On Fri, Apr 17, 2015 at 5:09 PM, Sun, Hui <[email protected]> wrote: > I'm not sure if I'm doing the right thing. But I have just > export PATH=$PATH:dir_to_valgind_bin > > And I rerun the command: > -@${PETSC_DIR}/bin/petscmpiexec -valgrind -n ${NP} ./test -mx ${ND} -my > ${ND} -mz ${ND} -ksp_monitor_short -ksp_type fgmres -pc_type asm > > Then it seems to output something, for example: > ==66450== Invalid write of size 8 > ==66450== at 0x100055225: Schur_SetMatrix (in ./test) > ==66450== by 0x10004F218: StokesSetup (in ./test) > ==66450== by 0x1000DC582: main (in ./test) > ==66450== Address 0x7fff5f93fb28 is on thread 1's stack > ==66450== in frame #0, created by Schur_SetMatrix (???) > ==66450== >
Yes, this worked, and it shows you have a memory overwrite in your code. You have no line numbers because you deleted the *.o files without running dsymutil. > And before those output, it has the following lines: > --66450-- run: /usr/bin/dsymutil "./test" > warning: (x86_64) /Users/hus003/projects/LS_BDRY/test/test.o unable to > open object file > warning: no debug symbols in executable (-arch x86_64) > --66450-- run: /usr/bin/dsymutil > "/Users/hus003/Documents/software/petsc-valgrind/petsc-valgrind-debug/lib/libpetsc.3.05.3.dylib" > --66450-- run: /usr/bin/dsymutil > "/Users/hus003/Documents/software/petsc-valgrind-install/lib/libmpicxx.12.dylib" > --66450-- run: /usr/bin/dsymutil > "/Users/hus003/Documents/software/petsc-valgrind-install/lib/libmpifort.12.dylib" > --66450-- run: /usr/bin/dsymutil > "/Users/hus003/Documents/software/petsc-valgrind-install/lib/libmpi.12.dylib" > --66450-- run: /usr/bin/dsymutil > "/Users/hus003/Documents/software/petsc-valgrind-install/lib/libpmpi.12.dylib" > > Does it mean that it's working? But what does these two warnings mean? > These warnings mean that symbols are missing from those libraries, which is no surprise. matt > Best, > Hui > > > ________________________________________ > From: Barry Smith [[email protected]] > Sent: Friday, April 17, 2015 2:57 PM > To: Matthew Knepley > Cc: Sun, Hui; [email protected] > Subject: Re: [petsc-users] install petsc with valgrind > > Or make sure valgrind is in your path > > > On Apr 17, 2015, at 4:56 PM, Matthew Knepley <[email protected]> wrote: > > > > As I said, it cannot find valgrind in your path. Remove it or install > valgrind. > > > > Matt > > > > On Fri, Apr 17, 2015 at 4:55 PM, Sun, Hui <[email protected]> wrote: > > Thank you, Matt and Barry. I was trying to run the following: > > -@${PETSC_DIR}/bin/petscmpiexec -valgrind -n ${NP} ./test -mx ${ND} -my > ${ND} -mz ${ND} -ksp_monitor_short -ksp_type fgmres -pc_type asm > > > > where NP=2, ND=32 > > > > And in the makefile I have specified the following: > > include ${PETSC_DIR}/lib/petsc/conf/variables > > include ${PETSC_DIR}/lib/petsc/conf/rules > > include ${PETSC_DIR}/lib/petsc/conf/test > > > > Best, > > Hui > > > > > > ________________________________________ > > From: Barry Smith [[email protected]] > > Sent: Friday, April 17, 2015 2:50 PM > > To: Sun, Hui > > Cc: [email protected] > > Subject: Re: [petsc-users] install petsc with valgrind > > > > Please please please always show WHAT YOU RAN with the error message. > Otherwise we just must guess > > > > > > > On Apr 17, 2015, at 3:58 PM, Sun, Hui <[email protected]> wrote: > > > > > > Thank you Barry. I just have it installed. And I was running a code, > and got the following error message: > > > > > > HYDU_create_process (utils/launch/launch.c:75): execvp error on file > valgrind: (No such file or directory) > > > > > > > =================================================================================== > > > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > > > = PID 66059 RUNNING AT math178.ucsd.edu > > > = EXIT CODE: 255 > > > = CLEANING UP REMAINING PROCESSES > > > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > > > =================================================================================== > > > > > > What does this mean? > > > > > > Best, > > > Hui > > > > > > ________________________________________ > > > From: Barry Smith [[email protected]] > > > Sent: Friday, April 17, 2015 1:08 PM > > > To: Sun, Hui > > > Cc: [email protected] > > > Subject: Re: [petsc-users] install petsc with valgrind > > > > > > The development copy of PETSc allows using --prefix with MPICH > http://www.mcs.anl.gov/petsc/developers/index.html > > > > > > > > > > > >> On Apr 17, 2015, at 2:38 PM, Sun, Hui <[email protected]> wrote: > > >> > > >> Hello, > > >> > > >> I want to install petsc with valgrind. And I read some > documentations, which suggests me to do > > >> ./configure --download-mpich --with-valgind-dir=… > > >> > > >> However, I also want to specify --prefix, but petsc doesn't allow me, > because --download-mpich option does not work with --prefix install. > > >> > > >> Is there anyway that I can have petsc --prefix, together with > valgrind? > > >> > > >> Best, > > >> Hui > > > > > > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > > -- Norbert Wiener > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
