[petsc-users] mesh refinement PETSc3.5.4 with HYPRE
Hao Zhang
hbcbh1999 at gmail.com
Fri Sep 29 22:51:44 CDT 2017
is there a builtin way in PETSc I can flush cache in C++, specifically
matrix entries so that I can look up? to check which entry is NaN. Thanks.
On Fri, Sep 29, 2017 at 11:16 PM, Hao Zhang <hbcbh1999 at gmail.com> wrote:
> Thanks!
>
> On Fri, Sep 29, 2017 at 11:14 PM, Satish Balay <balay at mcs.anl.gov> wrote:
>
>> On Sat, 30 Sep 2017, Hao Zhang wrote:
>>
>> > it seems that running petsc with download-mpich is a dead end for me.
>> I've
>> > re-compiled PETSc with mpich options but I can't reinstall TORQUE for
>> all
>> > users just for my own test. TORQUE needs root access.
>> > Do you have more suggestion on the issue?
>>
>> As mentioned - the previous log pointed to errors in your code. You
>> should look
>> at them - and try to fix your code.
>>
>> > just a quick refresh. my PETSc
>> > complained floating point exception. for coarse and medium mesh grid
>> > without fp_trap option, my program runs. with fp_trap, program crashed
>> > right away.
>>
>> After memory corruptions are eliminated - if the errors persist - you
>> might have to use the debugger to determine why NaNs are getting
>> generated.
>>
>> Satish
>>
>> >
>> > Thanks again!
>> >
>> > On Fri, Sep 29, 2017 at 9:33 PM, Hao Zhang <hbcbh1999 at gmail.com> wrote:
>> >
>> > > Thanks. I will recompile and submit a new debug log
>> > >
>> > > On Fri, Sep 29, 2017 at 9:31 PM, Satish Balay <balay at mcs.anl.gov>
>> wrote:
>> > >
>> > >> Most of this is from openmpi. Its best to use --download-mpich
>> > >> for valgrind clean mpi as mentioned below.
>> > >>
>> > >> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>> > >>
>> > >> [attempting to remove openmpi messages] - all messages below appear
>> to
>> > >> be from your appliation code. And I don't see any messages from PETSc
>> > >> code in this log.
>> > >>
>> > >> Once there is memory corruption we get random behavior from
>> > >> application. So its best to fix all these issues and make this
>> > >> application valgrind clean.
>> > >>
>> > >> Satish
>> > >>
>> > >> On Sat, 30 Sep 2017, Hao Zhang wrote:
>> > >>
>> > >> <snip>
>> > >>
>> > >> > ==31497== Invalid write of size 8
>> > >> > ==31497== at 0x643685: level_wave_func_Meniscus
>> (imkcurve.c:1826)
>> > >> > ==31497== by 0x65299B: assign_two_comp_domain (imksurf.c:2046)
>> > >> > ==31497== by 0x64623B: make_level_surface (imksurf.c:245)
>> > >> > ==31497== by 0x5458AF: FT_InitIntfc3d (finit.c:2137)
>> > >> > ==31497== by 0x544CA3: FT_InitIntfc (finit.c:1853)
>> > >> > ==31497== by 0x40C072: main (iFluid.cpp:218)
>> > >> > ==31497== Address 0x7fe859c38 is on thread 1's stack
>> > >> > ==31497==
>> > >> > ==31497== Invalid write of size 8
>> > >> > ==31497== at 0x64368C: level_wave_func_Meniscus
>> (imkcurve.c:1826)
>> > >> > ==31497== by 0x65299B: assign_two_comp_domain (imksurf.c:2046)
>> > >> > ==31497== by 0x64623B: make_level_surface (imksurf.c:245)
>> > >> > ==31497== by 0x5458AF: FT_InitIntfc3d (finit.c:2137)
>> > >> > ==31497== by 0x544CA3: FT_InitIntfc (finit.c:1853)
>> > >> > ==31497== by 0x40C072: main (iFluid.cpp:218)
>> > >> > ==31497== Address 0x7fe859c30 is on thread 1's stack
>> > >> > ==31497==
>> > >> > ==31497== Invalid read of size 8
>> > >> > ==31497== at 0x643693: level_wave_func_Meniscus
>> (imkcurve.c:1831)
>> > >> > ==31497== by 0x65299B: assign_two_comp_domain (imksurf.c:2046)
>> > >> > ==31497== by 0x64623B: make_level_surface (imksurf.c:245)
>> > >> > ==31497== by 0x5458AF: FT_InitIntfc3d (finit.c:2137)
>> > >> > ==31497== by 0x544CA3: FT_InitIntfc (finit.c:1853)
>> > >> > ==31497== by 0x40C072: main (iFluid.cpp:218)
>> > >> > ==31497== Address 0x7fe859c38 is on thread 1's stack
>> > >> > ==31497==
>> > >> > ==31497== Invalid write of size 8
>> > >> > ==31497== at 0x64372D: level_wave_func_Meniscus
>> (imkcurve.c:1848)
>> > >> > ==31497== by 0x65299B: assign_two_comp_domain (imksurf.c:2046)
>> > >> > ==31497== by 0x64623B: make_level_surface (imksurf.c:245)
>> > >> > ==31497== by 0x5458AF: FT_InitIntfc3d (finit.c:2137)
>> > >> > ==31497== by 0x544CA3: FT_InitIntfc (finit.c:1853)
>> > >> > ==31497== by 0x40C072: main (iFluid.cpp:218)
>> > >> > ==31497== Address 0x7fe859c18 is on thread 1's stack
>> > >> > ==31497==
>> > >> > ==31497== Invalid read of size 8
>> > >> > ==31497== at 0x7ED3127: tan (in /lib64/libm-2.12.so)
>> > >> > ==31497== by 0x65299B: assign_two_comp_domain (imksurf.c:2046)
>> > >> > ==31497== by 0x64623B: make_level_surface (imksurf.c:245)
>> > >> > ==31497== by 0x5458AF: FT_InitIntfc3d (finit.c:2137)
>> > >> > ==31497== by 0x544CA3: FT_InitIntfc (finit.c:1853)
>> > >> > ==31497== by 0x40C072: main (iFluid.cpp:218)
>> > >> > ==31497== Address 0x7fe859c18 is on thread 1's stack
>> > >> > ==31497==
>> > >> > ==31497== Invalid read of size 8
>> > >> > ==31497== at 0x643755: level_wave_func_Meniscus
>> (imkcurve.c:1853)
>> > >> > ==31497== by 0x65299B: assign_two_comp_domain (imksurf.c:2046)
>> > >> > ==31497== by 0x64623B: make_level_surface (imksurf.c:245)
>> > >> > ==31497== by 0x5458AF: FT_InitIntfc3d (finit.c:2137)
>> > >> > ==31497== by 0x544CA3: FT_InitIntfc (finit.c:1853)
>> > >> > ==31497== by 0x40C072: main (iFluid.cpp:218)
>> > >> > ==31497== Address 0x7fe859c30 is on thread 1's stack
>> > >> > ==31497==
>> > >> > ==31497== Invalid read of size 8
>> > >> > ==31497== at 0x643765: level_wave_func_Meniscus
>> (imkcurve.c:1854)
>> > >> > ==31497== by 0x65299B: assign_two_comp_domain (imksurf.c:2046)
>> > >> > ==31497== by 0x64623B: make_level_surface (imksurf.c:245)
>> > >> > ==31497== by 0x5458AF: FT_InitIntfc3d (finit.c:2137)
>> > >> > ==31497== by 0x544CA3: FT_InitIntfc (finit.c:1853)
>> > >> > ==31497== by 0x40C072: main (iFluid.cpp:218)
>> > >> > ==31497== Address 0x7fe859c30 is on thread 1's stack
>> > >> > ==31497==
>> > >> > ==31497== Invalid read of size 8
>> > >> > ==31497== at 0x643A7F: level_wave_func_Meniscus
>> (imkcurve.c:1944)
>> > >> > ==31497== by 0x65299B: assign_two_comp_domain (imksurf.c:2046)
>> > >> > ==31497== by 0x64623B: make_level_surface (imksurf.c:245)
>> > >> > ==31497== by 0x5458AF: FT_InitIntfc3d (finit.c:2137)
>> > >> > ==31497== by 0x544CA3: FT_InitIntfc (finit.c:1853)
>> > >> > ==31497== by 0x40C072: main (iFluid.cpp:218)
>> > >> > ==31497== Address 0x7fe859c30 is on thread 1's stack
>> > >> > ==31497==
>> > >> > ==31497== Invalid write of size 8
>> > >> > ==31497== at 0x643A92: level_wave_func_Meniscus
>> (imkcurve.c:1944)
>> > >> > ==31497== by 0x65299B: assign_two_comp_domain (imksurf.c:2046)
>> > >> > ==31497== by 0x64623B: make_level_surface (imksurf.c:245)
>> > >> > ==31497== by 0x5458AF: FT_InitIntfc3d (finit.c:2137)
>> > >> > ==31497== by 0x544CA3: FT_InitIntfc (finit.c:1853)
>> > >> > ==31497== by 0x40C072: main (iFluid.cpp:218)
>> > >> > ==31497== Address 0x7feffecf0 is on thread 1's stack
>> > >> > ==31497==
>> > >> > ==31497== Invalid read of size 8
>> > >> > ==31497== at 0x643AEB: level_wave_func_Meniscus
>> (imkcurve.c:1955)
>> > >> > ==31497== by 0x65299B: assign_two_comp_domain (imksurf.c:2046)
>> > >> > ==31497== by 0x64623B: make_level_surface (imksurf.c:245)
>> > >> > ==31497== by 0x5458AF: FT_InitIntfc3d (finit.c:2137)
>> > >> > ==31497== by 0x544CA3: FT_InitIntfc (finit.c:1853)
>> > >> > ==31497== by 0x40C072: main (iFluid.cpp:218)
>> > >> > ==31497== Address 0x7feffecf0 is on thread 1's stack
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x428B9F:
>> > >> > Incompress_Solver_Smooth_Basis::setAdvectionDt_vd()
>> (iFbasic.cpp:2799)
>> > >> > ==31497== by 0x4B8BB9:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::setInitialCondition_
>> > >> RSSY_vd(_LEVEL_FUNC_PACK*)
>> > >> > (iFcartsn3d.cpp:15253)
>> > >> > ==31497== by 0x40C485: main (iFluid.cpp:349)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x428BA9:
>> > >> > Incompress_Solver_Smooth_Basis::setAdvectionDt_vd()
>> (iFbasic.cpp:2799)
>> > >> > ==31497== by 0x4B8BB9:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::setInitialCondition_
>> > >> RSSY_vd(_LEVEL_FUNC_PACK*)
>> > >> > (iFcartsn3d.cpp:15253)
>> > >> > ==31497== by 0x40C485: main (iFluid.cpp:349)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x85B00E3: vfprintf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85BA189: printf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x486108:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::compDiffWithSmoothPro
>> > >> perty_velocity_MAC_coupled_vd()
>> > >> > (iFcartsn3d.cpp:6101)
>> > >> > ==31497== by 0x4CBF0D:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::solve_vd(double)
>> > >> > (iFcartsn3d.cpp:18574)
>> > >> > ==31497== by 0x40C72E: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:419)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x85B0101: vfprintf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85BA189: printf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x486108:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::compDiffWithSmoothPro
>> > >> perty_velocity_MAC_coupled_vd()
>> > >> > (iFcartsn3d.cpp:6101)
>> > >> > ==31497== by 0x4CBF0D:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::solve_vd(double)
>> > >> > (iFcartsn3d.cpp:18574)
>> > >> > ==31497== by 0x40C72E: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:419)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x4ED737:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::computeSubgridModel_vd()
>> > >> > (iFcartsn3d.cpp:24519)
>> > >> > ==31497== by 0x4CBFBC:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::solve_vd(double)
>> > >> > (iFcartsn3d.cpp:18594)
>> > >> > ==31497== by 0x40C72E: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:419)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x4ED754:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::computeSubgridModel_vd()
>> > >> > (iFcartsn3d.cpp:24519)
>> > >> > ==31497== by 0x4CBFBC:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::solve_vd(double)
>> > >> > (iFcartsn3d.cpp:18594)
>> > >> > ==31497== by 0x40C72E: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:419)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x85B4CF0: __printf_fp (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85B089F: vfprintf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85BA189: printf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x4ED9F7:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::computeSubgridModel_vd()
>> > >> > (iFcartsn3d.cpp:24549)
>> > >> > ==31497== by 0x4CBFBC:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::solve_vd(double)
>> > >> > (iFcartsn3d.cpp:18594)
>> > >> > ==31497== by 0x40C72E: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:419)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x85B4F91: __printf_fp (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85B089F: vfprintf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85BA189: printf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x4ED9F7:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::computeSubgridModel_vd()
>> > >> > (iFcartsn3d.cpp:24549)
>> > >> > ==31497== by 0x4CBFBC:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::solve_vd(double)
>> > >> > (iFcartsn3d.cpp:18594)
>> > >> > ==31497== by 0x40C72E: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:419)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x85AE396: __mpn_extract_double (in /lib64/
>> libc-2.12.so
>> > >> )
>> > >> > ==31497== by 0x85B51BD: __printf_fp (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85B089F: vfprintf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85BA189: printf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x4ED9F7:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::computeSubgridModel_vd()
>> > >> > (iFcartsn3d.cpp:24549)
>> > >> > ==31497== by 0x4CBFBC:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::solve_vd(double)
>> > >> > (iFcartsn3d.cpp:18594)
>> > >> > ==31497== by 0x40C72E: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:419)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x85AE39B: __mpn_extract_double (in /lib64/
>> libc-2.12.so
>> > >> )
>> > >> > ==31497== by 0x85B51BD: __printf_fp (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85B089F: vfprintf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85BA189: printf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x4ED9F7:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::computeSubgridModel_vd()
>> > >> > (iFcartsn3d.cpp:24549)
>> > >> > ==31497== by 0x4CBFBC:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::solve_vd(double)
>> > >> > (iFcartsn3d.cpp:18594)
>> > >> > ==31497== by 0x40C72E: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:419)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x85B59EC: __printf_fp (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85B089F: vfprintf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85BA189: printf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x4ED9F7:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::computeSubgridModel_vd()
>> > >> > (iFcartsn3d.cpp:24549)
>> > >> > ==31497== by 0x4CBFBC:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::solve_vd(double)
>> > >> > (iFcartsn3d.cpp:18594)
>> > >> > ==31497== by 0x40C72E: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:419)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x85B5A9D: __printf_fp (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85B089F: vfprintf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85BA189: printf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x4ED9F7:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::computeSubgridModel_vd()
>> > >> > (iFcartsn3d.cpp:24549)
>> > >> > ==31497== by 0x4CBFBC:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::solve_vd(double)
>> > >> > (iFcartsn3d.cpp:18594)
>> > >> > ==31497== by 0x40C72E: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:419)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x85B5C13: __printf_fp (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85B089F: vfprintf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85BA189: printf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x4ED9F7:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::computeSubgridModel_vd()
>> > >> > (iFcartsn3d.cpp:24549)
>> > >> > ==31497== by 0x4CBFBC:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::solve_vd(double)
>> > >> > (iFcartsn3d.cpp:18594)
>> > >> > ==31497== by 0x40C72E: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:419)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x85B5CA4: __printf_fp (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85B089F: vfprintf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85BA189: printf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x4ED9F7:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::computeSubgridModel_vd()
>> > >> > (iFcartsn3d.cpp:24549)
>> > >> > ==31497== by 0x4CBFBC:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::solve_vd(double)
>> > >> > (iFcartsn3d.cpp:18594)
>> > >> > ==31497== by 0x40C72E: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:419)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x85B625E: __printf_fp (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85B089F: vfprintf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85BA189: printf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x4ED9F7:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::computeSubgridModel_vd()
>> > >> > (iFcartsn3d.cpp:24549)
>> > >> > ==31497== by 0x4CBFBC:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::solve_vd(double)
>> > >> > (iFcartsn3d.cpp:18594)
>> > >> > ==31497== by 0x40C72E: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:419)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497==
>> > >> > ==31497== Conditional jump or move depends on uninitialised
>> value(s)
>> > >> > ==31497== at 0x85B6242: __printf_fp (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85B089F: vfprintf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85BA189: printf (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x4ED9F7:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::computeSubgridModel_vd()
>> > >> > (iFcartsn3d.cpp:24549)
>> > >> > ==31497== by 0x4CBFBC:
>> > >> > Incompress_Solver_Smooth_3D_Cartesian::solve_vd(double)
>> > >> > (iFcartsn3d.cpp:18594)
>> > >> > ==31497== by 0x40C72E: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:419)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497==
>> > >> > ==31497== Syscall param write(buf) points to uninitialised byte(s)
>> > >> > ==31497== at 0x86465ED: ??? (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x85DCAD2: _IO_file_write@@GLIBC_2.2.5 (in /lib64/
>> > >> > libc-2.12.so)
>> > >> > ==31497== by 0x85DE084: _IO_do_write@@GLIBC_2.2.5 (in /lib64/
>> > >> libc-2.12.so
>> > >> > )
>> > >> > ==31497== by 0x85DD287: _IO_file_sync@@GLIBC_2.2.5 (in /lib64/
>> > >> > libc-2.12.so)
>> > >> > ==31497== by 0x85D1999: fflush (in /lib64/libc-2.12.so)
>> > >> > ==31497== by 0x6FACFA: preserve_front_advance_front3d
>> (fadv.c:2255)
>> > >> > ==31497== by 0x6FA14E: mixed_advance_front3d (fadv.c:1895)
>> > >> > ==31497== by 0x6F9B2D: advance_front3d_tracking_control
>> > >> (fadv.c:1703)
>> > >> > ==31497== by 0x54E119: FrontAdvance (fmap.c:142)
>> > >> > ==31497== by 0x54DF27: FT_Propagate (fmap.c:80)
>> > >> > ==31497== by 0x40CA37: ifluid_driver(_Front*,
>> > >> > Incompress_Solver_Smooth_Basis*, _F_BASIC_DATA*) (iFluid.cpp:512)
>> > >> > ==31497== by 0x40C4F3: main (iFluid.cpp:369)
>> > >> > ==31497== Address 0x412308a is not stack'd, malloc'd or (recently)
>> > >> free'd
>> > >> > ==31497==
>> > >> >
>> > >> > On Fri, Sep 29, 2017 at 8:45 PM, Satish Balay <balay at mcs.anl.gov>
>> > >> wrote:
>> > >> >
>> > >> > > Can you run this code with valgrind and send the log?
>> > >> > >
>> > >> > > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>> > >> > >
>> > >> > > Satish
>> > >> > >
>> > >> > > On Sat, 30 Sep 2017, Hao Zhang wrote:
>> > >> > >
>> > >> > > > I've modified my source code accordingly using PETSc 3.8.0. It
>> > >> seems no
>> > >> > > > more useful info got printed out.
>> > >> > > >
>> > >> > > > On Fri, Sep 29, 2017 at 8:15 PM, Hao Zhang <
>> hbcbh1999 at gmail.com>
>> > >> wrote:
>> > >> > > >
>> > >> > > > > I'm using -fp_trap as I run the simulation. the output only
>> gives
>> > >> > > > >
>> > >> > > > > floating point exception
>> > >> > > > >
>> > >> > > > > It doesn't matter coarse grid or medium grid or more refined
>> > >> grid. the
>> > >> > > > > program crashed right away.
>> > >> > > > >
>> > >> > > > > On Fri, Sep 29, 2017 at 12:19 AM, Barry Smith <
>> bsmith at mcs.anl.gov
>> > >> >
>> > >> > > wrote:
>> > >> > > > >
>> > >> > > > >>
>> > >> > > > >> Please upgrade to the latest 3.8 version of PETSc. and
>> then
>> > >> run with
>> > >> > > > >> -fp_trap
>> > >> > > > >>
>> > >> > > > >> This message is usually an indication that a NaN or Inf
>> got
>> > >> into
>> > >> > > the
>> > >> > > > >> numerical computation. Using the latest PETSc will make it
>> much
>> > >> > > easier to
>> > >> > > > >> track down.
>> > >> > > > >>
>> > >> > > > >> Barry
>> > >> > > > >>
>> > >> > > > >> > On Sep 28, 2017, at 8:57 PM, Hao Zhang <
>> hbcbh1999 at gmail.com>
>> > >> wrote:
>> > >> > > > >> >
>> > >> > > > >> > I'm experiencing error when doing mesh refinement(mesh x2
>> for
>> > >> X, Y
>> > >> > > and
>> > >> > > > >> Z direction) for 3D poisson problem.
>> > >> > > > >> > PETSc produces no errors when no mesh refinement. I've
>> pasted
>> > >> some
>> > >> > > > >> debugging info here. Please advise.
>> > >> > > > >> >
>> > >> > > > >> >
>> > >> > > > >> > [0]PETSC ERROR: --------------------- Error Message
>> > >> > > > >> ------------------------------
>> --------------------------------
>> > >> > > > >> > [0]PETSC ERROR: Invalid argument
>> > >> > > > >> > [0]PETSC ERROR: Scalar value must be same on all
>> processes,
>> > >> > > argument # 3
>> > >> > > > >> > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/
>> > >> > > documentation/faq.html
>> > >> > > > >> for trouble shooting.
>> > >> > > > >> > [0]PETSC ERROR: Petsc Release Version 3.5.4, May, 23, 2015
>> > >> > > > >> > [0]PETSC ERROR: /home/haozhang/FT.NO.FULL/iFluid/iFluid
>> on a
>> > >> > > > >> arch-linux2-c-debug named vn18 by haozhang Thu Sep 28
>> 23:47:39
>> > >> 2017
>> > >> > > > >> > [0]PETSC ERROR: Configure options
>> --with-mpi-dir=/cm/shared/
>> > >> > > apps/openmpi/gcc/64/1.8.5/
>> > >> > > > >> --download-fblaslapack=/home/h
>> aozhang/tmp/fblaslapack-3.4.2.
>> > >> tar.gz
>> > >> > > > >> --download-hypre=/home/haozhang/tmp/hypre-2.9.1a.tar.gz
>> > >> > > > >> --with-valgrind-include=/home/haozhang/include/valgrind/
>> > >> > > > >> > [0]PETSC ERROR: #1 VecAXPBYPCZ() line 731 in
>> > >> > > > >> /home/haozhang/tmp/petsc-3.5.4
>> _HYPRE/src/vec/vec/interface/r
>> > >> vector.c
>> > >> > > > >> > [0]PETSC ERROR: #2 KSPSolve_BCGS() line 87 in
>> > >> > > > >> /home/haozhang/tmp/petsc-3.5.4
>> _HYPRE/src/ksp/ksp/impls/bcgs/
>> > >> bcgs.c
>> > >> > > > >> > [0]PETSC ERROR: #3 KSPSolve() line 460 in
>> > >> > > /home/haozhang/tmp/petsc-3.5.4
>> > >> > > > >> _HYPRE/src/ksp/ksp/interface/itfunc.c
>> > >> > > > >> > [vn18:99838] *** Process received signal ***
>> > >> > > > >> > [vn18:99838] Signal: Aborted (6)
>> > >> > > > >> > [vn18:99838] Signal code: (-6)
>> > >> > > > >> > [vn18:99848] *** Process received signal ***
>> > >> > > > >> > [vn18:99849] *** Process received signal ***
>> > >> > > > >> > [vn18:99849] Signal: Aborted (6)
>> > >> > > > >> > [vn18:99849] Signal code: (-6)
>> > >> > > > >> > [vn18:99848] Signal: Aborted (6)
>> > >> > > > >> > [vn18:99848] Signal code: (-6)
>> > >> > > > >> > [vn18:99838] [ 0] /lib64/libpthread.so.0(+0xf790
>> > >> )[0x2aaaadbb4790]
>> > >> > > > >> > [vn18:99838] [ 1] [vn18:99848] [ 0]
>> > >> /lib64/libpthread.so.0(+0xf790
>> > >> > > > >> )[0x2aaaadbb4790]
>> > >> > > > >> > [vn18:99848] [ 1] /lib64/libc.so.6(gsignal+0x35)
>> > >> [0x2aaaaddf5625]
>> > >> > > > >> > [vn18:99838] [ 2] /lib64/libc.so.6(abort+0x175)[
>> > >> 0x2aaaaddf6e05]
>> > >> > > > >> > [vn18:99838] [ 3] [vn18:99849] [ 0]
>> > >> /lib64/libpthread.so.0(+0xf790
>> > >> > > > >> )[0x2aaaadbb4790]
>> > >> > > > >> > [vn18:99849] [ 1] [vn15:122106] *** Process received
>> signal ***
>> > >> > > > >> > [vn15:122106] Signal: Aborted (6)
>> > >> > > > >> > [vn15:122106] Signal code: (-6)
>> > >> > > > >> > /lib64/libc.so.6(gsignal+0x35)[0x2aaaaddf5625]
>> > >> > > > >> > [vn18:99848] [ 2] /lib64/libc.so.6(abort+0x175)[
>> > >> 0x2aaaaddf6e05]
>> > >> > > > >> > [vn18:99848] [ 3] /home/haozhang/tmp/petsc-3.5.4
>> > >> > > > >> _HYPRE/arch-linux2-c-debug/lib
>> /libpetsc.so.3.5(PetscTraceBac
>> > >> > > > >> kErrorHandler+0x503)[0x2aaaaae1d7e1]
>> > >> > > > >> > [vn18:99838] [ 4] /lib64/libc.so.6(gsignal+0x35)
>> > >> [0x2aaaaddf5625]
>> > >> > > > >> > [vn18:99849] [ 2] /lib64/libc.so.6(abort+0x175)[
>> > >> 0x2aaaaddf6e05]
>> > >> > > > >> > [vn18:99849] [ 3] [vn15:122107] *** Process received
>> signal ***
>> > >> > > > >> > [vn15:122107] Signal: Aborted (6)
>> > >> > > > >> > [vn15:122107] Signal code: (-6)
>> > >> > > > >> > [vn16:86295] *** Process received signal ***
>> > >> > > > >> > [vn16:86295] Signal: Aborted (6)
>> > >> > > > >> > [vn16:86295] Signal code: (-6)
>> > >> > > > >> > [vn18:99824] *** Process received signal ***
>> > >> > > > >> > [vn18:99824] Signal: Aborted (6)
>> > >> > > > >> > [vn18:99824] Signal code: (-6)
>> > >> > > > >> > [vn18:99844] *** Process received signal ***
>> > >> > > > >> > [vn18:99844] Signal: Aborted (6)
>> > >> > > > >> > [vn18:99844] Signal code: (-6)
>> > >> > > > >> > /home/haozhang/tmp/petsc-3.5.4
>> _HYPRE/arch-linux2-c-debug/lib
>> > >> > > > >> /libpetsc.so.3.5(PetscError+0x338)[0x2aaaaae183b3]
>> > >> > > > >> >
>> > >> > > > >> >
>> > >> > > > >> >
>> > >> > > > >> > --
>> > >> > > > >> > Hao Zhang
>> > >> > > > >> > Dept. of Applid Mathematics and Statistics,
>> > >> > > > >> > Stony Brook University,
>> > >> > > > >> > Stony Brook, New York, 11790
>> > >> > > > >>
>> > >> > > > >>
>> > >> > > > >
>> > >> > > > >
>> > >> > > > > --
>> > >> > > > > Hao Zhang
>> > >> > > > > Dept. of Applid Mathematics and Statistics,
>> > >> > > > > Stony Brook University,
>> > >> > > > > Stony Brook, New York, 11790
>> > >> > > > >
>> > >> > > >
>> > >> > > >
>> > >> > > >
>> > >> > > >
>> > >> > >
>> > >> > >
>> > >> >
>> > >> >
>> > >> >
>> > >>
>> > >>
>> > >
>> > >
>> > > --
>> > > Hao Zhang
>> > > Dept. of Applid Mathematics and Statistics,
>> > > Stony Brook University,
>> > > Stony Brook, New York, 11790
>> > >
>> >
>> >
>> >
>> >
>>
>>
>
>
> --
> Hao Zhang
> Dept. of Applid Mathematics and Statistics,
> Stony Brook University,
> Stony Brook, New York, 11790
>
--
Hao Zhang
Dept. of Applid Mathematics and Statistics,
Stony Brook University,
Stony Brook, New York, 11790
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