February 2017 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] download problem p4est on Cori at NERSC
by Mark Adams 19 Feb '17

19 Feb '17

On Sat, Feb 18, 2017 at 10:29 PM, Jeff Hammond <jeff.science(a)gmail.com> wrote: > Please be more precise with your comments. Git works just fine on KNL and > I have hundreds of data to confirm this. > As I said, git is not loaded by default on the KNL nodes at NERSC. loading the git module solved that problem. > Any issues you have with Git on a KNL-based platform are the result of the > software configuration. Furthermore, every Haswell Xeon binary runs on > KNL* so there is no hardware-related reason why login-node packages won't > work on the KNL nodes. > > * KNL doesn't support TSX but the programming guide states that TSX users > must query cpuid to confirm support. > > Jeff > > On Wed, Feb 15, 2017 at 1:38 PM, Mark Adams <mfadams(a)lbl.gov> 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(a)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? >>> >> >> > > > -- > Jeff Hammond > jeff.science(a)gmail.com > http://jeffhammond.github.io/ >

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Re: [petsc-dev] download problem p4est on Cori at NERSC
by Jeff Hammond 18 Feb '17

18 Feb '17

Please be more precise with your comments. Git works just fine on KNL and I have hundreds of data to confirm this. Any issues you have with Git on a KNL-based platform are the result of the software configuration. Furthermore, every Haswell Xeon binary runs on KNL* so there is no hardware-related reason why login-node packages won't work on the KNL nodes. * KNL doesn't support TSX but the programming guide states that TSX users must query cpuid to confirm support. Jeff On Wed, Feb 15, 2017 at 1:38 PM, Mark Adams <mfadams(a)lbl.gov> 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(a)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? >> > > -- Jeff Hammond jeff.science(a)gmail.com http://jeffhammond.github.io/

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Re: [petsc-dev] SpMM question
by Jed Brown 18 Feb '17

18 Feb '17

Matthew Knepley <knepley(a)gmail.com> writes: > I took a look at the code. It is the worst kind of C-in-C++, It would > probably take 1 day to make a pure C version :) > The claim from Edgar is that it is intended to be used for this purpose > (have you read the arXiv thing with Torsten > about sparse tensor computing?). I haven't read it.

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Re: [petsc-dev] SpMM question
by Matthew Knepley 18 Feb '17

18 Feb '17

On Sat, Feb 18, 2017 at 3:38 PM, Jed Brown <jed(a)jedbrown.org> wrote: > Matthew Knepley <knepley(a)gmail.com> writes: > > > Have we considered using this > > > > https://github.com/solomonik/ctf > > > > as an alternative sparse matrix-matrix code for GAMG? Or was it > unsuitable > > for some reason. > > I don't think we considered it for that purpose. I'm not sure if its > dynamicism would work against us here. > I took a look at the code. It is the worst kind of C-in-C++, It would probably take 1 day to make a pure C version :) The claim from Edgar is that it is intended to be used for this purpose (have you read the arXiv thing with Torsten about sparse tensor computing?). Matt -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener

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Re: [petsc-dev] SpMM question
by Jed Brown 18 Feb '17

18 Feb '17

Matthew Knepley <knepley(a)gmail.com> writes: > Have we considered using this > > https://github.com/solomonik/ctf > > as an alternative sparse matrix-matrix code for GAMG? Or was it unsuitable > for some reason. I don't think we considered it for that purpose. I'm not sure if its dynamicism would work against us here.

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SpMM question
by Matthew Knepley 18 Feb '17

18 Feb '17

Have we considered using this https://github.com/solomonik/ctf as an alternative sparse matrix-matrix code for GAMG? Or was it unsuitable for some reason. Thanks, Matt -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener

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Re: [petsc-dev] download problem p4est on Cori at NERSC
by Satish Balay 17 Feb '17

17 Feb '17

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 <balay(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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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Re: [petsc-dev] download problem p4est on Cori at NERSC
by Mark Adams 17 Feb '17

17 Feb '17

That works, Thanks, On Fri, Feb 17, 2017 at 1:40 PM, Satish Balay <balay(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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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PETSc user
by Mahmud Hasan 17 Feb '17

17 Feb '17

Dear Sir/Madam, Good afternoon. I am trying to learn PETSc. Please add me to email list for future information about PETSc. Thank you. Have a nice day. Regards-- Mahmud Hasan, PhD, PE (Texas and Louisiana) Email: ahasan94(a)gmail.com Cell: 832-248-3770

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Re: [petsc-dev] download problem p4est on Cori at NERSC
by Tobin Isaac 17 Feb '17

17 Feb '17

On Fri, Feb 17, 2017 at 01:02:53PM -0600, Barry Smith wrote: > > > On Feb 17, 2017, at 12:58 PM, Tobin Isaac <tisaac(a)uchicago.edu> wrote: > > > > On Fri, Feb 17, 2017 at 01:28:25PM -0500, Mark Adams wrote: > >> p4est seems to work now, but I am getting a BLAS failure. But I download > >> blas.... > > > > I'm investigating how to pass the petsc discovered blas to p4est > > automatically. Until then, I think the configure logic says that if > > BLAS_LIBS is defined in the environment it will be be checked, so you > > could set that to whatever your know the blas libraries to be. > > Satish already fixed this :-) > *checks watch* yep, it's a day ending in 'y'.

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