[petsc-users] install petsc with valgrind

Fri Apr 17 17:26:56 CDT 2015

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

________________________________
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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto:bsmith at mcs.anl.gov>]
> Sent: Friday, April 17, 2015 2:50 PM
> To: Sun, Hui
> Cc: petsc-users at mcs.anl.gov<mailto: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<mailto: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<http://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<mailto:bsmith at mcs.anl.gov>]
> > Sent: Friday, April 17, 2015 1:08 PM
> > To: Sun, Hui
> > Cc: petsc-users at mcs.anl.gov<mailto: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<mailto: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
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