[petsc-dev] Valgrind MPI-Related Errors

Jacob Faibussowitsch jacob.fai at gmail.com
Tue Jun 2 12:09:34 CDT 2020 

> 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 <balay at mcs.anl.gov> 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 <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> <mailto: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><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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20200602/61033c78/attachment.html>

More information about the petsc-dev mailing list