[petsc-users] mesh refinement PETSc3.5.4 with HYPRE
Satish Balay
balay at mcs.anl.gov
Sat Sep 30 06:56:02 CDT 2017
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatView.html
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecView.html
Satish
On Sat, 30 Sep 2017, Hao Zhang wrote:
> 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
> >
>
>
>
>
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