[petsc-dev] Valgrind MPI-Related Errors

[Karl Rupp]

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 (My information might be outdated)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
> 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
> 
>