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

Satish Balay balay at mcs.anl.gov
Fri Feb 17 12:46:21 CST 2017 

Added the blas change now. There is also the following which petsc
configure should probably control.. [and specify to p4est configure..]

Satish

o---------------------------------------
| Checking libraries
o---------------------------------------
checking for library containing fabs... none required
checking for library containing adler32_combine... -lz
checking for library containing lua_createtable... no
configure: Checking BLAS
checking for dgemm_... yes
checking for BLAS by linking a C program without FLIBS... successful
configure: Checking LAPACK
checking for dgecon_... yes
checking for LAPACK by linking w/ BLAS_FLIBS but w/o FLIBS... successful
checking for getopt... successful
checking for obstack... successful
checking for library containing pthread_create... -lpthread
checking for POSIX threads... not used
checking for library containing omp_get_thread_num... -lgomp
checking for OpenMP... not used
checking size of void *... 8
checking for aligned_alloc... yes
checking for posix_memalign... yes
checking for memory alignment option... P4EST_SIZEOF_VOID_P
checking for metis... not used
checking for petscarch... no
checking for PETSc... not used
o---------------------------------------

On Fri, 17 Feb 2017, Barry Smith wrote:

> 
>    Satish,
> 
>     Whoever wrote p4est.py messed up. p4est has a dependency on blas that is missing in p4est.py so p4est is off hunting for its own blas. Can you please add the blas dependency to p4est.py?
> 
>    Barry
> 
> > On Feb 17, 2017, at 12:28 PM, Mark Adams <mfadams at lbl.gov> 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?
> > > > > > >>>>>>>>>
> > > > > > >>>>>>>>
> > > > > > >>>>>>>
> > > > > > >>>>>>>
> > > > > > >>>>>>
> > > > > > >>>>>>
> > > > > > >>>>>
> > > > > > >>>>
> > > > > > >>>
> > > > > >
> > > > >
> > >
> > >
> > >
> > 
> > 
> > <configure.log>
> 
>

More information about the petsc-dev mailing list