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

[Barry Smith]

> 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?

   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?
>>>>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>>