[petsc-dev] Valgrind MPI-Related Errors

Tue Jun 2 12:10:43 CDT 2020

It's not the most satisfying solution but you can also pretty quickly
generate and use suppression files to at least de-clutter the output:
https://valgrind.org/docs/manual/manual-core.html#manual-core.suppress

Am Di., 2. Juni 2020 um 18:59 Uhr schrieb Satish Balay via petsc-dev <
petsc-dev at mcs.anl.gov>:

> MPICH need to be built with the option --enable-g=meminit for it to be
> valgrind clean.
>
> --download-mpich does this [among other things that are useful during
> software developement]. Pre-configured MPICH is not likely to do this.
>
> You can verify with: mpichversion
>
> You can prebuild MPICH using PETSc with:
>
> ./configure --prefix=$HOME/soft/mpich --download-mpich CFLAGS= FFLAGS=
> CXXFLAGS= COPTFLAGS= CXXOPTFLAGS= FOPTFLAGS=
>
> And make this your default pre-installed MPI. [by adding $HOME/soft/mpich
> to PATH]
>
> Satish
>
>
> On Tue, 2 Jun 2020, Jacob Faibussowitsch wrote:
>
> > Yes I am using the pre-loaded MPICH from the docker image. Further proof
> from configure
> >
> > #define PETSC_HAVE_MPICH_NUMVERSION 30302300
> > #define PETSC_HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE MPIR_CVAR_CH3
> >
> > Best regards,
> >
> > Jacob Faibussowitsch
> > (Jacob Fai - booss - oh - vitch)
> > Cell: (312) 694-3391
> >
> > > On Jun 2, 2020, at 11:35 AM, Junchao Zhang <junchao.zhang at gmail.com>
> wrote:
> > >
> > > I guess Jacob already used MPICH, since
> MPIDI_CH3_EagerContigShortSend() is from MPICH.
> > >
> > > --Junchao Zhang
> > >
> > >
> > > On Tue, Jun 2, 2020 at 9:38 AM Satish Balay via petsc-dev <
> petsc-dev at mcs.anl.gov <mailto:petsc-dev at mcs.anl.gov>> wrote:
> > > use --download-mpich for valgrind.
> > >
> > > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind <
> https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind>
> > >
> > > Satish
> > >
> > > On Tue, 2 Jun 2020, Karl Rupp wrote:
> > >
> > > > Hi Jacob,
> > > >
> > > > the recommendation in the past was to use MPICH as it is (was?)
> > > > valgrind-clean. Which MPI do you use? OpenMPI used to have these
> kinds of
> > > > issues. (My information might be outdated)
> > > >
> > > > Best regards,
> > > > Karli
> > > >
> > > > On 6/2/20 2:43 AM, Jacob Faibussowitsch wrote:
> > > > > Hello All,
> > > > >
> > > > > TL;DR: valgrind always complains about "Syscall param write(buf)
> points to
> > > > > uninitialised byte(s)” for a LOT of MPI operations in petsc code,
> making
> > > > > debugging using valgrind fairly annoying since I have to sort
> through a ton
> > > > > of unrelated stuff. I have built valgrind from source, used apt
> install
> > > > > valgrind, apt install valgrind-mpi to no avail.
> > > > >
> > > > > I am using valgrind from docker. Dockerfile is attached below as
> well. I
> > > > > have been unsuccessfully trying to resolve these local valgrind
> errors, but
> > > > > I am running out of ideas. Googling the issue has also not
> provided entirely
> > > > > applicable solutions. Here is an example of the error:
> > > > >
> > > > > $ make -f gmakefile test VALGRIND=1
> > > > > ...
> > > > > #==54610== Syscall param write(buf) points to uninitialised byte(s)
> > > > > #==54610==    at 0x6F63317: write (write.c:26)
> > > > > #==54610==    by 0x9056AC9: MPIDI_CH3I_Sock_write (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==    by 0x9059FCD: MPIDI_CH3_iStartMsg (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==    by 0x903F298: MPIDI_CH3_EagerContigShortSend (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==    by 0x9049479: MPID_Send (in
> /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==    by 0x8FC9B2A: MPIC_Send (in
> /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==    by 0x8F86F2E: MPIR_Bcast_intra_binomial (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==    by 0x8EE204E: MPIR_Bcast_intra_auto (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==    by 0x8EE21F4: MPIR_Bcast_impl (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==    by 0x8F887FB: MPIR_Bcast_intra_smp (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==    by 0x8EE206E: MPIR_Bcast_intra_auto (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==    by 0x8EE21F4: MPIR_Bcast_impl (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==    by 0x8EE2A6F: PMPI_Bcast (in
> /usr/local/lib/libmpi.so.12.1.8)
> > > > > #==54610==    by 0x4B377B8: PetscOptionsInsertFile (options.c:525)
> > > > > #==54610==    by 0x4B39291: PetscOptionsInsert (options.c:672)
> > > > > #==54610==    by 0x4B5B1EF: PetscInitialize (pinit.c:996)
> > > > > #==54610==    by 0x10A6BA: main (ex9.c:75)
> > > > > #==54610==  Address 0x1ffeffa944 is on thread 1's stack
> > > > > #==54610==  in frame #3, created by MPIDI_CH3_EagerContigShortSend
> (???:)
> > > > > #==54610==  Uninitialised value was created by a stack allocation
> > > > > #==54610==    at 0x903F200: MPIDI_CH3_EagerContigShortSend (in
> > > > > /usr/local/lib/libmpi.so.12.1.8)
> > > > >
> > > > > There are probably 20 such errors every single time, regardless of
> what code
> > > > > is being run. I have tried using apt install valgrind, apt install
> > > > > valgrind-mpi, and building valgrind from source:
> > > > >
> > > > > # VALGRIND
> > > > > WORKDIR /
> > > > > RUN git clone git://sourceware.org/git/valgrind.git <
> http://sourceware.org/git/valgrind.git>
> > > > > WORKDIR /valgrind
> > > > > RUN git pull
> > > > > RUN ./autogen.sh
> > > > > RUN ./configure --with-mpicc=/usr/local/bin/mpicc
> > > > > RUN make -j 5
> > > > > RUN make install
> > > > >
> > > > > None of the those approaches lead to these errors disappearing.
> Perhaps I am
> > > > > missing some funky MPI args?
> > > > >
> > > > > Best regards,
> > > > >
> > > > > Jacob Faibussowitsch
> > > > > (Jacob Fai - booss - oh - vitch)
> > > > > Cell: (312) 694-3391
> > > > >
> > > > >
> > > >
> > > >
> >
> >
>
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