[petsc-dev] p4est configure error

[Tobin Isaac]

What is `libtool --version` on Cori?

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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