[petsc-users] VecView to hdf5 broken for large (complex) vectors

Smith, Barry F. bsmith at mcs.anl.gov
Tue Apr 16 20:42:49 CDT 2019

  Dang, I  ranted too soon. 

  I built mpich  using spack (master branch) and a very old Gnu C compiler and it produced valgrind clean code. Spack definitely is not passing the --enable-g=meminit to MPICH ./configure so this version of MPICH valgrind must be clean by default? MPICH's ./configure has 

meminit  - Preinitialize memory associated structures and unions to
                   eliminate access warnings from programs like valgrind

The default for enable-g is most and 


So it appears that at least some releases of MPICH are suppose to be valgrind clean by default ;).

Looking back at Sajid's valgrind output more carefully 

Conditional jump or move depends on uninitialised value(s)
==15359==    at 0x1331069A: __intel_sse4_strncmp (in /opt/intel/compilers_and_libraries_2019.1.144/linux/compiler/lib/intel64_lin/libintlc.so.5)

is the only valgrind error. Which I remember seeing from using Intel compilers for a long time, nothing to do with MPICH

Thus I conclude that Sajid's code is actually valgrind clean; and I withdraw my rant about MPICH/spack


> On Apr 16, 2019, at 5:13 PM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
>  So valgrind is printing all kinds of juicy information about uninitialized values but it is all worthless because MPICH was not built by spack to be valgrind clean. We can't know if any of the problems valgrind flags are real. MPICH needs to be configured with the option --enable-g=meminit to be valgrind clean. PETSc's --download-mpich always installs a valgrind clean MPI. 
> It is unfortunate Spack doesn't provide a variant of MPICH that is valgrind clean; actually it should default to valgrind clean MPICH.
>  Barry
>> On Apr 16, 2019, at 2:43 PM, Sajid Ali via petsc-users <petsc-users at mcs.anl.gov> wrote:
>> So, I tried running the debug version with valgrind to see if I can find the chunk size that's being set but I don't see it. Is there a better way to do it ?
>> `$ mpirun -np 32 valgrind ./ex_ms -prop_steps 1 -info &> out`. [The out file is attached.]
>> <out>

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