<div dir="ltr"><div dir="ltr"><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Apr 3, 2020 at 10:27 AM Satish Balay <<a href="mailto:balay@mcs.anl.gov">balay@mcs.anl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I attempted a rebase - and I get the following diff from yours. You might want to verify.<br>
<br></blockquote><div><br></div><div>These are small fixes that I did this morning. </div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
>>>>>>>>>>><br>
$ git diff origin/mark/feature-xgc-interface-rebase..mark/feature-xgc-interface-rebase-local<br>
diff --git a/include/petscdmplex.h b/include/petscdmplex.h<br>
index cb464bbe77..ed99700499 100644<br>
--- a/include/petscdmplex.h<br>
+++ b/include/petscdmplex.h<br>
@@ -474,7 +474,6 @@ PETSC_EXTERN PetscErrorCode DMPlexCellRefinerRefine(DMPlexCellRefiner, DMPolytop<br>
PETSC_EXTERN PetscErrorCode DMPlexCellRefinerGetAffineTransforms(DMPlexCellRefiner, DMPolytopeType, PetscInt *, PetscReal *[], PetscReal *[], PetscReal *[]);<br>
PETSC_EXTERN PetscErrorCode DMPlexCellRefinerGetAffineFaceTransforms(DMPlexCellRefiner, DMPolytopeType, PetscInt *, PetscReal *[], PetscReal *[], PetscReal *[], PetscReal *[]);<br>
PETSC_EXTERN PetscErrorCode DMPlexRefineUniform(DM, DMPlexCellRefiner, DM *);<br>
-<br>
PETSC_EXTERN PetscErrorCode DMPlexFPPrintNorms(Vec, PetscInt);<br>
PETSC_EXTERN PetscErrorCode DMPlexFPCreate2D(MPI_Comm, const PetscInt, const PetscInt, const PetscInt[], const double[], const double[], const PetscInt, const PetscInt[], const PetscScalar[/* ? */], DM *dm);<br>
PETSC_EXTERN PetscErrorCode DMPlexFPCreateVelocitySpace(MPI_Comm,PetscInt,const char[],Vec*,DM*);<br>
diff --git a/src/dm/impls/plex/tutorials/ex11.c b/src/dm/impls/plex/tutorials/ex11.c<br>
index b28864ac89..29ca44f422 100644<br>
--- a/src/dm/impls/plex/tutorials/ex11.c<br>
+++ b/src/dm/impls/plex/tutorials/ex11.c<br>
@@ -648,7 +648,6 @@ PetscPrintf(PETSC_COMM_SELF, "\t\t***** FormRHSSource: have new_imp_rate= %10.3e<br>
ierr = PetscObjectSetName((PetscObject)S, "src");CHKERRQ(ierr);<br>
ierr = VecViewFromOptions(S,NULL,"-vec_view_diagnostics");CHKERRQ(ierr);<br>
ierr = MatMult(ctx->M,S,rectx->imp_src);CHKERRQ(ierr);<br>
- ierr = VecCopy(S,rectx->imp_src);CHKERRQ(ierr);<br>
ierr = VecDestroy(&S);CHKERRQ(ierr);<br>
}<br>
ierr = VecCopy(rectx->imp_src,F);CHKERRQ(ierr);<br>
@@ -711,7 +710,7 @@ static PetscErrorCode stepSrc(PetscReal time, PetscInt step, PetscReal dt, Petsc<br>
REctx *rectx;<br>
PetscFunctionBegin;<br>
rectx = (REctx*)ctx->data;<br>
- if (time >= rectx->pulse_start) *rho = rectx->pulse_rate;<br>
+ if (time > 1.e+5) *rho = rectx->pulse_rate; /* turned off */<br>
else *rho = 0.;<br>
PetscFunctionReturn(0);<br>
}<br>
<<<<<<<<br>
<br>
$ ls src/dm/impls/plex/examples/tutorials/<br>
doc/ ex10.c ex10f90.F90 ex11.c output/<br>
<br></blockquote><div><br></div><div>Old files from move. I removed them. Thanks,</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
This should now be in src/dm/impls/plex/tutorials/<br>
<br>
Regarding the primary issue: configure, the primary error is not logged in configure.log. Running manually - I get:<br>
<br>
bfort terminating at 664: Exceeded output count limit!<br>
<br>
$ grep '/*@' *.c |wc -l<br>
600<br>
<br>
This single dir creates 600 man pages? Perhaps its time to reorganize plex into multiple dirs?<br>
<br>
Satish<br>
<br>
<br>
On Fri, 3 Apr 2020, Mark Adams wrote:<br>
<br>
> Satish, I tried again from scratch see the same thing.<br>
> I pushed this.<br>
> Thanks<br>
> <br>
> 09:35 mark/feature-xgc-interface-rebase= ~/Codes/petsc$ git rebase<br>
> origin/master<br>
> First, rewinding head to replay your work on top of it...<br>
> Applying: starting rebase branch<br>
> Using index info to reconstruct a base tree...<br>
> M include/petsc/private/dmpleximpl.h<br>
> M include/petscdmplex.h<br>
> M src/dm/impls/plex/makefile<br>
> .git/rebase-apply/patch:2620: trailing whitespace.<br>
> for (d=0;d<src->dim;d++) *pp++ = src->df[d][s][idx];<br>
> warning: 1 line adds whitespace errors.<br>
> Falling back to patching base and 3-way merge...<br>
> Auto-merging src/dm/impls/plex/makefile<br>
> Auto-merging include/petscdmplex.h<br>
> CONFLICT (content): Merge conflict in include/petscdmplex.h<br>
> Auto-merging include/petsc/private/dmpleximpl.h<br>
> error: Failed to merge in the changes.<br>
> Patch failed at 0001 starting rebase branch<br>
> hint: Use 'git am --show-current-patch' to see the failed patch<br>
> Resolve all conflicts manually, mark them as resolved with<br>
> "git add/rm <conflicted_files>", then run "git rebase --continue".<br>
> You can instead skip this commit: run "git rebase --skip".<br>
> To abort and get back to the state before "git rebase", run "git rebase<br>
> --abort".<br>
> 09:36 1 mark/feature-xgc-interface-rebase *+|REBASE 1/19 ~/Codes/petsc$ vi<br>
> include/petscdmplex.h<br>
> 09:37 mark/feature-xgc-interface-rebase *+|REBASE 1/19 ~/Codes/petsc$ git<br>
> add include/petscdmplex.h<br>
> 09:37 mark/feature-xgc-interface-rebase +|REBASE 1/19 ~/Codes/petsc$ git<br>
> rebase --continue<br>
> Applying: starting rebase branch<br>
> Applying: manual merge<br>
> Applying: RE test<br>
> Applying: remove Ehat<br>
> Applying: clean up interface, redo regression tests, found false negatives<br>
> Applying: change Ec<br>
> Applying: tweek griding<br>
> Applying: clean up, working on impurity injection<br>
> Applying: fixed quench and pulse test<br>
> Applying: hardwired CUDA kernel for DIM, added presolve in ex11<br>
> Applying: added guard<br>
> Applying: starting to get E field added<br>
> Applying: doc<br>
> Applying: fix test params<br>
> Applying: remove comment<br>
> Applying: updated test syntax<br>
> Applying: cleaned up flags<br>
> Applying: cleaned up flags<br>
> Applying: fixed soruce bug<br>
> <br>
> <br>
> 09:37 mark/feature-xgc-interface-rebase<> ~/Codes/petsc$ rm -fr<br>
> arch-macosx-gnu-g/<br>
> 09:38 mark/feature-xgc-interface-rebase<> ~/Codes/petsc$<br>
> ../arch-macosx-gnu-g.py<br>
> ===============================================================================<br>
> Configuring PETSc to compile on your system<br>
> <br>
> ===============================================================================<br>
> ===============================================================================<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> ***** WARNING: You have<br>
> an older version of Gnu make, it will work,<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> but may not support all the parallel testing<br>
> options. You can install the<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> latest Gnu make with your package manager, such as brew or macports,<br>
> or use<br>
> <br>
> <br>
> <br>
> <br>
> the<br>
> --download-make option to get the latest Gnu make *****<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> ===============================================================================<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> ===============================================================================<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> Trying to download git://<br>
> <a href="https://bitbucket.org/petsc/pkg-sowing.git" rel="noreferrer" target="_blank">https://bitbucket.org/petsc/pkg-sowing.git</a> for SOWING<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> ===============================================================================<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> ===============================================================================<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> Running configure on<br>
> SOWING; this may take several minutes<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> ===============================================================================<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> ===============================================================================<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> Running make on SOWING;<br>
> this may take several minutes<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> ===============================================================================<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> ===============================================================================<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> Running make install on<br>
> SOWING; this may take several minutes<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> ===============================================================================<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> TESTING: checkSharedLibrary<br>
> from config.packages.sowing(config/BuildSystem/config/package.py:926)<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> *******************************************************************************<br>
> CONFIGURATION CRASH (Please send configure.log to<br>
> <a href="mailto:petsc-maint@mcs.anl.gov" target="_blank">petsc-maint@mcs.anl.gov</a>)<br>
> *******************************************************************************<br>
> <br>
> 09:40 1 mark/feature-xgc-interface-rebase<> ~/Codes/petsc$<br>
> <br>
> <br>
> On Fri, Apr 3, 2020 at 8:17 AM Mark Adams <<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>> wrote:<br>
> <br>
> ><br>
> ><br>
> > On Thu, Apr 2, 2020 at 11:05 PM Satish Balay <<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>> wrote:<br>
> ><br>
> >> My OS build also went through. Looks like you haven't pushed [force<br>
> >> update] this branch - so I'm testing with something totally different.<br>
> >><br>
> >><br>
> > Yes, I have a <> after a rebase. Do you want me to push it? Or should I<br>
> > just start over? I thought I started with a clean version of my code from<br>
> > the repo.<br>
> > Thanks,<br>
> ><br>
> ><br>
> >> So likely something in your rebased sources is causing bfort to fail..<br>
> >><br>
> >> Satish<br>
> >><br>
> >> On Thu, 2 Apr 2020, Mark Adams wrote:<br>
> >><br>
> >> > I see:<br>
> >> > 22:46 128 mark/feature-xgc-interface-rebase<> ~/Codes/petsc$ git status<br>
> >> > On branch mark/feature-xgc-interface-rebase<br>
> >> > Your branch and 'origin/mark/feature-xgc-interface-rebase' have<br>
> >> diverged,<br>
> >> > and have 130 and 18 different commits each, respectively.<br>
> >> > (use "git pull" to merge the remote branch into yours)<br>
> >> ><br>
> >> > Untracked files:<br>
> >> > (use "git add <file>..." to include in what will be committed)<br>
> >> > out2.txt<br>
> >> > src/dm/impls/plex/examples/tutorials/Landau/<br>
> >> ><br>
> >> ><br>
> >> > On Thu, Apr 2, 2020 at 10:45 PM Mark Adams <<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>> wrote:<br>
> >> ><br>
> >> > ><br>
> >> > ><br>
> >> > > On Thu, Apr 2, 2020 at 10:33 PM Satish Balay <<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>><br>
> >> wrote:<br>
> >> > ><br>
> >> > >> Is this branch mark/feature-xgc-interface-rebase pushed?<br>
> >> > ><br>
> >> > ><br>
> >> > > yes.<br>
> >> > ><br>
> >> > ><br>
> >> > >> I had done a build with the current state of it - and the build went<br>
> >> > >> through fine. This was on linux.<br>
> >> > >><br>
> >> > >> Will try OSX now.<br>
> >> > >><br>
> >> > >> Satish<br>
> >> > >><br>
> >> > >> On Thu, 2 Apr 2020, Mark Adams wrote:<br>
> >> > >><br>
> >> > >> > Note, when I rebased I got one conflict, in a header where I added<br>
> >> > >> stuff at<br>
> >> > >> > the end and master did also so I just kept them both and continued.<br>
> >> > >> > Other than that it was a clean rebase.<br>
> >> > >> ><br>
> >> > >> > On Thu, Apr 2, 2020 at 10:15 PM Mark Adams <<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>><br>
> >> wrote:<br>
> >> > >> ><br>
> >> > >> > ><br>
> >> > >> > ><br>
> >> > >> > > On Thu, Apr 2, 2020 at 9:32 PM Satish Balay <<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>><br>
> >> > >> wrote:<br>
> >> > >> > ><br>
> >> > >> > >> can you try this in a local clone [same branch] and see if that<br>
> >> > >> works?<br>
> >> > >> > >><br>
> >> > >> > >> cd /Users/markadams/Codes<br>
> >> > >> > >> git clone petsc petsc-test<br>
> >> > >> > >> cd petsc-test<br>
> >> > >> > >> ./configure ...<br>
> >> > >> > >><br>
> >> > >> > >> Satish<br>
> >> > >> > >><br>
> >> > >> > >><br>
> >> > >> > >> On Thu, 2 Apr 2020, Mark Adams wrote:<br>
> >> > >> > >><br>
> >> > >> > >> > I tried to rebase mark/feature-xgc-interface-rebase with<br>
> >> master<br>
> >> > >> and I<br>
> >> > >> > >> get<br>
> >> > >> > >> > this.<br>
> >> > >> > >> > I of course deleted the arch directory.<br>
> >> > >> > >> > Thanks,<br>
> >> > >> > >> > Mark<br>
> >> > >> > >> ><br>
> >> > >> > >><br>
> >> > >> > >><br>
> >> > >> ><br>
> >> > >><br>
> >> > >><br>
> >> ><br>
> >><br>
> >><br>
> <br>
<br>
</blockquote></div></div>