> MPICH need to be built with the option --enable-g=meminit for it to be > valgrind clean. I see. Two questions:
1. I am using Jeds docker image for MPICH (actually this is the main reason for using Jeds image, as configuring and building MPICH takes an absolute age on docker), will this re-build the MPICH already installed in the image or download and build an entirely new MPICH? 2. (More a question for Jed) If I am using Jeds docker image anyways and we have CI/CD builds also using his docker images (correct me if I am wrong here) and a valgrind build in stage 3 why not include those build arguments in the MPICH included in the images? I think the valgrind build for CI/CD actually downloads and builds MPICH through petsc configure, is this because of the errors I detailed below? Best regards, Jacob Faibussowitsch (Jacob Fai - booss - oh - vitch) Cell: (312) 694-3391 > On Jun 2, 2020, at 11:59 AM, Satish Balay <[email protected]> wrote: > > 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 <[email protected]> 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 >>> <[email protected] <mailto:[email protected]> >>> <mailto:[email protected] <mailto:[email protected]>>> 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><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 >>>>> <git://sourceware.org/git/valgrind.git> >>>>> <http://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
