[petsc-dev] p4est configure error

[Mark Adams]

On Fri, Jul 8, 2016 at 1:30 PM, Tobin Isaac <tisaac at uchicago.edu> wrote:

>
> What is `libtool --version` on Cori?
>

 2.4.2

on Edison:

07:59 edison09 maint= ~/petsc_install/petsc$ libtool --version
libtool (GNU libtool) 2.4.6


On Fri, Jul 08, 2016 at 08:37:15AM -0400, Mark Adams wrote:
> > And here is the good configure on Cori,
> >
> > On Fri, Jul 8, 2016 at 8:23 AM, Mark Adams <mfadams at lbl.gov> wrote:
> >
> > > As I said, I need two passes to get this to work, here is the first
> > > (failed) configure on Cori.  With any luck my current configure will
> work
> > > and I can send that along.
> > > Note, this used to work on Edison, so it might be something not worth,
> or
> > > even possible, to fix with NERSC's help.
> > > Thanks,
> > >
> > > On Thu, Jul 7, 2016 at 9:12 PM, Tobin Isaac <tisaac at uchicago.edu>
> wrote:
> > >
> > >> I'd be happy to help some more if you send a successful log from Cori.
> > >>
> > >> On July 7, 2016 7:18:30 PM CDT, Mark Adams <mfadams at lbl.gov> wrote:
> > >> >Yes, if fails on debug=0. This used to work on Edison and it does
> work
> > >> >now
> > >> >on Cori.
> > >> >
> > >> >On Fri, Jul 8, 2016 at 1:07 AM, Mark Adams <mfadams at lbl.gov> wrote:
> > >> >
> > >> >> whoops, that did not have p4est
> > >> >>
> > >> >>
> > >> >> On Fri, Jul 8, 2016 at 1:04 AM, Mark Adams <mfadams at lbl.gov>
> wrote:
> > >> >>
> > >> >>>
> > >> >>>
> > >> >>> On Fri, Jul 8, 2016 at 12:18 AM, Tobin Isaac <tisaac at uchicago.edu
> >
> > >> >wrote:
> > >> >>>
> > >> >>>> Interesting, you'd think that --disable-shared would be all that
> > >> >>>> matters.  Could you please send that configure.log for
> comparison?
> > >> >>>>
> > >> >>>> On July 7, 2016 5:14:13 PM CDT, Mark Adams <mfadams at lbl.gov>
> wrote:
> > >> >>>> >Well, this did not work as you suspected ... FYI, it seems to
> work
> > >> >>>> >with-debugging=0.
> > >> >>>> >
> > >> >>>> >On Thu, Jul 7, 2016 at 11:13 PM, Satish Balay <
> balay at mcs.anl.gov>
> > >> >>>> >wrote:
> > >> >>>> >
> > >> >>>> >>
> > >> >>>> >>
> > >> >>>> >> >>>>>>>
> > >> >>>> >> /bin/sh ./libtool  --tag=CC   --mode=link cc  -no-ipo -g -O0
> > >> >-o
> > >> >>>> >> libb64/sc_b64enc libb64/libb64_sc_b64enc-b64enc.o ./src/
> libsc.la
> > >> >>>> >-lgomp
> > >> >>>> >> libtool: link: cc -no-ipo -g -O0 -o libb64/sc_b64enc
> > >> >>>> >> libb64/libb64_sc_b64enc-b64enc.o  ./src/.libs/libsc.a
> > >> >>>> >> /opt/gcc/5.2.0/snos/lib/../lib64/libgomp.so -lrt -ldl
> -Wl,-rpath
> > >> >>>> >> -Wl,/opt/gcc/5.2.0/snos/lib/../lib64 -Wl,-rpath
> > >> >>>> >> -Wl,/opt/gcc/5.2.0/snos/lib/../lib64
> > >> >>>> >> <<<<<<<
> > >> >>>> >>
> > >> >>>> >> For some reason libtool is converting "-lgomp" into
> > >> >>>> >> "/opt/gcc/5.2.0/snos/lib/../lib64/libgomp.so" - and giving an
> ld
> > >> >>>> >error.
> > >> >>>> >>
> > >> >>>> >> On my linux box - I see:
> > >> >>>> >> >>>>>>>
> > >> >>>> >> /bin/sh ./libtool  --tag=CC   --mode=link mpicc  -g3   -o
> > >> >>>> >libb64/sc_b64enc
> > >> >>>> >> libb64/libb64_sc_b64enc-b64enc.o ./src/libsc.la -lgomp
> -lpthread
> > >> >-lz
> > >> >>>> >-lm
> > >> >>>> >> libtool: link: mpicc -g3 -o libb64/sc_b64enc
> > >> >>>> >> libb64/libb64_sc_b64enc-b64enc.o  ./src/.libs/libsc.a -lgomp
> > >> >>>> >-lpthread -lz
> > >> >>>> >> -lm
> > >> >>>> >> <<<<<<
> > >> >>>> >>
> > >> >>>> >> I don't really understand libtool - or this error..
> > >> >>>> >>
> > >> >>>> >> Satish
> > >> >>>> >>
> > >> >>>> >> On Thu, 7 Jul 2016, Tobin Isaac wrote:
> > >> >>>> >>
> > >> >>>> >> > Nope, different error: p4est autotools found an openmp
> library
> > >> >and
> > >> >>>> >tried
> > >> >>>> >> to link it, but there's a shared/static mismatch.  I'll try to
> > >> >get to
> > >> >>>> >the
> > >> >>>> >> bottom of this.
> > >> >>>> >> >
> > >> >>>> >> >
> > >> >>>> >> > On July 7, 2016 3:27:23 PM CDT, Mark Adams <mfadams at lbl.gov
> >
> > >> >wrote:
> > >> >>>> >> > >I nuked and ran this twice:
> > >> >>>> >> > >
> > >> >>>> >> > >1013  rm -fr arch-xc30-dbg64-intel
> > >> >>>> >> > > 1014  ../arch-xc30-dbg64-intel.py
> > >> >>>> >> > > 1015  h
> > >> >>>> >> > > 1016  ../arch-xc30-dbg64-intel.py
> > >> >>>> >> > >
> > >> >>>> >> > >Same error.
> > >> >>>> >> > >
> > >> >>>> >> > >
> > >> >>>> >> > >On Thu, Jul 7, 2016 at 9:36 PM, Satish Balay
> > >> ><balay at mcs.anl.gov>
> > >> >>>> >wrote:
> > >> >>>> >> > >
> > >> >>>> >> > >> perhaps configure was not rerun - so a stale p4est was
> > >> >being
> > >> >>>> >used..
> > >> >>>> >> > >>
> > >> >>>> >> > >> Satish
> > >> >>>> >> > >>
> > >> >>>> >> > >> On Thu, 7 Jul 2016, Tobin Isaac wrote:
> > >> >>>> >> > >>
> > >> >>>> >> > >> > p4est.py automatically pulls from whatever p4est
> branch I
> > >> >call
> > >> >>>> >> > >'petsc'
> > >> >>>> >> > >> > in my repo, so I don't see how this problem persists if
> > >> >you
> > >> >>>> >really
> > >> >>>> >> > >> > nuked it.
> > >> >>>> >> > >> >
> > >> >>>> >> > >> > - Did you nuke the right directory?
> > >> >>>> >> > >> > - Did you send me the right configure.log?
> > >> >>>> >> > >> > - Is the new failure the same (the same stale p4est
> > >> >commit is
> > >> >>>> >being
> > >> >>>> >> > >> >   used)?
> > >> >>>> >> > >> >
> > >> >>>> >> > >> > On Thu, Jul 07, 2016 at 08:33:57PM +0200, Mark Adams
> > >> >wrote:
> > >> >>>> >> > >> > > It sounds like I have not merged your fix.  Should I
> > >> >pull
> > >> >>>> >from
> > >> >>>> >> > >master?
> > >> >>>> >> > >> > >
> > >> >>>> >> > >> > > I have nuked this many times.
> > >> >>>> >> > >> > >
> > >> >>>> >> > >> > > On Thu, Jul 7, 2016 at 4:26 PM, Tobin Isaac
> > >> >>>> ><tisaac at uchicago.edu>
> > >> >>>> >> > >> wrote:
> > >> >>>> >> > >> > >
> > >> >>>> >> > >> > > >
> > >> >>>> >> > >> > > > On Thu, Jul 07, 2016 at 03:16:40PM +0200, Mark
> Adams
> > >> >>>> >wrote:
> > >> >>>> >> > >> > > > > p4est on Edison configures in w/o debugging,
> > >> >although I
> > >> >>>> >have
> > >> >>>> >> > >to run
> > >> >>>> >> > >> > > > > configure twice.
> > >> >>>> >> > >> > > > > But with debugging it fails.  I can not see any
> > >> >>>> >difference
> > >> >>>> >> > >between
> > >> >>>> >> > >> the
> > >> >>>> >> > >> > > > two
> > >> >>>> >> > >> > > > > configures other than debugging.
> > >> >>>> >> > >> > > > > Mark
> > >> >>>> >> > >> > > >
> > >> >>>> >> > >> > > > The log shows that you are configuring a p4est
> commit
> > >> >>>> >(3d3e1)
> > >> >>>> >> > >that is
> > >> >>>> >> > >> > > > before the one I pushed specifically to avoid the
> > >> >fortran
> > >> >>>> >> > >> > > > configuration error (f54bb3).  Please clear the
> > >> >git.p4est
> > >> >>>> >> > >directory,
> > >> >>>> >> > >> > > > and confirm that you are configuring with the
> current
> > >> >>>> >'petsc'
> > >> >>>> >> > >branch
> > >> >>>> >> > >> > > > of p4est (`grep 'checking Point version'
> > >> >configure.log`
> > >> >>>> >should
> > >> >>>> >> > >show
> > >> >>>> >> > >> > > > X.XXX-a9f22).
> > >> >>>> >> > >> > > >
> > >> >>>> >> > >> > > > Cheers,
> > >> >>>> >> > >> > > >   Toby
> > >> >>>> >> > >> > > >
> > >> >>>> >> > >> >
> > >> >>>> >> > >>
> > >> >>>> >> > >>
> > >> >>>> >> >
> > >> >>>> >> >
> > >> >>>> >>
> > >> >>>> >>
> > >> >>>>
> > >> >>>>
> > >> >>>
> > >> >>
> > >>
> > >>
> > >
>
>
>
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