[petsc-dev] p4est configure error

[Mark Adams]

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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