November 2021 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] PTScotch problem on Mac
by Matthew Knepley 23 Nov '21

23 Nov '21

On Tue, Nov 23, 2021 at 4:36 PM Lawrence Mitchell <wence(a)gmx.li> wrote: > > > > On 23 Nov 2021, at 21:29, Satish Balay via petsc-dev < > petsc-dev(a)mcs.anl.gov> wrote: > > > > perhaps "dtruss -f" ? > > > > > https://stackoverflow.com/questions/1925978/equivalent-of-strace-feopen-com… > > > > 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 > > Yeah, you need boot into recovery mode (holding Command-R on startup) and > turn off the SIP: > > csrutil enable --without dtrace > > Remind me why we use apple hardware again? > Ah ha! master *:~/Downloads/tmp/hpc1$ dtruss -f ls dtrace: failed to initialize dtrace: DTrace requires additional privileges 1master *:~/Downloads/tmp/hpc1$ sudo dtruss -f ls Password: PID/THRD SYSCALL(args) = return .DS_Store makefile mesh.xmf meshtest.c ex13.c mesh.h5 meshtest meshtest.o 76662/0x16881f3: issetugid(0x0, 0x0, 0x0) = 0 0 76662/0x16881f3: getentropy(0x7FFEE560E120, 0x20, 0x0) = 0 0 76662/0x16881f3: getentropy(0x7FFEE560E170, 0x40, 0x0) = 0 0 76662/0x16881f3: getpid(0x0, 0x0, 0x0) = 76662 0 76662/0x16881f3: stat64("/AppleInternal\0", 0x7FFEE560E710, 0x0) = -1 Err#2 76662/0x16881f3: csops_audittoken(0x12B76, 0x7, 0x7FFEE560E260) = 0 0 76662/0x16881f3: proc_info(0x2, 0x12B76, 0xD) = 64 0 76662/0x16881f3: csops_audittoken(0x12B76, 0x7, 0x7FFEE560DAE0) = 0 0 76662/0x16881f3: open_nocancel("/usr/share/locale/en_US.UTF-8/LC_COLLATE\0", 0x0, 0x7) = 3 0 76662/0x16881f3: fcntl_nocancel(0x3, 0x3, 0x0) = 0 0 76662/0x16881f3: getrlimit(0x1008, 0x7FFEE560EDF0, 0x0) = 0 0 76662/0x16881f3: fstat64(0x3, 0x7FFEE560ED68, 0x0) = 0 0 76662/0x16881f3: read_nocancel(0x3, "1.1A\n\0", 0x1000) = 2086 0 76662/0x16881f3: close_nocancel(0x3) = 0 0 76662/0x16881f3: open_nocancel("/usr/share/locale/en_US.UTF-8/LC_CTYPE\0", 0x0, 0x5) = 3 0 76662/0x16881f3: fcntl_nocancel(0x3, 0x3, 0x0) = 0 0 76662/0x16881f3: fstat64(0x3, 0x7FFEE560EEA8, 0x0) = 0 0 76662/0x16881f3: fstat64(0x3, 0x7FFEE560ECA8, 0x0) = 0 0 76662/0x16881f3: lseek(0x3, 0x0, 0x1) = 0 0 76662/0x16881f3: lseek(0x3, 0x0, 0x0) = 0 0 76662/0x16881f3: read_nocancel(0x3, "RuneMagAUTF-8\0", 0x1000) = 4096 0 76662/0x16881f3: read_nocancel(0x3, "\0", 0x1000) = 4096 0 76662/0x16881f3: read_nocancel(0x3, "\0", 0x1000) = 4096 0 76662/0x16881f3: read_nocancel(0x3, "\0", 0x1000) = 4096 0 76662/0x16881f3: read_nocancel(0x3, "\0", 0x1000) = 4096 0 76662/0x16881f3: read_nocancel(0x3, "\0", 0x1000) = 4096 0 76662/0x16881f3: read_nocancel(0x3, "\0", 0x1000) = 4096 0 76662/0x16881f3: read_nocancel(0x3, "@\004\211\0", 0xF5D0) = 62928 0 76662/0x16881f3: close_nocancel(0x3) = 0 0 76662/0x16881f3: open_nocancel("/usr/share/locale/en_US.UTF-8/LC_MONETARY\0", 0x0, 0x8) = 3 0 76662/0x16881f3: fstat64(0x3, 0x7FFEE560EEB8, 0x0) = 0 0 76662/0x16881f3: read_nocancel(0x3, "USD \n$\n.\n,\n3;3\n\n-\n2\n2\n1\n0\n1\n0\n1\n1\n\b\0", 0x22) = 34 0 76662/0x16881f3: close_nocancel(0x3) = 0 0 76662/0x16881f3: open_nocancel("/usr/share/locale/en_US.UTF-8/LC_NUMERIC\0", 0x0, 0x7) = 3 0 76662/0x16881f3: fstat64(0x3, 0x7FFEE560EEB8, 0x0) = 0 0 76662/0x16881f3: read_nocancel(0x3, ".\n,\n3;3\n@$\b\0", 0x8) = 8 0 76662/0x16881f3: close_nocancel(0x3) = 0 0 76662/0x16881f3: open_nocancel("/usr/share/locale/en_US.UTF-8/LC_TIME\0", 0x0, 0x4) = 3 0 76662/0x16881f3: fstat64(0x3, 0x7FFEE560EEB8, 0x0) = 0 0 76662/0x16881f3: read_nocancel(0x3, "Jan\nFeb\nMar\nApr\nMay\nJun\nJul\nAug\nSep\nOct\nNov\nDec\nJanuary\nFebruary\nMarch\nApril\nMay\nJune\nJuly\nAugust\nSeptember\nOctober\nNovember\nDecember\nSun\nMon\nTue\nWed\nThu\nFri\nSat\nSunday\nMonday\nTuesday\nWednesday\nThursday\nFriday\nSaturday\n%H:%M:%S\n%m/%d/%Y\n%a %b %e %X %Y\nAM\nP", 0x179) = 377 0 76662/0x16881f3: close_nocancel(0x3) = 0 0 76662/0x16881f3: open_nocancel("/usr/share/locale/en_US.UTF-8/LC_MESSAGES/LC_MESSAGES\0", 0x0, 0xFFFFFFFFFFFFFFF4) = 3 0 76662/0x16881f3: fstat64(0x3, 0x7FFEE560EEB8, 0x0) = 0 0 76662/0x16881f3: read_nocancel(0x3, "^[yYsS].*\n^[nN].*\n(\0", 0x12) = 18 0 76662/0x16881f3: close_nocancel(0x3) = 0 0 76662/0x16881f3: ioctl(0x1, 0x4004667A, 0x7FFEE560F404) = 0 0 76662/0x16881f3: ioctl(0x1, 0x40087468, 0x7FFEE560FA78) = 0 0 76662/0x16881f3: getuid(0x0, 0x0, 0x0) = 0 0 76662/0x16881f3: fstatat64(0xFFFFFFFFFFFFFFFE, 0x7FCD30C062A8, 0x7FFEE560F318) = 0 0 76662/0x16881f3: open_nocancel(".\0", 0x1000000, 0x0) = 3 0 76662/0x16881f3: fchdir(0x3, 0x0, 0x0) = 0 0 76662/0x16881f3: open_nocancel(".\0", 0x1000000, 0x0) = 4 0 76662/0x16881f3: open_nocancel(".\0", 0x1100004, 0x0) = 5 0 76662/0x16881f3: getattrlistbulk(0x5, 0x7FFEE560F368, 0x7FCD3100B600) = 8 0 76662/0x16881f3: getattrlistbulk(0x5, 0x7FFEE560F368, 0x7FCD3100B600) = 0 0 76662/0x16881f3: close_nocancel(0x5) = 0 0 76662/0x16881f3: fchdir(0x4, 0x0, 0x0) = 0 0 76662/0x16881f3: close_nocancel(0x4) = 0 0 76662/0x16881f3: fstat64(0x1, 0x7FFEE560EBC8, 0x0) = 0 0 76662/0x16881f3: ioctl(0x1, 0x4004667A, 0x7FFEE560EC14) = 0 0 76662/0x16881f3: write_nocancel(0x1, ".DS_Store\tmakefile\tmesh.xmf\tmeshtest.c\n\0", 0x27) = 39 0 76662/0x16881f3: write_nocancel(0x1, "ex13.c\t\tmesh.h5\t\tmeshtest\tmeshtest.o\n\004\0", 0x25) = 37 0 76662/0x16881f3: fchdir(0x3, 0x0, 0x0) = 0 0 76662/0x16881f3: close_nocancel(0x3) = 0 0 master *:~/Downloads/tmp/hpc1$ Matt > Lawrence -- 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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Re: [petsc-dev] PTScotch problem on Mac
by Barry Smith 23 Nov '21

23 Nov '21

> On Nov 23, 2021, at 4:36 PM, Lawrence Mitchell <wence(a)gmx.li> wrote: > > > >> On 23 Nov 2021, at 21:29, Satish Balay via petsc-dev <petsc-dev(a)mcs.anl.gov> wrote: >> >> perhaps "dtruss -f" ? >> >> https://stackoverflow.com/questions/1925978/equivalent-of-strace-feopen-com… >> >> 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 > > Yeah, you need boot into recovery mode (holding Command-R on startup) and turn off the SIP: > > csrutil enable --without dtrace > > Remind me why we use apple hardware again? Because it is not Linux? > > Lawrence

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Re: [petsc-dev] PTScotch problem on Mac
by Lawrence Mitchell 23 Nov '21

23 Nov '21

> On 23 Nov 2021, at 21:29, Satish Balay via petsc-dev <petsc-dev(a)mcs.anl.gov> wrote: > > perhaps "dtruss -f" ? > > https://stackoverflow.com/questions/1925978/equivalent-of-strace-feopen-com… > > 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 Yeah, you need boot into recovery mode (holding Command-R on startup) and turn off the SIP: csrutil enable --without dtrace Remind me why we use apple hardware again? Lawrence

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Re: [petsc-dev] PTScotch problem on Mac
by Satish Balay 23 Nov '21

23 Nov '21

perhaps "dtruss -f" ? https://stackoverflow.com/questions/1925978/equivalent-of-strace-feopen-com… 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 <knepley(a)gmail.com> wrote: > > > > On Tue, Nov 23, 2021 at 2:05 PM Satish Balay <balay(a)mcs.anl.gov <mailto:[email protected]>> wrote: > > On Tue, 23 Nov 2021, Matthew Knepley wrote: > > > > > On Tue, Nov 23, 2021 at 12:56 PM Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> wrote: > > > > > > > On Tue, Nov 23, 2021 at 12:29 PM Satish Balay <balay(a)mcs.anl.gov <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 <balay(a)mcs.anl.gov <mailto:[email protected]>> > > > >> wrote: > > > >> > > > > >> > > On Tue, 23 Nov 2021, Matthew Knepley wrote: > > > >> > > > > > >> > > > On Tue, Nov 23, 2021 at 11:28 AM Satish Balay <balay(a)mcs.anl.gov <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/> > >

1 0

Re: [petsc-dev] PTScotch problem on Mac
by Barry Smith 23 Nov '21

23 Nov '21

>> 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(a)gmail.com> wrote: > > On Tue, Nov 23, 2021 at 2:05 PM Satish Balay <balay(a)mcs.anl.gov <mailto:[email protected]>> wrote: > On Tue, 23 Nov 2021, Matthew Knepley wrote: > > > On Tue, Nov 23, 2021 at 12:56 PM Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> wrote: > > > > > On Tue, Nov 23, 2021 at 12:29 PM Satish Balay <balay(a)mcs.anl.gov <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 <balay(a)mcs.anl.gov <mailto:[email protected]>> > > >> wrote: > > >> > > > >> > > On Tue, 23 Nov 2021, Matthew Knepley wrote: > > >> > > > > >> > > > On Tue, Nov 23, 2021 at 11:28 AM Satish Balay <balay(a)mcs.anl.gov <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/>

1 0

Re: [petsc-dev] PTScotch problem on Mac
by Barry Smith 23 Nov '21

23 Nov '21

Ahh, it is the perl :-) > On Nov 23, 2021, at 2:05 PM, Satish Balay via petsc-dev <petsc-dev(a)mcs.anl.gov> wrote: > > On Tue, 23 Nov 2021, Matthew Knepley wrote: > >> On Tue, Nov 23, 2021 at 12:56 PM Matthew Knepley <knepley(a)gmail.com> wrote: >> >>> On Tue, Nov 23, 2021 at 12:29 PM Satish Balay <balay(a)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(a)mcs.anl.gov> >>>> wrote: >>>>> >>>>>> On Tue, 23 Nov 2021, Matthew Knepley wrote: >>>>>> >>>>>>> On Tue, Nov 23, 2021 at 11:28 AM Satish Balay <balay(a)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@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/ >>> <http://www.cse.buffalo.edu/~knepley/> >>> >> >> >> >

1 0

Re: [petsc-dev] PTScotch problem on Mac
by Matthew Knepley 23 Nov '21

23 Nov '21

On Tue, Nov 23, 2021 at 2:05 PM Satish Balay <balay(a)mcs.anl.gov> wrote: > On Tue, 23 Nov 2021, Matthew Knepley wrote: > > > On Tue, Nov 23, 2021 at 12:56 PM Matthew Knepley <knepley(a)gmail.com> > wrote: > > > > > On Tue, Nov 23, 2021 at 12:29 PM Satish Balay <balay(a)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(a)mcs.anl.gov> > > >> wrote: > > >> > > > >> > > On Tue, 23 Nov 2021, Matthew Knepley wrote: > > >> > > > > >> > > > On Tue, Nov 23, 2021 at 11:28 AM Satish Balay < > balay(a)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@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/ > > > <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/>

1 0

Re: [petsc-dev] PTScotch problem on Mac
by Satish Balay 23 Nov '21

23 Nov '21

On Tue, 23 Nov 2021, Matthew Knepley wrote: > On Tue, Nov 23, 2021 at 12:56 PM Matthew Knepley <knepley(a)gmail.com> wrote: > > > On Tue, Nov 23, 2021 at 12:29 PM Satish Balay <balay(a)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(a)mcs.anl.gov> > >> wrote: > >> > > >> > > On Tue, 23 Nov 2021, Matthew Knepley wrote: > >> > > > >> > > > On Tue, Nov 23, 2021 at 11:28 AM Satish Balay <balay(a)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@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/ > > <http://www.cse.buffalo.edu/~knepley/> > > > > >

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Re: [petsc-dev] PTScotch problem on Mac
by Barry Smith 23 Nov '21

23 Nov '21

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(a)gmail.com> wrote: > > On Tue, Nov 23, 2021 at 12:56 PM Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> wrote: > On Tue, Nov 23, 2021 at 12:29 PM Satish Balay <balay(a)mcs.anl.gov <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? > > 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(a)mcs.anl.gov <mailto:[email protected]>> wrote: > > > > > On Tue, 23 Nov 2021, Matthew Knepley wrote: > > > > > > > On Tue, Nov 23, 2021 at 11:28 AM Satish Balay <balay(a)mcs.anl.gov <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/ <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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Re: [petsc-dev] DMPlexCreateNaturalVector
by Alexis Marboeuf 23 Nov '21

23 Nov '21

Hi Matt, Thank you for your help. We can continue this conversation under your merge request on gitlab. Thanks, Alexis ________________________________ De : Matthew Knepley <knepley(a)gmail.com> Envoyé : mardi 23 novembre 2021 01:24 À : Alexis Marboeuf <alexis.marboeuf(a)hotmail.fr> Cc : petsc-dev(a)mcs.anl.gov <petsc-dev(a)mcs.anl.gov> Objet : Re: [petsc-dev] DMPlexCreateNaturalVector On Mon, Nov 22, 2021 at 7:24 PM Matthew Knepley <knepley(a)gmail.com<mailto:[email protected]>> wrote: On Mon, Nov 22, 2021 at 7:21 PM Alexis Marboeuf <alexis.marboeuf(a)hotmail.fr<mailto:[email protected]>> wrote: Dear PETSc Team, I am writing a DMPlexCreateNaturalVector routine in src/dm/impls/plex/plexnatural.c. What is the way to properly interface the call such as for DMCreateGlobalVector? In particular, do you want to unify the call with its DMDA counterpart DMDACreateNaturalVector of src/dm/impls/da/dadist.c? This exists currently. However, we are debating how it should behave. Currently the natural vector has a global order that matches the original global order, but has the current partition. It could be that we want a vector that matches the original partition, so we are discussing this online. I forgot to point you to the discussion: https://gitlab.com/petsc/petsc/-/merge_requests/4547 Thanks, Matt Thanks, Matt Thanks, Alexis -- 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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