<div dir="ltr">And here is the good configure on Cori,</div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jul 8, 2016 at 8:23 AM, Mark Adams <span dir="ltr"><<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">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.<div>Note, this used to work on Edison, so it might be something not worth, or even possible, to fix with NERSC's help.<br><div>Thanks, </div></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jul 7, 2016 at 9:12 PM, Tobin Isaac <span dir="ltr"><<a href="mailto:tisaac@uchicago.edu" target="_blank">tisaac@uchicago.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I'd be happy to help some more if you send a successful log from Cori.<br>
<div><div><br>
On July 7, 2016 7:18:30 PM CDT, Mark Adams <<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>> wrote:<br>
>Yes, if fails on debug=0. This used to work on Edison and it does work<br>
>now<br>
>on Cori.<br>
><br>
>On Fri, Jul 8, 2016 at 1:07 AM, Mark Adams <<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>> wrote:<br>
><br>
>> whoops, that did not have p4est<br>
>><br>
>><br>
>> On Fri, Jul 8, 2016 at 1:04 AM, Mark Adams <<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>> wrote:<br>
>><br>
>>><br>
>>><br>
>>> On Fri, Jul 8, 2016 at 12:18 AM, Tobin Isaac <<a href="mailto:tisaac@uchicago.edu" target="_blank">tisaac@uchicago.edu</a>><br>
>wrote:<br>
>>><br>
>>>> Interesting, you'd think that --disable-shared would be all that<br>
>>>> matters. Could you please send that configure.log for comparison?<br>
>>>><br>
>>>> On July 7, 2016 5:14:13 PM CDT, Mark Adams <<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>> wrote:<br>
>>>> >Well, this did not work as you suspected ... FYI, it seems to work<br>
>>>> >with-debugging=0.<br>
>>>> ><br>
>>>> >On Thu, Jul 7, 2016 at 11:13 PM, Satish Balay <<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>><br>
>>>> >wrote:<br>
>>>> ><br>
>>>> >><br>
>>>> >><br>
>>>> >> >>>>>>><br>
>>>> >> /bin/sh ./libtool --tag=CC --mode=link cc -no-ipo -g -O0<br>
>-o<br>
>>>> >> libb64/sc_b64enc libb64/libb64_sc_b64enc-b64enc.o ./src/<a href="http://libsc.la" rel="noreferrer" target="_blank">libsc.la</a><br>
>>>> >-lgomp<br>
>>>> >> libtool: link: cc -no-ipo -g -O0 -o libb64/sc_b64enc<br>
>>>> >> libb64/libb64_sc_b64enc-b64enc.o ./src/.libs/libsc.a<br>
>>>> >> /opt/gcc/5.2.0/snos/lib/../lib64/libgomp.so -lrt -ldl -Wl,-rpath<br>
>>>> >> -Wl,/opt/gcc/5.2.0/snos/lib/../lib64 -Wl,-rpath<br>
>>>> >> -Wl,/opt/gcc/5.2.0/snos/lib/../lib64<br>
>>>> >> <<<<<<<<br>
>>>> >><br>
>>>> >> For some reason libtool is converting "-lgomp" into<br>
>>>> >> "/opt/gcc/5.2.0/snos/lib/../lib64/libgomp.so" - and giving an ld<br>
>>>> >error.<br>
>>>> >><br>
>>>> >> On my linux box - I see:<br>
>>>> >> >>>>>>><br>
>>>> >> /bin/sh ./libtool --tag=CC --mode=link mpicc -g3 -o<br>
>>>> >libb64/sc_b64enc<br>
>>>> >> libb64/libb64_sc_b64enc-b64enc.o ./src/<a href="http://libsc.la" rel="noreferrer" target="_blank">libsc.la</a> -lgomp -lpthread<br>
>-lz<br>
>>>> >-lm<br>
>>>> >> libtool: link: mpicc -g3 -o libb64/sc_b64enc<br>
>>>> >> libb64/libb64_sc_b64enc-b64enc.o ./src/.libs/libsc.a -lgomp<br>
>>>> >-lpthread -lz<br>
>>>> >> -lm<br>
>>>> >> <<<<<<<br>
>>>> >><br>
>>>> >> I don't really understand libtool - or this error..<br>
>>>> >><br>
>>>> >> Satish<br>
>>>> >><br>
>>>> >> On Thu, 7 Jul 2016, Tobin Isaac wrote:<br>
>>>> >><br>
>>>> >> > Nope, different error: p4est autotools found an openmp library<br>
>and<br>
>>>> >tried<br>
>>>> >> to link it, but there's a shared/static mismatch. I'll try to<br>
>get to<br>
>>>> >the<br>
>>>> >> bottom of this.<br>
>>>> >> ><br>
>>>> >> ><br>
>>>> >> > On July 7, 2016 3:27:23 PM CDT, Mark Adams <<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>><br>
>wrote:<br>
>>>> >> > >I nuked and ran this twice:<br>
>>>> >> > ><br>
>>>> >> > >1013 rm -fr arch-xc30-dbg64-intel<br>
>>>> >> > > 1014 ../arch-xc30-dbg64-intel.py<br>
>>>> >> > > 1015 h<br>
>>>> >> > > 1016 ../arch-xc30-dbg64-intel.py<br>
>>>> >> > ><br>
>>>> >> > >Same error.<br>
>>>> >> > ><br>
>>>> >> > ><br>
>>>> >> > >On Thu, Jul 7, 2016 at 9:36 PM, Satish Balay<br>
><<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>><br>
>>>> >wrote:<br>
>>>> >> > ><br>
>>>> >> > >> perhaps configure was not rerun - so a stale p4est was<br>
>being<br>
>>>> >used..<br>
>>>> >> > >><br>
>>>> >> > >> Satish<br>
>>>> >> > >><br>
>>>> >> > >> On Thu, 7 Jul 2016, Tobin Isaac wrote:<br>
>>>> >> > >><br>
>>>> >> > >> > p4est.py automatically pulls from whatever p4est branch I<br>
>call<br>
>>>> >> > >'petsc'<br>
>>>> >> > >> > in my repo, so I don't see how this problem persists if<br>
>you<br>
>>>> >really<br>
>>>> >> > >> > nuked it.<br>
>>>> >> > >> ><br>
>>>> >> > >> > - Did you nuke the right directory?<br>
>>>> >> > >> > - Did you send me the right configure.log?<br>
>>>> >> > >> > - Is the new failure the same (the same stale p4est<br>
>commit is<br>
>>>> >being<br>
>>>> >> > >> > used)?<br>
>>>> >> > >> ><br>
>>>> >> > >> > On Thu, Jul 07, 2016 at 08:33:57PM +0200, Mark Adams<br>
>wrote:<br>
>>>> >> > >> > > It sounds like I have not merged your fix. Should I<br>
>pull<br>
>>>> >from<br>
>>>> >> > >master?<br>
>>>> >> > >> > ><br>
>>>> >> > >> > > I have nuked this many times.<br>
>>>> >> > >> > ><br>
>>>> >> > >> > > On Thu, Jul 7, 2016 at 4:26 PM, Tobin Isaac<br>
>>>> ><<a href="mailto:tisaac@uchicago.edu" target="_blank">tisaac@uchicago.edu</a>><br>
>>>> >> > >> wrote:<br>
>>>> >> > >> > ><br>
>>>> >> > >> > > ><br>
>>>> >> > >> > > > On Thu, Jul 07, 2016 at 03:16:40PM +0200, Mark Adams<br>
>>>> >wrote:<br>
>>>> >> > >> > > > > p4est on Edison configures in w/o debugging,<br>
>although I<br>
>>>> >have<br>
>>>> >> > >to run<br>
>>>> >> > >> > > > > configure twice.<br>
>>>> >> > >> > > > > But with debugging it fails. I can not see any<br>
>>>> >difference<br>
>>>> >> > >between<br>
>>>> >> > >> the<br>
>>>> >> > >> > > > two<br>
>>>> >> > >> > > > > configures other than debugging.<br>
>>>> >> > >> > > > > Mark<br>
>>>> >> > >> > > ><br>
>>>> >> > >> > > > The log shows that you are configuring a p4est commit<br>
>>>> >(3d3e1)<br>
>>>> >> > >that is<br>
>>>> >> > >> > > > before the one I pushed specifically to avoid the<br>
>fortran<br>
>>>> >> > >> > > > configuration error (f54bb3). Please clear the<br>
>git.p4est<br>
>>>> >> > >directory,<br>
>>>> >> > >> > > > and confirm that you are configuring with the current<br>
>>>> >'petsc'<br>
>>>> >> > >branch<br>
>>>> >> > >> > > > of p4est (`grep 'checking Point version'<br>
>configure.log`<br>
>>>> >should<br>
>>>> >> > >show<br>
>>>> >> > >> > > > X.XXX-a9f22).<br>
>>>> >> > >> > > ><br>
>>>> >> > >> > > > Cheers,<br>
>>>> >> > >> > > > Toby<br>
>>>> >> > >> > > ><br>
>>>> >> > >> ><br>
>>>> >> > >><br>
>>>> >> > >><br>
>>>> >> ><br>
>>>> >> ><br>
>>>> >><br>
>>>> >><br>
>>>><br>
>>>><br>
>>><br>
>><br>
<br>
</div></div></blockquote></div><br></div>
</div></div></blockquote></div><br></div>