[petsc-dev] download problem p4est on Cori at NERSC

Mark Adams mfadams at lbl.gov
Fri Feb 17 11:21:50 CST 2017 

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?
> > >>>>>>>>>
> > >>>>>>>>
> > >>>>>>>
> > >>>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>
> > >>>>
> > >>>
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20170217/a18bbd70/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: configure.log
Type: application/octet-stream
Size: 3609071 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20170217/a18bbd70/attachment.obj>

More information about the petsc-dev mailing list