[petsc-dev] p4est configure error

[Tobin Isaac]

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
>>>> >> > >> > > >
>>>> >> > >> >
>>>> >> > >>
>>>> >> > >>
>>>> >> >
>>>> >> >
>>>> >>
>>>> >>
>>>>
>>>>
>>>
>>