[petsc-dev] download problem p4est on Cori at NERSC
Mark Adams
mfadams at lbl.gov
Fri Feb 17 16:45:06 CST 2017
That works,
Thanks,
On Fri, Feb 17, 2017 at 1:40 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> Sorry - forgot the attachment..
>
> On Fri, 17 Feb 2017, Satish Balay wrote:
>
> > Can you try the attached patch? If it works - I'll push it to master.
> >
> > BTW: why use --download-fblaslapack=1 on cray? Shouldn't you be using
> > one of the blas impls provied by cray? [libsci?]
> >
> > Satish
> >
> > On Fri, 17 Feb 2017, Mark Adams wrote:
> >
> > > p4est seems to work now, but I am getting a BLAS failure. But I
> download
> > > blas....
> > >
> > > On Fri, Feb 17, 2017 at 12:48 PM, Satish Balay <balay at mcs.anl.gov>
> wrote:
> > >
> > > > >>>
> > > > File "/global/u2/m/madams/petsc/config/BuildSystem/config/
> packages/p4est.py",
> > > > line 51, in updateGitDir
> > > > raise RuntimeError('Could not initialize sc submodule needed by
> p4est')
> > > > <<<
> > > >
> > > > So 'git submoudle' stuff failed. Presumably this install of git
> doesn't
> > > > support submodule?
> > > >
> > > > >>>>>>
> > > > Checking for program /usr/common/software/git/2.9.1/bin/git...found
> > > > Defined make macro "GIT" to "git"
> > > > Executing: git --version
> > > > stdout: git version 2.9.1
> > > > <<<<<<<
> > > >
> > > > You should be able to use the taball - if you use the patch I
> mentioned
> > > > eariler [which is already in master]
> > > >
> > > > If you want everything else to be from git - and use tarball with
> only
> > > > p4est - then do:
> > > >
> > > > --download-p4est=https://github.com/p4est/p4est.github.
> > > > io/raw/master/release/p4est-2.0.tar.gz
> > > >
> > > > Satish
> > > >
> > > > On Fri, 17 Feb 2017, Tobin Isaac wrote:
> > > >
> > > > > The configure.log doesn't really tell me why it is failing. Did
> you
> > > > > start with a clean git.p4est after trying to use the tarball?
> > > > >
> > > > > On Fri, Feb 17, 2017 at 12:21:50PM -0500, Mark Adams wrote:
> > > > > > It turns out that Cori-KNL does have git, it is just not loaded
> by
> > > > default.
> > > > > >
> > > > > > It still does not work, but the error looks different.
> > > > > >
> > > > > > ************************************************************
> > > > *******************
> > > > > > UNABLE to CONFIGURE with GIVEN OPTIONS (see
> configure.log
> > > > for
> > > > > > details):
> > > > > > ------------------------------------------------------------
> > > > -------------------
> > > > > > Could not initialize sc submodule needed by p4est
> > > > > > ************************************************************
> > > > *******************
> > > > > >
> > > > > >
> > > > > > On Thu, Feb 16, 2017 at 10:20 PM, Tobin Isaac <
> tisaac at uchicago.edu>
> > > > wrote:
> > > > > >
> > > > > > >
> > > > > > > On Thu, Feb 16, 2017 at 05:48:57PM -0600, Barry Smith wrote:
> > > > > > > >
> > > > > > > > > On Feb 16, 2017, at 5:01 PM, Tobin Isaac <
> tisaac at uchicago.edu>
> > > > wrote:
> > > > > > > > >
> > > > > > > > > The bootstrap script predates/supercedes autoreconf to
> get the
> > > > > > > necessary m4 scripts and write configure. The tarballs have
> the m4
> > > > scripts
> > > > > > > and configure, so they should be treated as standard gnu
> configure
> > > > && make
> > > > > > > && make install scripts. I think that's what I accomplished in
> > > > p4est.py.
> > > > > > > I'm on my phone, when I'm at a computer I'll look at this
> thread's
> > > > history
> > > > > > > to see if I can figure out what's going on.
> > > > > > > >
> > > > > > > > You are confusing two errors. One is the issue you mention
> > > > above, we
> > > > > > > don't care about that. The only error we care about is that
> p4est
> > > > > > > ./configure needs to run a compiled program to gather some
> > > > information
> > > > > > > about the machine. On systems with cross-compiling this
> doesn't work
> > > > since
> > > > > > > after ./configure compiles the program it cannot run it
> because it
> > > > is not
> > > > > > > compatible with the hardware. So the question is: is there an
> easy
> > > > way to
> > > > > > > hack the p4est configure so that we can provide the needed
> > > > information
> > > > > > > directly and not have ./configure try to run an executable?
> > > > > > >
> > > > > > > Okay, I get it now. There should be `config.log` in
> > > > > > > externalpackags/git.p4est that would let me know what
> particular
> > > > check
> > > > > > > it was working on when cross-compilation errors cropped up,
> and I
> > > > > > > could try to help come up with a solution.
> > > > > > >
> > > > > > > >
> > > > > > > > Barry
> > > > > > > >
> > > > > > > > Note that this problem is common for many autoconf based
> build
> > > > systems,
> > > > > > > its solution depends on the details of how the particular
> system is
> > > > using
> > > > > > > using executables to gather information.
> > > > > > > >
> > > > > > > > >
> > > > > > > > > On February 16, 2017 4:34:35 PM CST, Barry Smith <
> > > > bsmith at mcs.anl.gov>
> > > > > > > wrote:
> > > > > > > > >>
> > > > > > > > >> The best long term fix is to find out what things p4est
> needs to
> > > > > > > > >> determine by a running a program and providing them some
> other
> > > > way.
> > > > > > > > >>
> > > > > > > > >> Toby
> > > > > > > > >>
> > > > > > > > >> So what things is p4est trying to determine by running a
> > > > program?
> > > > > > > > >>
> > > > > > > > >> Barry
> > > > > > > > >>
> > > > > > > > >>
> > > > > > > > >>
> > > > > > > > >>> On Feb 16, 2017, at 3:25 PM, Satish Balay <
> balay at mcs.anl.gov>
> > > > wrote:
> > > > > > > > >>>
> > > > > > > > >>> I don't understand autoconf well enough for cross
> compiling.
> > > > Some
> > > > > > > > >>> packages appear to require this - but others don't.
> > > > > > > > >>>
> > > > > > > > >>>
> > > > > > > > >> https://www.gnu.org/software/
> autoconf/manual/autoconf-2.69/
> > > > > > > html_node/Hosts-and-Cross_002dCompilation.html
> > > > > > > > >>>
> > > > > > > > >>> So one would run 'config.guess' script on the compute
> node -
> > > > and use
> > > > > > > > >> this value on the compile node with configure?
> > > > > > > > >>>
> > > > > > > > >>> I don't know how we could automate that..
> > > > > > > > >>>
> > > > > > > > >>> Satish
> > > > > > > > >>>
> > > > > > > > >>> On Wed, 15 Feb 2017, Mark Adams wrote:
> > > > > > > > >>>
> > > > > > > > >>>> OK, that did not work. It says something about --host
> now.
> > > > > > > > >>>>
> > > > > > > > >>>> On Wed, Feb 15, 2017 at 5:06 PM, Mark Adams <
> mfadams at lbl.gov>
> > > > > > > wrote:
> > > > > > > > >>>>
> > > > > > > > >>>>> I think this will work because I have git when I
> configure
> > > > on a
> > > > > > > > >> login node
> > > > > > > > >>>>> (Haswell). I build KNL by submitting a batch script (it
> > > > takes to
> > > > > > > > >> long to
> > > > > > > > >>>>> fit in 30 minutes of an interactive session). That
> fails
> > > > because
> > > > > > > > >> git is not
> > > > > > > > >>>>> available (can I just load the module ...) on a KNL
> compute
> > > > node.
> > > > > > > > >> It is
> > > > > > > > >>>>> reconfiguring now, I'll let you know if it fails.
> > > > > > > > >>>>> Thanks,
> > > > > > > > >>>>>
> > > > > > > > >>>>> On Wed, Feb 15, 2017 at 4:59 PM, Satish Balay <
> > > > balay at mcs.anl.gov>
> > > > > > > > >> wrote:
> > > > > > > > >>>>>
> > > > > > > > >>>>>> Sorry - this won't work - as p4est appears to require
> git
> > > > > > > > >> [submodules?]..
> > > > > > > > >>>>>>
> > > > > > > > >>>>>>>>>>>>>>>>>> p4est.py <<<<<<<<<<<<<
> > > > > > > > >>>>>> def updateGitDir(self):
> > > > > > > > >>>>>> config.package.GNUPackage.updateGitDir(self)
> > > > > > > > >>>>>> Dir = self.getDir()
> > > > > > > > >>>>>> try:
> > > > > > > > >>>>>> libsc = self.libsc
> > > > > > > > >>>>>> except AttributeError:
> > > > > > > > >>>>>> try:
> > > > > > > > >>>>>> self.executeShellCommand([
> self.sourceControl.git,
> > > > > > > > >> 'submodule',
> > > > > > > > >>>>>> 'update', '--init'], cwd=Dir, log=self.log)
> > > > > > > > >>>>>> import os
> > > > > > > > >>>>>> if os.path.isfile(os.path.join(
> Dir,'sc','README')):
> > > > > > > > >>>>>> self.libsc = os.path.join(Dir,'sc')
> > > > > > > > >>>>>> else:
> > > > > > > > >>>>>> raise RuntimeError
> > > > > > > > >>>>>> except RuntimeError:
> > > > > > > > >>>>>> raise RuntimeError('Could not initialize sc
> submodule
> > > > > > > > >> needed by
> > > > > > > > >>>>>> p4est')
> > > > > > > > >>>>>> return
> > > > > > > > >>>>>> <<<<<<
> > > > > > > > >>>>>>
> > > > > > > > >>>>>> Satish
> > > > > > > > >>>>>>
> > > > > > > > >>>>>> On Wed, 15 Feb 2017, Satish Balay wrote:
> > > > > > > > >>>>>>
> > > > > > > > >>>>>>> batch won't help here. its git vs tarball - and p4est
> > > > curently
> > > > > > > > >> doesn't
> > > > > > > > >>>>>> have a taball.
> > > > > > > > >>>>>>>
> > > > > > > > >>>>>>> The following should give you a tarball - if you
> don't
> > > > have git.
> > > > > > > > >>>>>>>
> > > > > > > > >>>>>>> diff --git a/config/BuildSystem/config/
> packages/p4est.py
> > > > > > > > >>>>>> b/config/BuildSystem/config/packages/p4est.py
> > > > > > > > >>>>>>> index 4735ff4..1f9507c 100644
> > > > > > > > >>>>>>> --- a/config/BuildSystem/config/packages/p4est.py
> > > > > > > > >>>>>>> +++ b/config/BuildSystem/config/packages/p4est.py
> > > > > > > > >>>>>>> @@ -4,7 +4,7 @@ class Configure(config.package.
> > > > GNUPackage):
> > > > > > > > >>>>>>> def __init__(self, framework):
> > > > > > > > >>>>>>> config.package.GNUPackage.__init__(self,
> framework)
> > > > > > > > >>>>>>> self.gitcommit = 'v2.0'
> > > > > > > > >>>>>>> - self.download = ['git://
> > > > https://github.com/cbu
> > > > > > > > >>>>>> rstedde/p4est']
> > > > > > > > >>>>>>> + self.download = ['git://
> > > > https://github.com/cbu
> > > > > > > > >>>>>> rstedde/p4est','https://github.com/cburstedde/p4est/
> > > > archive/
> > > > > > > > >>>>>> '+self.gitcommit+'.tar.gz']
> > > > > > > > >>>>>>> self.functions = ['p4est_init']
> > > > > > > > >>>>>>> self.includes = ['p4est_bits.h']
> > > > > > > > >>>>>>> self.liblist = [['libp4est.a',
> 'libsc.a']]
> > > > > > > > >>>>>>>
> > > > > > > > >>>>>>> I can push this to master.
> > > > > > > > >>>>>>>
> > > > > > > > >>>>>>> Satish
> > > > > > > > >>>>>>>
> > > > > > > > >>>>>>> On Wed, 15 Feb 2017, Mark Adams wrote:
> > > > > > > > >>>>>>>
> > > > > > > > >>>>>>>> Oh, this is because git does not work on KNL. Maybe
> I
> > > > should do
> > > > > > > > >>>>>>>> with-batch=1,
> > > > > > > > >>>>>>>>
> > > > > > > > >>>>>>>>
> > > > > > > > >>>>>>>> On Wed, Feb 15, 2017 at 4:36 PM, Mark Adams <
> > > > mfadams at lbl.gov>
> > > > > > > > >> wrote:
> > > > > > > > >>>>>>>>
> > > > > > > > >>>>>>>>> I get this error on the KNL partition at NERSC.
> P4est
> > > > works on
> > > > > > > > >> the
> > > > > > > > >>>>>>>>> Haswell partition and other downloads seem to work
> on
> > > > the KNL
> > > > > > > > >>>>>> partition.
> > > > > > > > >>>>>>>>> Any ideas?
> > > > > > > > >>>>>>>>>
> > > > > > > > >>>>>>>>
> > > > > > > > >>>>>>>
> > > > > > > > >>>>>>>
> > > > > > > > >>>>>>
> > > > > > > > >>>>>>
> > > > > > > > >>>>>
> > > > > > > > >>>>
> > > > > > > > >>>
> > > > > > > >
> > > > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > > >
> > >
> >
> >
>
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