On Fri, Apr 17, 2015 at 5:26 PM, Sun, Hui <[email protected]> wrote: > How do I run dsymutil so as to get the line numbers? >
dsymutil ./test Matt > ------------------------------ > *From:* Matthew Knepley [[email protected]] > *Sent:* Friday, April 17, 2015 3:10 PM > *To:* Sun, Hui > *Cc:* Barry Smith; [email protected] > *Subject:* Re: [petsc-users] install petsc with valgrind > > 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 > -- 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
