[Q-e-developers] Using Valgrind and GDB with QE
Ye Luo
xw111luoye at gmail.com
Thu May 5 20:20:24 CEST 2016
Hi Hsin-Yu,
I'm sorry that I didn't explain myself clearly.
Meanwhile, I also got confused with libc and glibc
I think It is neither a problem of glibc nor libc.
I thought you mentioned that it might be a libc bug based on the reference
you provided.
[1] http://valgrind-users.narkive.com/MPnV7HOw/gcc-pg-valgrind-errors
In this reference, the call stack shows that all the error comes from
inside the libc.
In the problem of this discussion, the call stack shows that the problem
comes from the user program rather than any libraries.
I hope now I explain myself well.
Best,
Ye
===================
Ye Luo, Ph.D.
Leadership Computing Facility
Argonne National Laboratory
2016-05-05 13:06 GMT-05:00 Hsin-Yu Ko <hsinyu at princeton.edu>:
> Hi Ye,
>
> Thanks a lot for the clarification. Yes, you are right. It is glibc
> instead of libc.
>
> Best,
> Hsin-Yu
>
>
> On 05/05/2016 01:56 PM, Ye Luo wrote:
> > Hi Hsin-Yu,
> > I mean neither of them/.
> > /
> > I thought you mentioned that it might be a glibc bug based on the
> > reference you provided.
> > [1] http://valgrind-users.narkive.com/MPnV7HOw/gcc-pg-valgrind-errors
> > But in this case, all the error comes from inside the glibc.
> > So I think the problem here has nothing to do with the one you mentioned.
> >
> > Ye
> >
> > ===================
> > Ye Luo, Ph.D.
> > Leadership Computing Facility
> > Argonne National Laboratory
> >
> > 2016-05-05 12:40 GMT-05:00 Hsin-Yu Ko <hsinyu at princeton.edu
> > <mailto:hsinyu at princeton.edu>>:
> >
> > Hi Ye,
> >
> > Thanks a lot for the comment. Just for clarification: did you mean
> that
> > the failure to generate debug symbols not libc bug, or the "==10233==
> > Invalid write of size 8" warning not a libc bug?
> >
> > Thanks a lot,
> > Hsin-Yu
> >
> > On 05/05/2016 01:31 PM, Ye Luo wrote:
> > > It doesn't seem to be a libc bug.
> > > The call stack shows that in the subroutine check_quantity_dh
> ofyour
> > > module mbdvdw,
> > > the code failed in writing something into tgg_complex which seems
> to be
> > > a variable belongs to your module.
> > > Is this variable dynamically allocatable and not initialized?
> > >
> > > Ye
> > >
> > > ===================
> > > Ye Luo, Ph.D.
> > > Leadership Computing Facility
> > > Argonne National Laboratory
> > >
> > > 2016-05-05 12:14 GMT-05:00 Hsin-Yu Ko <hsinyu at princeton.edu
> <mailto:hsinyu at princeton.edu>
> > > <mailto:hsinyu at princeton.edu <mailto:hsinyu at princeton.edu>>>:
> > >
> > > Thomas,
> > >
> > > That is interesting. What you are seeing seems to be a libc
> > bug [1]. I
> > > have encountered something similar last month. I fixed the
> > problem on my
> > > machine by recompiling glibc with debug features enabled (I am
> > not sure
> > > how useful gentoo documentation is but I put the reference
> > here just in
> > > case [2]). I think removing -pg may be a quick fix according
> > to [1].
> > >
> > > Best,
> > > Hsin-Yu
> > >
> > > [1]
> > http://valgrind-users.narkive.com/MPnV7HOw/gcc-pg-valgrind-errors
> > > [2] https://wiki.gentoo.org/wiki/Debugging
> > >
> > > On 05/05/2016 12:34 PM, Thomas Markovich wrote:
> > > > Hsin-Yu,
> > > >
> > > > Thank you for the suggestion!
> > > >
> > > > I had -g in LDFLAGS:
> > > > LDFLAGS = -g -pthread -fopenmp
> > > >
> > > > but nothing equivalent in CFLAGS, which was defined as:
> > > > CFLAGS = -O3 $(DFLAGS) $(IFLAGS)
> > > >
> > > > I have since gone ahead and changed CFLAGS to
> > > > CFLAGS = -Og -g $(DFLAGS) $(IFLAGS)
> > > >
> > > > The resulting fortran compile statements look something like:
> > > > mpif90 -Og -g -pg -fopenmp -Wall -Wextra -Warray-temporaries
> > > > -Wconversion -fbacktrace -ffree-line-length-0 -finit-real=nan
> > > > -ffpe-trap=zero,invalid,zero,overflow -x f95-cpp-input
> -fopenmp
> > > > -D__GFORTRAN -D__STD_F95 -D__FFTW -D__MPI -D__PARA
> -D__SCALAPACK
> > > > -D__OPENMP -I../include -I../iotk/src -I../ELPA/src -I. -c
> > mbdvdw.f90
> > > >
> > > > and reran valgrind. It gave the following output:
> > > >
> > > > ==30486== Invalid write of size 8
> > > > ==30486== at 0x1002735ED:
> > __mbdvdw_module_MOD_mbdvdw_tgg_complex (in
> > > > /Users/tmarkovich/bin/pw.x)
> > > > ==30486== by 0x100290F58:
> > > > __mbdvdw_module_MOD_mbdvdw_check_quantity_dh (in
> > /Users/tmarkovich/bin/pw.x)
> > > > ==30486== Address 0x1037989f0 is 0 bytes after a block of
> > size 1,728
> > > > alloc'd
> > > > ==30486== at 0x10092B4AB: malloc (in
> > > >
> >
> /usr/local/Cellar/valgrind/HEAD/lib/valgrind/vgpreload_memcheck-amd64-darwin.so)
> > > > ==30486== by 0x10028FEE2:
> > > > __mbdvdw_module_MOD_mbdvdw_check_quantity_dh (in
> > /Users/tmarkovich/bin/pw.x)
> > > > ==30486== by 0x1001D4567: v_of_rho_ (in
> > /Users/tmarkovich/bin/pw.x)
> > > > ==30486== by 0x10007C0BE: electrons_scf_ (in
> > /Users/tmarkovich/bin/pw.x)
> > > > ==30486== by 0x10007D385: electrons_ (in
> > /Users/tmarkovich/bin/pw.x)
> > > > ==30486== by 0x10018B30B: run_pwscf_ (in
> > /Users/tmarkovich/bin/pw.x)
> > > > ==30486== by 0x100001157: MAIN__ (pwscf.f90:30)
> > > > ==30486== by 0x1004EC496: main (pwscf.f90:14)
> > > >
> > > > This appears to not have changed much.
> > > >
> > > > Best,
> > > > Thomas
> > > >
> > > > On Thu, May 5, 2016 at 10:15 AM, Hsin-Yu Ko
> > <hsinyu at princeton.edu <mailto:hsinyu at princeton.edu>
> > <mailto:hsinyu at princeton.edu <mailto:hsinyu at princeton.edu>>
> > > > <mailto:hsinyu at princeton.edu <mailto:hsinyu at princeton.edu>
> > <mailto:hsinyu at princeton.edu <mailto:hsinyu at princeton.edu>>>> wrote:
> > > >
> > > > Hi Thomas,
> > > >
> > > > Did you put -g in CFLAGS and LDFLAGS? Valgrind seems to
> > > recognize some
> > > > lines inside MAIN__ while failing to find the linked
> ones.
> > > >
> > > > Best,
> > > > Hsin-Yu
> > > >
> > > > On 05/05/2016 09:48 AM, Thomas Markovich wrote:
> > > > > Hi,
> > > > >
> > > > > I'm preparing to push my module that implements the
> > Many Body
> > > > Dispersion
> > > > > van der Waals correction, and all associated forces.
> > As a last
> > > > thing, I
> > > > > ran my code through valgrind, and it seems to have
> > popped up a
> > > > couple of
> > > > > remaining things that I would like to fix before
> > release[1].
> > > > > Unfortunately, the valgrind output below is less than
> > clear
> > > on where
> > > > > exactly the error is, and it doesn't give any
> > important line
> > > numbers.
> > > > > Beyond this, addr2line gives thoroughly unhelpful
> output:
> > > > > ▶ gaddr2line -e pw.x 0x100520518
> > > > > ??:0.
> > > > >
> > > > > I have compiled QE given the following flags with
> > gfortran 4.9:
> > > > > FFLAGS = -Og -g -pg -fopenmp -fbacktrace
> > -fcheck=all
> > > > > -finit-real=nan -ffpe-trap=zero,invalid,zero,overflow
> > > > >
> > > > > Is there any way to compile QE such that it generates
> > all the
> > > > debugging
> > > > > symbols, so that I can get more readable and
> informative
> > > output from
> > > > > valgrind? I thought all I needed was the -g flag, but
> > it appears
> > > > that I
> > > > > might need more?
> > > > >
> > > > > Best,
> > > > > Thomas Markovich
> > > > >
> > > > > [1]
> > > > > ==10233== Invalid write of size 8
> > > > > ==10233== at 0x100520518:
> > > > __mbdvdw_module_MOD_mbdvdw_tgg_complex (in
> > > > > /Users/tmarkovich/bin/pw.x)
> > > > > ==10233== by 0x100555A88:
> > > > > __mbdvdw_module_MOD_mbdvdw_check_quantity_dh (in
> > > > /Users/tmarkovich/bin/pw.x)
> > > > > ==10233== Address 0x103131248 is 8 bytes after a
> block of
> > > size 1,728
> > > > > alloc'd
> > > > > ==10233== at 0x1011814AB: malloc (in
> > > > >
> > > >
> > >
> >
> /usr/local/Cellar/valgrind/HEAD/lib/valgrind/vgpreload_memcheck-amd64-darwin.so)
> > > > > ==10233== by 0x1005547B0:
> > > > > __mbdvdw_module_MOD_mbdvdw_check_quantity_dh (in
> > > > /Users/tmarkovich/bin/pw.x)
> > > > > ==10233== by 0x1003D56E4: v_of_rho_ (in
> > > /Users/tmarkovich/bin/pw.x)
> > > > > ==10233== by 0x1000F540B: electrons_scf_ (in
> > > > /Users/tmarkovich/bin/pw.x)
> > > > > ==10233== by 0x1000F6E18: electrons_ (in
> > > > /Users/tmarkovich/bin/pw.x)
> > > > > ==10233== by 0x10032AA28: run_pwscf_ (in
> > > > /Users/tmarkovich/bin/pw.x)
> > > > > ==10233== by 0x1000010BB: MAIN__ (pwscf.f90:30)
> > > > > ==10233== by 0x100B67C1F: main (pwscf.f90:14)
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