[Q-e-developers] Using Valgrind and GDB with QE

[Thomas Markovich]

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> 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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