[petsc-dev] Valgrind MPI-Related Errors

[Satish Balay]

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 (My information might be outdated)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
> > > > 
> > > > 
> > > 
> > > 
> 
>