015
>>> [1]PETSC ERROR: Configure options PETSC_ARCH=linux-gnu-dbg --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack --download-mpich --download-mumps --download-hypre --download-superlu_dist --download-metis --download-parmetis --download-scalapack
>>> [1]PETSC ERROR: #1 VecValidValues() line 34 in /home/dsu/Soft/PETSc/petsc-3.5.2/src/vec/vec/interface/rvector.c
>>> ../min3p_thcm_petsc_dbg on a linux-gnu-dbg named nwmop by dsu Thu Apr 23 15:38:52 2015
>>> [2]PETSC ERROR: Configure options PETSC_ARCH=linux-gnu-dbg --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack --download-mpich --download-mumps --download-hypre --download-superlu_dist --download-metis --download-parmetis --download-scalapack
>>> [2]PETSC ERROR: #1 VecValidValues() line 34 in /home/dsu/Soft/PETSc/petsc-3.5.2/src/vec/vec/interface/rvector.c
>>> [2]PETSC ERROR: [1]PETSC ERROR: #2 PCApply() line 442 in /home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/pc/interface/precon.c
>>> [1]PETSC ERROR: #2 PCApply() line 442 in /home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/pc/interface/precon.c
>>> [2]PETSC ERROR: #3 KSP_PCApply() line 230 in /home/dsu/Soft/PETSc/petsc-3.5.2/include/petsc-private/kspimpl.h
>>> #3 KSP_PCApply() line 230 in /home/dsu/Soft/PETSc/petsc-3.5.2/include/petsc-private/kspimpl.h
>>> [1]PETSC ERROR: #4 KSPInitialResidual() line 63 in /home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/ksp/interface/itres.c
>>> [2]PETSC ERROR: #4 KSPInitialResidual() line 63 in /home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/ksp/interface/itres.c
>>> [1]PETSC ERROR: #5 KSPSolve_GMRES() line 234 in /home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/ksp/impls/gmres/gmres.c
>>> [2]PETSC ERROR: #5 KSPSolve_GMRES() line 234 in /home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/ksp/impls/gmres/gmres.c
>>> [2]PETSC ERROR: #6 KSPSolve() line 459 in /home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/ksp/interface/itfunc.c
>>> [1]PETSC ERROR: #6 KSPSolve() line 459 in /home/dsu/Soft/PETSc/petsc-3.5.2/src/ksp/ksp/interface/itfunc.c
>>> ^C[mpiexec at nwmop] Sending Ctrl-C to processes as requested
>>> [mpiexec at nwmop] Press Ctrl-C again to force abort
>
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