Re: [petsc-dev] PTScotch problem on Mac

23 Nov 2021

Ahh, it is the perl :-)
...
On Nov 23, 2021, at 2:05 PM, Satish Balay via petsc-dev <[email protected]> wrote:
On Tue, 23 Nov 2021, Matthew Knepley wrote:
...
On Tue, Nov 23, 2021 at 12:56 PM Matthew Knepley <[email protected]> wrote:
...
On Tue, Nov 23, 2021 at 12:29 PM Satish Balay <[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/
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 <[email protected]>
wrote:
...
On Tue, 23 Nov 2021, Matthew Knepley wrote:
...
On Tue, Nov 23, 2021 at 11:28 AM Satish Balay <[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/>


    

Barry Smith

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