Re: [petsc-dev] download problem p4est on Cori at NERSC
Great! pushed to master. Satish On Fri, 17 Feb 2017, Mark Adams wrote:
That works, Thanks,
On Fri, Feb 17, 2017 at 1:40 PM, Satish Balay <[email protected]> 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 <[email protected]> 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 <
[email protected]> wrote:
On Thu, Feb 16, 2017 at 05:48:57PM -0600, Barry Smith wrote:
On Feb 16, 2017, at 5:01 PM, Tobin Isaac <
[email protected]> 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 <
[email protected]> 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 < [email protected]> 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 <
[email protected]> 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 < [email protected]> 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 < [email protected]> 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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Satish Balay