[petsc-users] Running moose/scripts/update_and_rebuild_petsc.sh on HPC

[Tomas Mondragon]

Thanks, that does sound useful!

On Fri, Jan 31, 2020, 6:23 PM Smith, Barry F. <bsmith at mcs.anl.gov> wrote:

>
>    You might find this option useful.
>
>    --with-packages-download-dir=<dir>
>        Skip network download of package tarballs and locate them in
> specified dir. If not found in dir, print package URL - so it can be
> obtained manually.
>
>
>    This generates a list of URLs to download so you don't need to look
> through the xxx.py files for that information. Conceivably a script could
> gather this information from the run of configure and get the tarballs for
> you.
>
>     Barry
>
>
>
> > On Jan 31, 2020, at 11:58 AM, Tomas Mondragon <
> tom.alex.mondragon at gmail.com> wrote:
> >
> > Hypre problem resolved. PETSc commit 05f86fb made in August 05, 2019
> added the line 'self.installwithbatch  = 0' to the __init__ method of the
> Configure class in the file
> petsc/config/BuildSystem/config/packages/hypre.py to fix a bug with hypre
> installation on Cray KNL systems. Since the machine I was installing os was
> an SGI system, I decided to try switching to 'self.installwithbatch = 1'
> and it worked! The configure script was finally able to run to completion.
> >
> > Perhaps there can be a Cray flag for configure that can control this,
> since it is only Cray's that have this problem with Hypre?
> >
> > For my benefit when I have to do this again -
> > To get moose/petsc/scripts/update_and_rebuild_petsc.sh to run on an SGI
> system as a batch job, I had to:
> >
> > Make sure the git (gnu version) module was loaded
> > git clone moose
> > cd to the petsc directory and git clone the petsc submodule, but make
> sure to pull the latest commit. The commit that the moose repo refers to is
> outdated.
> > cd back to the moose directory, git add petsc and git commit so that the
> newest petsc commit gets used by the update script. otherwise the old
> commit will be used.
> > download the tarballs for fblaspack, hypre, metis, mumps, parmetis,
> scalapack, (PT)scotch, slepc, and superLU_dist. The URLS are in the
> __init__ methods of the relevant files
> inmost/petsc/config/BuildSystem/config/packages/
> > alter moose/scripts/update_and_rebuild_petsc.sh script so that it is a
> working PBS batch job. Be sure to module swap to the gcc compiler and
> module load git (gnu version) and alter the ./configure command arguments
> >      adding
> >              --with-cudac=0
> >              --with-batch=1
> >     changing
> >              --download-<package>=/path/to/thirdparty/package/tarball
> > If the supercomputer is not a Cray KNL system, change line 26 of
> moose/petsc/config/BuildSystem/config/packages/hypre.py from
> 'self.installwithbath = 0' to 'self.installwithbatch = 1', otherwise,
> install hypre on its own and use --with-hypre-dir=/path/to/hypre in the
> ./configure command
> >
> > On Fri, Jan 31, 2020 at 10:06 AM Tomas Mondragon <
> tom.alex.mondragon at gmail.com> wrote:
> > Thanks for the change to base.py. Pulling the commit, confirm was able
> to skip over lgrind and c2html. I did have a problem with Parmetis, but
> that was because I was using an old ParMetis commit accidentally. Fixed by
> downloading the right commit of ParMetis.
> >
> > My current problem is with Hypre. Apparently --download-hypre cannot be
> used with --with-batch=1 even if the download URL is on the local machine.
> The configuration.log that resulted is attached for anyone who may be
> interested.
> >
> > --
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> .
>
>
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