[petsc-users] Floating point exception
Barry Smith
bsmith at mcs.anl.gov
Sat Apr 25 13:55:15 CDT 2015
> On Apr 25, 2015, at 1:51 PM, Danyang Su <danyang.su at gmail.com> wrote:
>
>
>
> On 15-04-25 11:32 AM, Barry Smith wrote:
>> 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
> Yes, I did change the code in fp.c and run 'make gnumake' in the PETSc directory. I just did a double check and ran make gnumake again and got the following information this time.
>
> dsu at nwmop:~/Soft/PETSc/petsc-3.5.2$ make gnumake
> Building PETSc using GNU Make with 10 build threads
> ==========================================
> make[1]: Entering directory `/home/dsu/Soft/PETSc/petsc-3.5.2'
> make[1]: Nothing to be done for `all'.
> make[1]: Leaving directory `/home/dsu/Soft/PETSc/petsc-3.5.2'
> =========================================
>
>
> Then I recompiled the codes, ran with -fp_trap and still got the following error
>
> Backtrace for this error:
> Note: The EXACT line numbers in the stack are not available,
> [2]PETSC ERROR: INSTEAD the line number of the start of the function
> [2]PETSC ERROR: is given.
> [2]PETSC ERROR: [2] PetscDefaultFPTrap line 379 /home/dsu/Soft/PETSc/petsc-3.5.2/src/sys/error/fp.c
> INSTEAD the line number of the start of the function
> [3]PETSC ERROR: is given.
> [3]PETSC ERROR: [3] PetscDefaultFPTrap line 379 /home/dsu/Soft/PETSc/petsc-3.5.2/src/sys/error/fp.c
> [2]PETSC ERROR: User provided function() line 0 in Unknown file trapped floating point error
> [3]PETSC ERROR: User provided function() line 0 in Unknown file trapped floating point error
>
This is different then what you sent a few minutes ago where it crashed in hypre.
Anyways you need to use the -start_in_debugger business I sent in the previous email to see the exact place the problem occurs.
> Thanks,
>
> Danyang
>>> 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
More information about the petsc-users
mailing list