[petsc-dev] failed rebase
Satish Balay
balay at mcs.anl.gov
Fri Apr 3 09:27:05 CDT 2020
I attempted a rebase - and I get the following diff from yours. You might want to verify.
>>>>>>>>>>>
$ git diff origin/mark/feature-xgc-interface-rebase..mark/feature-xgc-interface-rebase-local
diff --git a/include/petscdmplex.h b/include/petscdmplex.h
index cb464bbe77..ed99700499 100644
--- a/include/petscdmplex.h
+++ b/include/petscdmplex.h
@@ -474,7 +474,6 @@ PETSC_EXTERN PetscErrorCode DMPlexCellRefinerRefine(DMPlexCellRefiner, DMPolytop
PETSC_EXTERN PetscErrorCode DMPlexCellRefinerGetAffineTransforms(DMPlexCellRefiner, DMPolytopeType, PetscInt *, PetscReal *[], PetscReal *[], PetscReal *[]);
PETSC_EXTERN PetscErrorCode DMPlexCellRefinerGetAffineFaceTransforms(DMPlexCellRefiner, DMPolytopeType, PetscInt *, PetscReal *[], PetscReal *[], PetscReal *[], PetscReal *[]);
PETSC_EXTERN PetscErrorCode DMPlexRefineUniform(DM, DMPlexCellRefiner, DM *);
-
PETSC_EXTERN PetscErrorCode DMPlexFPPrintNorms(Vec, PetscInt);
PETSC_EXTERN PetscErrorCode DMPlexFPCreate2D(MPI_Comm, const PetscInt, const PetscInt, const PetscInt[], const double[], const double[], const PetscInt, const PetscInt[], const PetscScalar[/* ? */], DM *dm);
PETSC_EXTERN PetscErrorCode DMPlexFPCreateVelocitySpace(MPI_Comm,PetscInt,const char[],Vec*,DM*);
diff --git a/src/dm/impls/plex/tutorials/ex11.c b/src/dm/impls/plex/tutorials/ex11.c
index b28864ac89..29ca44f422 100644
--- a/src/dm/impls/plex/tutorials/ex11.c
+++ b/src/dm/impls/plex/tutorials/ex11.c
@@ -648,7 +648,6 @@ PetscPrintf(PETSC_COMM_SELF, "\t\t***** FormRHSSource: have new_imp_rate= %10.3e
ierr = PetscObjectSetName((PetscObject)S, "src");CHKERRQ(ierr);
ierr = VecViewFromOptions(S,NULL,"-vec_view_diagnostics");CHKERRQ(ierr);
ierr = MatMult(ctx->M,S,rectx->imp_src);CHKERRQ(ierr);
- ierr = VecCopy(S,rectx->imp_src);CHKERRQ(ierr);
ierr = VecDestroy(&S);CHKERRQ(ierr);
}
ierr = VecCopy(rectx->imp_src,F);CHKERRQ(ierr);
@@ -711,7 +710,7 @@ static PetscErrorCode stepSrc(PetscReal time, PetscInt step, PetscReal dt, Petsc
REctx *rectx;
PetscFunctionBegin;
rectx = (REctx*)ctx->data;
- if (time >= rectx->pulse_start) *rho = rectx->pulse_rate;
+ if (time > 1.e+5) *rho = rectx->pulse_rate; /* turned off */
else *rho = 0.;
PetscFunctionReturn(0);
}
<<<<<<<
$ ls src/dm/impls/plex/examples/tutorials/
doc/ ex10.c ex10f90.F90 ex11.c output/
This should now be in src/dm/impls/plex/tutorials/
Regarding the primary issue: configure, the primary error is not logged in configure.log. Running manually - I get:
bfort terminating at 664: Exceeded output count limit!
$ grep '/*@' *.c |wc -l
600
This single dir creates 600 man pages? Perhaps its time to reorganize plex into multiple dirs?
Satish
On Fri, 3 Apr 2020, Mark Adams wrote:
> Satish, I tried again from scratch see the same thing.
> I pushed this.
> Thanks
>
> 09:35 mark/feature-xgc-interface-rebase= ~/Codes/petsc$ git rebase
> origin/master
> First, rewinding head to replay your work on top of it...
> Applying: starting rebase branch
> Using index info to reconstruct a base tree...
> M include/petsc/private/dmpleximpl.h
> M include/petscdmplex.h
> M src/dm/impls/plex/makefile
> .git/rebase-apply/patch:2620: trailing whitespace.
> for (d=0;d<src->dim;d++) *pp++ = src->df[d][s][idx];
> warning: 1 line adds whitespace errors.
> Falling back to patching base and 3-way merge...
> Auto-merging src/dm/impls/plex/makefile
> Auto-merging include/petscdmplex.h
> CONFLICT (content): Merge conflict in include/petscdmplex.h
> Auto-merging include/petsc/private/dmpleximpl.h
> error: Failed to merge in the changes.
> Patch failed at 0001 starting rebase branch
> hint: Use 'git am --show-current-patch' to see the failed patch
> Resolve all conflicts manually, mark them as resolved with
> "git add/rm <conflicted_files>", then run "git rebase --continue".
> You can instead skip this commit: run "git rebase --skip".
> To abort and get back to the state before "git rebase", run "git rebase
> --abort".
> 09:36 1 mark/feature-xgc-interface-rebase *+|REBASE 1/19 ~/Codes/petsc$ vi
> include/petscdmplex.h
> 09:37 mark/feature-xgc-interface-rebase *+|REBASE 1/19 ~/Codes/petsc$ git
> add include/petscdmplex.h
> 09:37 mark/feature-xgc-interface-rebase +|REBASE 1/19 ~/Codes/petsc$ git
> rebase --continue
> Applying: starting rebase branch
> Applying: manual merge
> Applying: RE test
> Applying: remove Ehat
> Applying: clean up interface, redo regression tests, found false negatives
> Applying: change Ec
> Applying: tweek griding
> Applying: clean up, working on impurity injection
> Applying: fixed quench and pulse test
> Applying: hardwired CUDA kernel for DIM, added presolve in ex11
> Applying: added guard
> Applying: starting to get E field added
> Applying: doc
> Applying: fix test params
> Applying: remove comment
> Applying: updated test syntax
> Applying: cleaned up flags
> Applying: cleaned up flags
> Applying: fixed soruce bug
>
>
> 09:37 mark/feature-xgc-interface-rebase<> ~/Codes/petsc$ rm -fr
> arch-macosx-gnu-g/
> 09:38 mark/feature-xgc-interface-rebase<> ~/Codes/petsc$
> ../arch-macosx-gnu-g.py
> ===============================================================================
> Configuring PETSc to compile on your system
>
> ===============================================================================
> ===============================================================================
>
>
>
>
>
> ***** WARNING: You have
> an older version of Gnu make, it will work,
>
>
>
>
>
> but may not support all the parallel testing
> options. You can install the
>
>
>
>
>
> latest Gnu make with your package manager, such as brew or macports,
> or use
>
>
>
>
> the
> --download-make option to get the latest Gnu make *****
>
>
>
>
>
>
> ===============================================================================
>
>
>
>
>
>
> ===============================================================================
>
>
>
>
>
> Trying to download git://
> https://bitbucket.org/petsc/pkg-sowing.git for SOWING
>
>
>
>
>
>
> ===============================================================================
>
>
>
>
>
>
> ===============================================================================
>
>
>
>
>
> Running configure on
> SOWING; this may take several minutes
>
>
>
>
>
>
> ===============================================================================
>
>
>
>
>
>
> ===============================================================================
>
>
>
>
>
> Running make on SOWING;
> this may take several minutes
>
>
>
>
>
>
> ===============================================================================
>
>
>
>
>
>
> ===============================================================================
>
>
>
>
>
> Running make install on
> SOWING; this may take several minutes
>
>
>
>
>
>
> ===============================================================================
>
>
>
>
>
> TESTING: checkSharedLibrary
> from config.packages.sowing(config/BuildSystem/config/package.py:926)
>
>
>
>
>
>
> *******************************************************************************
> CONFIGURATION CRASH (Please send configure.log to
> petsc-maint at mcs.anl.gov)
> *******************************************************************************
>
> 09:40 1 mark/feature-xgc-interface-rebase<> ~/Codes/petsc$
>
>
> On Fri, Apr 3, 2020 at 8:17 AM Mark Adams <mfadams at lbl.gov> wrote:
>
> >
> >
> > On Thu, Apr 2, 2020 at 11:05 PM Satish Balay <balay at mcs.anl.gov> wrote:
> >
> >> My OS build also went through. Looks like you haven't pushed [force
> >> update] this branch - so I'm testing with something totally different.
> >>
> >>
> > Yes, I have a <> after a rebase. Do you want me to push it? Or should I
> > just start over? I thought I started with a clean version of my code from
> > the repo.
> > Thanks,
> >
> >
> >> So likely something in your rebased sources is causing bfort to fail..
> >>
> >> Satish
> >>
> >> On Thu, 2 Apr 2020, Mark Adams wrote:
> >>
> >> > I see:
> >> > 22:46 128 mark/feature-xgc-interface-rebase<> ~/Codes/petsc$ git status
> >> > On branch mark/feature-xgc-interface-rebase
> >> > Your branch and 'origin/mark/feature-xgc-interface-rebase' have
> >> diverged,
> >> > and have 130 and 18 different commits each, respectively.
> >> > (use "git pull" to merge the remote branch into yours)
> >> >
> >> > Untracked files:
> >> > (use "git add <file>..." to include in what will be committed)
> >> > out2.txt
> >> > src/dm/impls/plex/examples/tutorials/Landau/
> >> >
> >> >
> >> > On Thu, Apr 2, 2020 at 10:45 PM Mark Adams <mfadams at lbl.gov> wrote:
> >> >
> >> > >
> >> > >
> >> > > On Thu, Apr 2, 2020 at 10:33 PM Satish Balay <balay at mcs.anl.gov>
> >> wrote:
> >> > >
> >> > >> Is this branch mark/feature-xgc-interface-rebase pushed?
> >> > >
> >> > >
> >> > > yes.
> >> > >
> >> > >
> >> > >> I had done a build with the current state of it - and the build went
> >> > >> through fine. This was on linux.
> >> > >>
> >> > >> Will try OSX now.
> >> > >>
> >> > >> Satish
> >> > >>
> >> > >> On Thu, 2 Apr 2020, Mark Adams wrote:
> >> > >>
> >> > >> > Note, when I rebased I got one conflict, in a header where I added
> >> > >> stuff at
> >> > >> > the end and master did also so I just kept them both and continued.
> >> > >> > Other than that it was a clean rebase.
> >> > >> >
> >> > >> > On Thu, Apr 2, 2020 at 10:15 PM Mark Adams <mfadams at lbl.gov>
> >> wrote:
> >> > >> >
> >> > >> > >
> >> > >> > >
> >> > >> > > On Thu, Apr 2, 2020 at 9:32 PM Satish Balay <balay at mcs.anl.gov>
> >> > >> wrote:
> >> > >> > >
> >> > >> > >> can you try this in a local clone [same branch] and see if that
> >> > >> works?
> >> > >> > >>
> >> > >> > >> cd /Users/markadams/Codes
> >> > >> > >> git clone petsc petsc-test
> >> > >> > >> cd petsc-test
> >> > >> > >> ./configure ...
> >> > >> > >>
> >> > >> > >> Satish
> >> > >> > >>
> >> > >> > >>
> >> > >> > >> On Thu, 2 Apr 2020, Mark Adams wrote:
> >> > >> > >>
> >> > >> > >> > I tried to rebase mark/feature-xgc-interface-rebase with
> >> master
> >> > >> and I
> >> > >> > >> get
> >> > >> > >> > this.
> >> > >> > >> > I of course deleted the arch directory.
> >> > >> > >> > Thanks,
> >> > >> > >> > Mark
> >> > >> > >> >
> >> > >> > >>
> >> > >> > >>
> >> > >> >
> >> > >>
> >> > >>
> >> >
> >>
> >>
>
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