[petsc-dev] PTScotch problem on Mac

Satish Balay balay at mcs.anl.gov
Tue Nov 23 15:29:10 CST 2021 

perhaps "dtruss -f" ?

https://stackoverflow.com/questions/1925978/equivalent-of-strace-feopen-command-on-mac-os-x

balay at ypro petsc % dtruss -f ./configure
dtrace: system integrity protection is on, some features will not be available
dtrace: failed to initialize dtrace: DTrace requires additional privileges

Oh well..

Satish

On Tue, 23 Nov 2021, Barry Smith wrote:

> 
> >> Hmm, I cannot figure out how to do that. Developer tools on Mac are embarrassing.
> 
> I think you are probably looking in the wrong place. The GUI based Xcode Instruments tools likely have this type of capability but it may not be accessible from the command line.
> 
> 
> > On Nov 23, 2021, at 3:02 PM, Matthew Knepley <knepley at gmail.com> wrote:
> > 
> > On Tue, Nov 23, 2021 at 2:05 PM Satish Balay <balay at mcs.anl.gov <mailto:balay at mcs.anl.gov>> wrote:
> > On Tue, 23 Nov 2021, Matthew Knepley wrote:
> > 
> > > On Tue, Nov 23, 2021 at 12:56 PM Matthew Knepley <knepley at gmail.com <mailto:knepley at gmail.com>> wrote:
> > > 
> > > > On Tue, Nov 23, 2021 at 12:29 PM Satish Balay <balay at mcs.anl.gov <mailto:balay at mcs.anl.gov>> wrote:
> > > >
> > > >> The primary difference I can spot [as you say] is the older xcode you
> > > >> have. Eventhough it says the same version of flex - perhaps its buggy?
> > > >>
> > > >> Apple clang version 11.0.3 (clang-1103.0.32.59)
> > > >> vs
> > > >> Apple clang version 12.0.0 (clang-1200.0.32.2)
> > > >>
> > > >>
> > > >> >
> > > >> PATH=/PETSc3/cig/bin:/PETSc3/petsc/petsc-pylith/arch-pylith-debug/bin:/PETSc3/petsc/apple/bin:/Library/Frameworks/Python.framework/Versions/3.8/bin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/texbin:/opt/X11/bin:/usr/local/git/bin:/Library/Frameworks/Python.framework/Versions/3.8/bin:/opt/local/bin:/opt/local/sbin:/usr/X11/bin:/usr/local/texlive/2019/bin/x86_64-darwin:/usr/local/cuda/bin:/usr/local/gmt/bin:/usr/local/bin:/usr/X11/bin:/usr/local/texlive/2019/bin/x86_64-darwin:/usr/local/cuda/bin:/usr/local/gmt/bin
> > > >>
> > > >> BTW: Can you try a build with the following and see if it makes a
> > > >> difference?
> > > >>
> > > >> PATH=/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
> > > >> ./configure PETSC_ARCH=arch-test --with-mpi-dir=/PETSc3/petsc/apple
> > > >> --download-c2html --download-ptscotch
> > > >>
> > > >
> > > > Damn damn damn damn. Now I have to bisect the PATH to see how in the world
> > > > that can make a difference.
> > > >
> > > 
> > > Okay, the configure succeeds by taking out /opt/local/bin:/opt/local/sbin,
> > > but I cannot figure out why this would be the case?
> > 
> > 
> > If you can do 'strace --follow-forks' or equivalent on Mac - you might
> > be able to see what gets used from /opt/local/bin/
> > 
> > Hmm, I cannot figure out how to do that. Developer tools on Mac are embarrassing.
> >  
> > Also you might be better off using brew instead of what you currently
> > have.. [likely you don't need most of the binaries below. 'brew
> > leaves' gives a nice way to keep track of whats really needed]
> > 
> > I do not use MacPorts. I edited my .profile years ago and I missed that when abandoning it.
> >  
> > Or a brute force bisection by moving binaries out of (and back into) this location.
> > 
> > That sounds like something for "grad student time"
> > 
> >    Thanks,
> > 
> >      Matt
> >  
> > Satish
> > 
> > > 
> > > knepley/feature-plex-multiple-hybrid *$:/PETSc3/petsc/petsc-pylith$ ls
> > > /opt/local/sbin/
> > > knepley/feature-plex-multiple-hybrid *$:/PETSc3/petsc/petsc-pylith$ ls
> > > /opt/local/bin/
> > > a2p                     envsubst                libnetcfg-5.12
> > >  perlivp-5.8             prove
> > > a2p-5.12                find2perl               libnetcfg-5.8
> > > perlthanks              prove-5.12
> > > a2p-5.8                 find2perl-5.12          msgattrib
> > > perlthanks-5.12         prove-5.8
> > > autoconf263             find2perl-5.8           msgcat
> > >  perlthanks-5.8          psed
> > > 
> > > autoheader263           gettext                 msgcmp
> > >  piconv                  psed-5.12
> > > autom4te263             gettext.sh              msgcomm
> > > piconv-5.12             psed-5.8
> > > autopoint               gettextize              msgconv
> > > piconv-5.8              pstruct
> > > autoreconf263           ghc                     msgen
> > > pl2pm                   pstruct-5.12
> > > autoscan263             ghc-6.10.4              msgexec
> > > pl2pm-5.12              pstruct-5.8
> > > autoupdate263           ghc-pkg                 msgfilter
> > > pl2pm-5.8               ptar-5.12
> > > c2ph                    ghc-pkg-6.10.4          msgfmt
> > >  pod2html                ptardiff-5.12
> > > c2ph-5.12               ghci                    msggrep
> > > pod2html-5.12           recode-sr-latin
> > > c2ph-5.8                ghci-6.10.4             msginit
> > > pod2html-5.8            reset
> > > c_rehash                gm4                     msgmerge
> > >  pod2latex               runghc
> > > captoinfo               gperf                   msgunfmt
> > >  pod2latex-5.12          runhaskell
> > > clear                   h2ph                    msguniq
> > > pod2latex-5.8           s2p
> > > config_data-5.12        h2ph-5.12               ncurses5-config
> > > pod2man                 s2p-5.12
> > > corelist-5.12           h2ph-5.8                ncursesw5-config
> > >  pod2man-5.12            s2p-5.8
> > > corelist-5.8            h2xs                    ngettext
> > >  pod2man-5.8             shasum-5.12
> > > cpan                    h2xs-5.12               openssl
> > > pod2text                splain
> > > cpan-5.12               h2xs-5.8                perl
> > >  pod2text-5.12           splain-5.12
> > > cpan-5.8                haddock                 perl5
> > > pod2text-5.8            splain-5.8
> > > cpan2dist               hasktags                perl5.12
> > >  pod2usage               tabs
> > > cpan2dist-5.12          help2man                perl5.12.3
> > >  pod2usage-5.12          tic
> > > cpanp                   hp2ps                   perl5.8
> > > pod2usage-5.8           toe
> > > cpanp-5.12              hpc                     perl5.8.9
> > > podchecker              tput
> > > cpanp-run-perl          hsc2hs                  perlbug
> > > podchecker-5.12         tset
> > > cpanp-run-perl-5.12     iconv                   perlbug-5.12
> > >  podchecker-5.8          wget
> > > daemondo                idn                     perlbug-5.8
> > > podselect               xgettext
> > > dprofpp                 ifnames263              perlcc-5.8
> > >  podselect-5.12          xmlwf
> > > dprofpp-5.12            infocmp                 perldoc
> > > podselect-5.8           xsubpp
> > > dprofpp-5.8             infotocap               perldoc-5.12
> > >  port                    xsubpp-5.12
> > > enc2xs                  instmodsh-5.12          perldoc-5.8
> > > portf                   xsubpp-5.8
> > > enc2xs-5.12             instmodsh-5.8           perlivp
> > > portindex
> > > enc2xs-5.8              libnetcfg               perlivp-5.12
> > >  portmirror
> > > 
> > >   Thanks,
> > > 
> > >      Matt
> > > 
> > > 
> > > >   Thanks,
> > > >
> > > >      Matt
> > > >
> > > >
> > > >> Satish
> > > >>
> > > >>
> > > >> On Tue, 23 Nov 2021, Matthew Knepley wrote:
> > > >>
> > > >> > Here it is.
> > > >> >
> > > >> >   Matt
> > > >> >
> > > >> > On Tue, Nov 23, 2021 at 11:44 AM Satish Balay <balay at mcs.anl.gov <mailto:balay at mcs.anl.gov>>
> > > >> wrote:
> > > >> >
> > > >> > > On Tue, 23 Nov 2021, Matthew Knepley wrote:
> > > >> > >
> > > >> > > > On Tue, Nov 23, 2021 at 11:28 AM Satish Balay <balay at mcs.anl.gov <mailto:balay at mcs.anl.gov>>
> > > >> wrote:
> > > >> > > >
> > > >> > > > > Well we don't have this issue on our (macos) CI boxes where both
> > > >> c2html
> > > >> > > > > and scotch build and run daily [in CI]
> > > >> > > > >
> > > >> > > > > what 'flex' are you using? And why does it behave differently on
> > > >> your
> > > >> > > box?
> > > >> > > > >
> > > >> > > >
> > > >> > > > main *$:/PETSc3/petsc/petsc-dev$ which flex
> > > >> > > > /usr/bin/flex
> > > >> > > > main *$:/PETSc3/petsc/petsc-dev$ flex --version
> > > >> > > > flex 2.5.35 Apple(flex-32)
> > > >> > > >
> > > >> > > >
> > > >> > > > > And what errors do you get?
> > > >> > > > >
> > > >> > > >
> > > >> > > > Without the extra input define in PTScotch.py, I get the yylval
> > > >> symbol
> > > >> > > > undefined and the lexer symbol. When I give
> > > >> > > > that define as input, only the lexer symbol is undefined.
> > > >> > >
> > > >> > > BTW: Can you send the log?
> > > >> > >
> > > >> > > Satish
> > > >> > >
> > > >> > > >
> > > >> > > >
> > > >> > > > > Perhaps CI is using older xcode (command line tools) - and you are
> > > >> > > using
> > > >> > > > > newer? Or something else?
> > > >> > > > >
> > > >> > > >
> > > >> > > > Probably the other way around. I am on Catalina 10.15.6
> > > >> > > >
> > > >> > > >    Matt
> > > >> > > >
> > > >> > > >
> > > >> > > > > Barry - do you have this issue on your machine?
> > > >> > > > >
> > > >> > > > > balay at ypro ~ % which flex
> > > >> > > > > /usr/bin/flex
> > > >> > > > > balay at ypro ~ % /usr/bin/flex --version
> > > >> > > > > flex 2.5.35 Apple(flex-32)
> > > >> > > > > balay at ypro petsc % clang -v
> > > >> > > > > Apple clang version 12.0.0 (clang-1200.0.32.2)
> > > >> > > > > Target: x86_64-apple-darwin19.6.0
> > > >> > > > > Thread model: posix
> > > >> > > > > InstalledDir: /Library/Developer/CommandLineTools/usr/bin
> > > >> > > > > balay at ypro ~ % balay at ypro petsc % ./configure
> > > >> > > > > --with-mpi-dir=$HOME/mpich-3.4.2 --download-c2html
> > > >> --download-ptscotch
> > > >> > > > >
> > > >> > > > > <log attached>
> > > >> > > > >
> > > >> > > > >
> > > >> > > > > Satish
> > > >> > > > >
> > > >> > > > > On Tue, 23 Nov 2021, Matthew Knepley wrote:
> > > >> > > > >
> > > >> > > > > > This is the same flex problem as I had for c2html, but I was
> > > >> more
> > > >> > > > > > determined tracking it down this time. The first problem is
> > > >> that we
> > > >> > > were
> > > >> > > > > > not renaming in the parser,
> > > >> > > > > >
> > > >> > > > > > main *$:/PETSc3/petsc/petsc-dev$ git diff
> > > >> > > > > > diff --git a/config/BuildSystem/config/packages/PTScotch.py
> > > >> > > > > > b/config/BuildSystem/config/packages/PTScotch.py
> > > >> > > > > > index d1c277b6e9f..e046804c17f 100644
> > > >> > > > > > --- a/config/BuildSystem/config/packages/PTScotch.py
> > > >> > > > > > +++ b/config/BuildSystem/config/packages/PTScotch.py
> > > >> > > > > > @@ -70,7 +70,7 @@ class Configure(config.package.Package):
> > > >> > > > > >      if self.libraries.add('-lrt','timer_create'): ldflags += '
> > > >> -lrt'
> > > >> > > > > >      self.cflags = self.cflags + ' -DCOMMON_RANDOM_FIXED_SEED'
> > > >> > > > > >      # do not use -DSCOTCH_PTHREAD because requires MPI built
> > > >> for
> > > >> > > > > threads.
> > > >> > > > > > -    self.cflags = self.cflags + ' -DSCOTCH_RENAME
> > > >> > > > > > -Drestrict="'+self.compilers.cRestrict+'"'
> > > >> > > > > > +    self.cflags = self.cflags + ' -DSCOTCH_RENAME
> > > >> > > -DSCOTCH_RENAME_PARSER
> > > >> > > > > > -Drestrict="'+self.compilers.cRestrict+'"'
> > > >> > > > > >      # this is needed on the Mac, because common2.c includes
> > > >> common.h
> > > >> > > > > which
> > > >> > > > > > DOES NOT include mpi.h because
> > > >> > > > > >      # SCOTCH_PTSCOTCH is NOT defined above Mac does not know
> > > >> what
> > > >> > > > > > clock_gettime() is!
> > > >> > > > > >      if self.setCompilers.isDarwin(self.log):
> > > >> > > > > >
> > > >> > > > > > Second, they were not treating this case completely correctly:
> > > >> > > > > >
> > > >> > > > > >
> > > >> > > > >
> > > >> > >
> > > >> (93454e8...):/PETSc3/petsc/petsc-dev/arch-master-debug/externalpackages/git.ptscotch/src/libscotch$
> > > >> > > > > > git diff HEAD~1
> > > >> > > > > > diff --git a/src/libscotch/parser_yy.h
> > > >> b/src/libscotch/parser_yy.h
> > > >> > > > > > index 931315d..95b8160 100644
> > > >> > > > > > --- a/src/libscotch/parser_yy.h
> > > >> > > > > > +++ b/src/libscotch/parser_yy.h
> > > >> > > > > > @@ -62,6 +62,9 @@
> > > >> > > > > >
> > > >> > > > > >  #if ((defined SCOTCH_RENAME_PARSER) || (defined yylex)) /* If
> > > >> prefix
> > > >> > > > > > renaming    */
> > > >> > > > > >  #define scotchyyparse               stratParserParse2 /* Parser
> > > >> > > function
> > > >> > > > > > name    */
> > > >> > > > > > +#if !defined(yylex)
> > > >> > > > > > +#define yylex                       scotchyylex
> > > >> > > > > > +#endif
> > > >> > > > > >  #ifndef yylval
> > > >> > > > > >  #define yylval                      SCOTCH_NAME_MACRO3
> > > >> (scotchyy,
> > > >> > > > > > SCOTCH_NAME_SUFFIXC, lval) /* It should be Yacc/Bison's job to
> > > >> > > redefine
> > > >> > > > > it!
> > > >> > > > > >  */
> > > >> > > > > >  #endif /* yylval              */
> > > >> > > > > >
> > > >> > > > > > How should we go about getting this fix in? Do you need to have
> > > >> our
> > > >> > > own
> > > >> > > > > > branch of PTScotch?
> > > >> > > > > >
> > > >> > > > > >   Thanks,
> > > >> > > > > >
> > > >> > > > > >      Matt
> > > >> > > > > >
> > > >> > > > > >
> > > >> > > > >
> > > >> > > >
> > > >> > > >
> > > >> > > >
> > > >> > >
> > > >> > >
> > > >> >
> > > >> >
> > > >>
> > > >>
> > > >
> > > > --
> > > > 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
> > > >
> > > > https://www.cse.buffalo.edu/~knepley/ <https://www.cse.buffalo.edu/~knepley/>
> > > > <http://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>>
> > > >
> > > 
> > > 
> > > 
> > 
> > 
> > 
> > -- 
> > 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
> > 
> > https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
> 
>

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