[petsc-users] install petsc with valgrind

[Matthew Knepley]

On Fri, Apr 17, 2015 at 5:26 PM, Sun, Hui <hus003 at ucsd.edu> wrote:

>  How do I run dsymutil so as to get the line numbers?
>

dsymutil ./test

   Matt


>  ------------------------------
> *From:* Matthew Knepley [knepley at gmail.com]
> *Sent:* Friday, April 17, 2015 3:10 PM
> *To:* Sun, Hui
> *Cc:* Barry Smith; petsc-users at mcs.anl.gov
> *Subject:* Re: [petsc-users] install petsc with valgrind
>
>    On Fri, Apr 17, 2015 at 5:09 PM, Sun, Hui <hus003 at ucsd.edu> 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 [bsmith at mcs.anl.gov]
>> Sent: Friday, April 17, 2015 2:57 PM
>> To: Matthew Knepley
>> Cc: Sun, Hui; petsc-users at mcs.anl.gov
>> 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 <knepley at gmail.com> 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 <hus003 at ucsd.edu> 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 [bsmith at mcs.anl.gov]
>> > Sent: Friday, April 17, 2015 2:50 PM
>> > To: Sun, Hui
>> > Cc: petsc-users at mcs.anl.gov
>> > 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 <hus003 at ucsd.edu> 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 [bsmith at mcs.anl.gov]
>> > > Sent: Friday, April 17, 2015 1:08 PM
>> > > To: Sun, Hui
>> > > Cc: petsc-users at mcs.anl.gov
>> > > 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 <hus003 at ucsd.edu> 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
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