<div dir="ltr">p4est seems to work now, but I am getting a BLAS failure. But I download blas....</div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Feb 17, 2017 at 12:48 PM, Satish Balay <span dir="ltr"><<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">>>><br>
File "/global/u2/m/madams/petsc/<wbr>config/BuildSystem/config/<wbr>packages/p4est.py", line 51, in updateGitDir<br>
<span class=""> raise RuntimeError('Could not initialize sc submodule needed by p4est')<br>
<<<<br>
<br>
</span>So 'git submoudle' stuff failed. Presumably this install of git doesn't support submodule?<br>
<br>
>>>>>><br>
Checking for program /usr/common/software/git/2.9.<wbr>1/bin/git...found<br>
Defined make macro "GIT" to "git"<br>
Executing: git --version<br>
stdout: git version 2.9.1<br>
<<<<<<<<br>
<br>
You should be able to use the taball - if you use the patch I mentioned eariler [which is already in master]<br>
<br>
If you want everything else to be from git - and use tarball with only p4est - then do:<br>
<br>
--download-p4est=<a href="https://github.com/p4est/p4est.github.io/raw/master/release/p4est-2.0.tar.gz" rel="noreferrer" target="_blank">https://<wbr>github.com/p4est/p4est.github.<wbr>io/raw/master/release/p4est-2.<wbr>0.tar.gz</a><br>
<span class="HOEnZb"><font color="#888888"><br>
Satish<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
On Fri, 17 Feb 2017, Tobin Isaac wrote:<br>
<br>
> The configure.log doesn't really tell me why it is failing. Did you<br>
> start with a clean git.p4est after trying to use the tarball?<br>
><br>
> On Fri, Feb 17, 2017 at 12:21:50PM -0500, Mark Adams wrote:<br>
> > It turns out that Cori-KNL does have git, it is just not loaded by default.<br>
> ><br>
> > It still does not work, but the error looks different.<br>
> ><br>
> > ******************************<wbr>******************************<wbr>*******************<br>
> > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for<br>
> > details):<br>
> > ------------------------------<wbr>------------------------------<wbr>-------------------<br>
> > Could not initialize sc submodule needed by p4est<br>
> > ******************************<wbr>******************************<wbr>*******************<br>
> ><br>
> ><br>
> > On Thu, Feb 16, 2017 at 10:20 PM, Tobin Isaac <<a href="mailto:tisaac@uchicago.edu">tisaac@uchicago.edu</a>> wrote:<br>
> ><br>
> > ><br>
> > > On Thu, Feb 16, 2017 at 05:48:57PM -0600, Barry Smith wrote:<br>
> > > ><br>
> > > > > On Feb 16, 2017, at 5:01 PM, Tobin Isaac <<a href="mailto:tisaac@uchicago.edu">tisaac@uchicago.edu</a>> wrote:<br>
> > > > ><br>
> > > > > The bootstrap script predates/supercedes autoreconf to get the<br>
> > > necessary m4 scripts and write configure. The tarballs have the m4 scripts<br>
> > > and configure, so they should be treated as standard gnu configure && make<br>
> > > && make install scripts. I think that's what I accomplished in p4est.py.<br>
> > > I'm on my phone, when I'm at a computer I'll look at this thread's history<br>
> > > to see if I can figure out what's going on.<br>
> > > ><br>
> > > > You are confusing two errors. One is the issue you mention above, we<br>
> > > don't care about that. The only error we care about is that p4est<br>
> > > ./configure needs to run a compiled program to gather some information<br>
> > > about the machine. On systems with cross-compiling this doesn't work since<br>
> > > after ./configure compiles the program it cannot run it because it is not<br>
> > > compatible with the hardware. So the question is: is there an easy way to<br>
> > > hack the p4est configure so that we can provide the needed information<br>
> > > directly and not have ./configure try to run an executable?<br>
> > ><br>
> > > Okay, I get it now. There should be `config.log` in<br>
> > > externalpackags/git.p4est that would let me know what particular check<br>
> > > it was working on when cross-compilation errors cropped up, and I<br>
> > > could try to help come up with a solution.<br>
> > ><br>
> > > ><br>
> > > > Barry<br>
> > > ><br>
> > > > Note that this problem is common for many autoconf based build systems,<br>
> > > its solution depends on the details of how the particular system is using<br>
> > > using executables to gather information.<br>
> > > ><br>
> > > > ><br>
> > > > > On February 16, 2017 4:34:35 PM CST, Barry Smith <<a href="mailto:bsmith@mcs.anl.gov">bsmith@mcs.anl.gov</a>><br>
> > > wrote:<br>
> > > > >><br>
> > > > >> The best long term fix is to find out what things p4est needs to<br>
> > > > >> determine by a running a program and providing them some other way.<br>
> > > > >><br>
> > > > >> Toby<br>
> > > > >><br>
> > > > >> So what things is p4est trying to determine by running a program?<br>
> > > > >><br>
> > > > >> Barry<br>
> > > > >><br>
> > > > >><br>
> > > > >><br>
> > > > >>> On Feb 16, 2017, at 3:25 PM, Satish Balay <<a href="mailto:balay@mcs.anl.gov">balay@mcs.anl.gov</a>> wrote:<br>
> > > > >>><br>
> > > > >>> I don't understand autoconf well enough for cross compiling. Some<br>
> > > > >>> packages appear to require this - but others don't.<br>
> > > > >>><br>
> > > > >>><br>
> > > > >> <a href="https://www.gnu.org/software/autoconf/manual/autoconf-2.69/" rel="noreferrer" target="_blank">https://www.gnu.org/software/<wbr>autoconf/manual/autoconf-2.69/</a><br>
> > > html_node/Hosts-and-Cross_<wbr>002dCompilation.html<br>
> > > > >>><br>
> > > > >>> So one would run 'config.guess' script on the compute node - and use<br>
> > > > >> this value on the compile node with configure?<br>
> > > > >>><br>
> > > > >>> I don't know how we could automate that..<br>
> > > > >>><br>
> > > > >>> Satish<br>
> > > > >>><br>
> > > > >>> On Wed, 15 Feb 2017, Mark Adams wrote:<br>
> > > > >>><br>
> > > > >>>> OK, that did not work. It says something about --host now.<br>
> > > > >>>><br>
> > > > >>>> On Wed, Feb 15, 2017 at 5:06 PM, Mark Adams <<a href="mailto:mfadams@lbl.gov">mfadams@lbl.gov</a>><br>
> > > wrote:<br>
> > > > >>>><br>
> > > > >>>>> I think this will work because I have git when I configure on a<br>
> > > > >> login node<br>
> > > > >>>>> (Haswell). I build KNL by submitting a batch script (it takes to<br>
> > > > >> long to<br>
> > > > >>>>> fit in 30 minutes of an interactive session). That fails because<br>
> > > > >> git is not<br>
> > > > >>>>> available (can I just load the module ...) on a KNL compute node.<br>
> > > > >> It is<br>
> > > > >>>>> reconfiguring now, I'll let you know if it fails.<br>
> > > > >>>>> Thanks,<br>
> > > > >>>>><br>
> > > > >>>>> On Wed, Feb 15, 2017 at 4:59 PM, Satish Balay <<a href="mailto:balay@mcs.anl.gov">balay@mcs.anl.gov</a>><br>
> > > > >> wrote:<br>
> > > > >>>>><br>
> > > > >>>>>> Sorry - this won't work - as p4est appears to require git<br>
> > > > >> [submodules?]..<br>
> > > > >>>>>><br>
> > > > >>>>>>>>>>>>>>>>>> p4est.py <<<<<<<<<<<<<<br>
> > > > >>>>>> def updateGitDir(self):<br>
> > > > >>>>>> config.package.GNUPackage.<wbr>updateGitDir(self)<br>
> > > > >>>>>> Dir = self.getDir()<br>
> > > > >>>>>> try:<br>
> > > > >>>>>> libsc = self.libsc<br>
> > > > >>>>>> except AttributeError:<br>
> > > > >>>>>> try:<br>
> > > > >>>>>> self.executeShellCommand([<wbr>self.sourceControl.git,<br>
> > > > >> 'submodule',<br>
> > > > >>>>>> 'update', '--init'], cwd=Dir, log=self.log)<br>
> > > > >>>>>> import os<br>
> > > > >>>>>> if os.path.isfile(os.path.join(<wbr>Dir,'sc','README')):<br>
> > > > >>>>>> self.libsc = os.path.join(Dir,'sc')<br>
> > > > >>>>>> else:<br>
> > > > >>>>>> raise RuntimeError<br>
> > > > >>>>>> except RuntimeError:<br>
> > > > >>>>>> raise RuntimeError('Could not initialize sc submodule<br>
> > > > >> needed by<br>
> > > > >>>>>> p4est')<br>
> > > > >>>>>> return<br>
> > > > >>>>>> <<<<<<<br>
> > > > >>>>>><br>
> > > > >>>>>> Satish<br>
> > > > >>>>>><br>
> > > > >>>>>> On Wed, 15 Feb 2017, Satish Balay wrote:<br>
> > > > >>>>>><br>
> > > > >>>>>>> batch won't help here. its git vs tarball - and p4est curently<br>
> > > > >> doesn't<br>
> > > > >>>>>> have a taball.<br>
> > > > >>>>>>><br>
> > > > >>>>>>> The following should give you a tarball - if you don't have git.<br>
> > > > >>>>>>><br>
> > > > >>>>>>> diff --git a/config/BuildSystem/config/<wbr>packages/p4est.py<br>
> > > > >>>>>> b/config/BuildSystem/config/<wbr>packages/p4est.py<br>
> > > > >>>>>>> index 4735ff4..1f9507c 100644<br>
> > > > >>>>>>> --- a/config/BuildSystem/config/<wbr>packages/p4est.py<br>
> > > > >>>>>>> +++ b/config/BuildSystem/config/<wbr>packages/p4est.py<br>
> > > > >>>>>>> @@ -4,7 +4,7 @@ class Configure(config.package.<wbr>GNUPackage):<br>
> > > > >>>>>>> def __init__(self, framework):<br>
> > > > >>>>>>> config.package.GNUPackage.__<wbr>init__(self, framework)<br>
> > > > >>>>>>> self.gitcommit = 'v2.0'<br>
> > > > >>>>>>> - self.download = ['git://<a href="https://github.com/cbu" rel="noreferrer" target="_blank">https://github.com/cbu</a><br>
> > > > >>>>>> rstedde/p4est']<br>
> > > > >>>>>>> + self.download = ['git://<a href="https://github.com/cbu" rel="noreferrer" target="_blank">https://github.com/cbu</a><br>
> > > > >>>>>> rstedde/p4est','<a href="https://github.com/cburstedde/p4est/archive/" rel="noreferrer" target="_blank">https://<wbr>github.com/cburstedde/p4est/<wbr>archive/</a><br>
> > > > >>>>>> '+self.gitcommit+'.tar.gz']<br>
> > > > >>>>>>> self.functions = ['p4est_init']<br>
> > > > >>>>>>> self.includes = ['p4est_bits.h']<br>
> > > > >>>>>>> self.liblist = [['libp4est.a', 'libsc.a']]<br>
> > > > >>>>>>><br>
> > > > >>>>>>> I can push this to master.<br>
> > > > >>>>>>><br>
> > > > >>>>>>> Satish<br>
> > > > >>>>>>><br>
> > > > >>>>>>> On Wed, 15 Feb 2017, Mark Adams wrote:<br>
> > > > >>>>>>><br>
> > > > >>>>>>>> Oh, this is because git does not work on KNL. Maybe I should do<br>
> > > > >>>>>>>> with-batch=1,<br>
> > > > >>>>>>>><br>
> > > > >>>>>>>><br>
> > > > >>>>>>>> On Wed, Feb 15, 2017 at 4:36 PM, Mark Adams <<a href="mailto:mfadams@lbl.gov">mfadams@lbl.gov</a>><br>
> > > > >> wrote:<br>
> > > > >>>>>>>><br>
> > > > >>>>>>>>> I get this error on the KNL partition at NERSC. P4est works on<br>
> > > > >> the<br>
> > > > >>>>>>>>> Haswell partition and other downloads seem to work on the KNL<br>
> > > > >>>>>> partition.<br>
> > > > >>>>>>>>> Any ideas?<br>
> > > > >>>>>>>>><br>
> > > > >>>>>>>><br>
> > > > >>>>>>><br>
> > > > >>>>>>><br>
> > > > >>>>>><br>
> > > > >>>>>><br>
> > > > >>>>><br>
> > > > >>>><br>
> > > > >>><br>
> > > ><br>
> > ><br>
><br>
><br>
><br>
<br>
</div></div></blockquote></div><br></div>