[petsc-dev] PTScotch problem on Mac
Matthew Knepley
knepley at gmail.com
Tue Nov 23 12:30:08 CST 2021
On Tue, Nov 23, 2021 at 12:56 PM Matthew Knepley <knepley at gmail.com> wrote:
> On Tue, Nov 23, 2021 at 12:29 PM Satish Balay <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>
>> 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>
>> 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/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20211123/c49195b3/attachment.html>
More information about the petsc-dev
mailing list