[petsc-dev] p4est configure error

[Mark Adams]

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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