use --download-mpich for 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 (My information might be outdated) 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 > > 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 > > > > > >
