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

[Hsin-Yu Ko]

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>> 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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