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 (My information might be outdated)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
