[petsc-dev] PTScotch problem on Mac
Barry Smith
bsmith at petsc.dev
Tue Nov 23 12:48:07 CST 2021
Matt,
The make that comes with Apple is ancient; I use a much more recent gnumake I compiled from source (probably brew's make is fine too).
> On Nov 23, 2021, at 1:30 PM, Matthew Knepley <knepley at gmail.com> 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?
>
> 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/ <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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