[petsc-users] Floating point exception
Barry Smith
bsmith at mcs.anl.gov
Sat Apr 25 13:32:07 CDT 2015
I told you this yesterday.
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.
Did you do this?
Barry
> On Apr 25, 2015, at 1:05 AM, Danyang Su <danyang.su at gmail.com> wrote:
>
> Hi Barry and Satish,
>
> How can I get rid of unknown floating point error when a very small value is multiplied.
>
> e.g.,
> cinfrt_dg(i1) and diff(ic,idim) are 1.0250235986806329E-008 8.6178408169776945E-317 respectively,
>
> cinfrt = cinfrt_dg(i1) * diff(ic,idim)
>
> I get the following error when run with "-fp_trap -start_in_debugger".
>
> Backtrace for this error:
> *** unknown floating point error occurred ***
> [2]PETSC ERROR: The specific exception can be determined by running in a debugger. When the
> [2]PETSC ERROR: debugger traps the signal, the exception can be found with fetestexcept(0x3d)
> [2]PETSC ERROR: cinfrt_dg(i1),diff(ic,idim) 1.0250235986806329E-008 8.6178408169776945E-317
> where the result is a bitwise OR of the following flags:
> [2]PETSC ERROR: FE_INVALID=0x1 FE_DIVBYZERO=0x4 FE_OVERFLOW=0x8 FE_UNDERFLOW=0x10 FE_INEXACT=0x20
> [2]PETSC ERROR: Try option -start_in_debugger
> [2]PETSC ERROR: likely location of problem given in stack below
>
> Thanks,
>
> Danyang
>
> On 15-04-24 01:54 PM, Danyang Su wrote:
>> On 15-04-24 01:23 PM, Satish Balay wrote:
>>> c 4 1.0976214263087059E-067
>>>
>>> I don't think this number can be stored in a real*4.
>>>
>>> Satish
>> Thanks, Satish. It is caused by this number.
>>>
>>> On Fri, 24 Apr 2015, Danyang Su 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
>>>>>> timestep: max.sia: 0.000E+00 tol.sia: 0.000E+00
>>>>>> timestep: 2731 time: 7.675E+00 years delt: 1.000E-02 years iter: 1
>>>>>> timestep: max.sia: 0.000E+00 tol.sia: 0.000E+00
>>>>>> timestep: 2732 time: 7.685E+00 years delt: 1.000E-02 years iter: 1
>>>>>> timestep: max.sia: 0.000E+00 tol.sia: 0.000E+00
>>>>>> timestep: 2733 time: 7.695E+00 years delt: 1.000E-02 years iter: 1
>>>>>> timestep: max.sia: 0.000E+00 tol.sia: 0.000E+00
>>>>>> timestep: 2734 time: 7.705E+00 years delt: 1.000E-02 years iter: 1
>>>>>> timestep: 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
>>>>>> timestep: 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
>>>>>> timestep: 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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