perhaps "dtruss -f" ? https://stackoverflow.com/questions/1925978/equivalent-of-strace-feopen-command-on-mac-os-x
balay@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 <[email protected]> wrote: > > > > On Tue, Nov 23, 2021 at 2:05 PM Satish Balay <[email protected] > > <mailto:[email protected]>> wrote: > > On Tue, 23 Nov 2021, Matthew Knepley wrote: > > > > > On Tue, Nov 23, 2021 at 12:56 PM Matthew Knepley <[email protected] > > > <mailto:[email protected]>> wrote: > > > > > > > On Tue, Nov 23, 2021 at 12:29 PM Satish Balay <[email protected] > > > > <mailto:[email protected]>> 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 <[email protected] > > > >> > <mailto:[email protected]>> > > > >> wrote: > > > >> > > > > >> > > On Tue, 23 Nov 2021, Matthew Knepley wrote: > > > >> > > > > > >> > > > On Tue, Nov 23, 2021 at 11:28 AM Satish Balay <[email protected] > > > >> > > > <mailto:[email protected]>> > > > >> 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@ypro ~ % which flex > > > >> > > > > /usr/bin/flex > > > >> > > > > balay@ypro ~ % /usr/bin/flex --version > > > >> > > > > flex 2.5.35 Apple(flex-32) > > > >> > > > > balay@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@ypro ~ % balay@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/> > >
