[petsc-dev] PTScotch problem on Mac
Barry Smith
bsmith at petsc.dev
Tue Nov 23 14:02:08 CST 2021
Ahh, it is the perl :-)
> On Nov 23, 2021, at 2:05 PM, Satish Balay via petsc-dev <petsc-dev 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> 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?
>
>
> If you can do 'strace --follow-forks' or equivalent on Mac - you might
> be able to see what gets used from /opt/local/bin/
>
> 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]
>
> Or a brute force bisection by moving binaries out of (and back into) this location.
>
> 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>
>>>> 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/>
>>>
>>
>>
>>
>
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