Re: [petsc-dev] *unwind* next branch

[Lisandro Dalcin]

I had a branch (PR 755) merged into next BEFORE (by looking at the
commit list in Bitbucket) the commits related to the release were
pushed. So this PR did not make in for the new release.

On 27 September 2017 at 05:01, Balay, Satish  wrote:
> ref: https://lists.mcs.anl.gov/pipermail/petsc-dev/2016-April/019013.html
>
> I've recreated 'next' branch - and have a backup for current 'next' at
> 'next-sep-2017'.
>
> So *all git repo users* (if you have/use 'next' branch in your clone)
> - please do the following (in all your git clones):
>
> git checkout master
> git fetch
> git branch -D next
> git checkout next
>
> Please *do not push* to 'next' from a stale next branch in your clone.
>
> $ git log --oneline v3.8..next|wc -l
> 2
> $ git log --oneline v3.8..next-sep-2017|wc -l
> 300
>
> [i.e a 'small' number vs a 'huge' number in the diff].
>
> Satish
>
> --
> Ref:currently merged branches in old next
>
> $ comm -12 <(git branch -r --merged origin/next-sep-2017 | sort) <(git branch 
> -r --no-merged origin/master | sort)
>   origin/dalcinl/add-tsrestart
>   origin/dalcinl/fix-dmplex-draw
>   origin/hongzh/add-ell-format



-- 
Lisandro Dalcin

Research Scientist
Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/

4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 0109
Thuwal 23955-6900, Kingdom of Saudi Arabia
http://www.kaust.edu.sa

Office Phone: +966 12 808-0459

[petsc-dev] why am I getting this message?

[Mark Adams]

I just pulled maint but still get a message that I am out of date:

1072  git pull origin
 1073  h
05:12 cori01 maint= ~/petsc_install/petsc$ ../arch-cori-knl-opt-intel.py
PETSC_DIR=$PWD
+++
The version of PETSc you are using is out-of-date, we recommend updating to
the new release
 Available Version: 3.8   Installed Version: 3.7.6
http://www.mcs.anl.gov/petsc/download/index.html
+++
===
 Configuring PETSc to compile on your system

===

Re: [petsc-dev] why am I getting this message?

[Satish Balay]

What url do you have for origin? Send output from:

git config --local -l

And do you have to list 'origin' in pull? [I guess you need to do that
if you have multiple remotes?]

And what do you have for:

git fetch origin
git describe origin/maint
git describe maint

Satish

On Wed, 27 Sep 2017, Mark Adams wrote:

> I just pulled maint but still get a message that I am out of date:
> 
> 1072  git pull origin
>  1073  h
> 05:12 cori01 maint= ~/petsc_install/petsc$ ../arch-cori-knl-opt-intel.py
> PETSC_DIR=$PWD
> +++
> The version of PETSc you are using is out-of-date, we recommend updating to
> the new release
>  Available Version: 3.8   Installed Version: 3.7.6
> http://www.mcs.anl.gov/petsc/download/index.html
> +++
> ===
>  Configuring PETSc to compile on your system
> 
> ===
> 

Re: [petsc-dev] why am I getting this message?

[Mark Adams]

This message seems to have gone away ...

On Wed, Sep 27, 2017 at 8:14 AM, Mark Adams  wrote:

> I just pulled maint but still get a message that I am out of date:
>
> 1072  git pull origin
>  1073  h
> 05:12 cori01 maint= ~/petsc_install/petsc$ ../arch-cori-knl-opt-intel.py
> PETSC_DIR=$PWD
> 
> +++
> The version of PETSc you are using is out-of-date, we recommend updating
> to the new release
>  Available Version: 3.8   Installed Version: 3.7.6
> http://www.mcs.anl.gov/petsc/download/index.html
> 
> +++
> 
> ===
>  Configuring PETSc to compile on your system
>
> 
> ===
>
>

Re: [petsc-dev] *unwind* next branch

[Lisandro Dalcin]

Satish, please revert the merge to next of my branch
dalcinl/add-tsrestart. This branch has fixes that should go to new
maint, but now I need to rework the commits, as they introduce new
APIs.

On 27 September 2017 at 11:02, Lisandro Dalcin  wrote:
> I had a branch (PR 755) merged into next BEFORE (by looking at the
> commit list in Bitbucket) the commits related to the release were
> pushed. So this PR did not make in for the new release.
>
> On 27 September 2017 at 05:01, Balay, Satish  wrote:
>> ref: https://lists.mcs.anl.gov/pipermail/petsc-dev/2016-April/019013.html
>>
>> I've recreated 'next' branch - and have a backup for current 'next' at
>> 'next-sep-2017'.
>>
>> So *all git repo users* (if you have/use 'next' branch in your clone)
>> - please do the following (in all your git clones):
>>
>> git checkout master
>> git fetch
>> git branch -D next
>> git checkout next
>>
>> Please *do not push* to 'next' from a stale next branch in your clone.
>>
>> $ git log --oneline v3.8..next|wc -l
>> 2
>> $ git log --oneline v3.8..next-sep-2017|wc -l
>> 300
>>
>> [i.e a 'small' number vs a 'huge' number in the diff].
>>
>> Satish
>>
>> --
>> Ref:currently merged branches in old next
>>
>> $ comm -12 <(git branch -r --merged origin/next-sep-2017 | sort) <(git 
>> branch -r --no-merged origin/master | sort)
>>   origin/dalcinl/add-tsrestart
>>   origin/dalcinl/fix-dmplex-draw
>>   origin/hongzh/add-ell-format
>
>
>
> --
> Lisandro Dalcin
> 
> Research Scientist
> Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
> Extreme Computing Research Center (ECRC)
> King Abdullah University of Science and Technology (KAUST)
> http://ecrc.kaust.edu.sa/
>
> 4700 King Abdullah University of Science and Technology
> al-Khawarizmi Bldg (Bldg 1), Office # 0109
> Thuwal 23955-6900, Kingdom of Saudi Arabia
> http://www.kaust.edu.sa
>
> Office Phone: +966 12 808-0459



-- 
Lisandro Dalcin

Research Scientist
Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/

4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 0109
Thuwal 23955-6900, Kingdom of Saudi Arabia
http://www.kaust.edu.sa

Office Phone: +966 12 808-0459

Re: [petsc-dev] *unwind* next branch

[Lisandro Dalcin]

Also revert the merge of dalcinl/fix-dmplex-draw, I have to decline
the PR and make a new one targeting maint.

On 27 September 2017 at 16:16, Lisandro Dalcin  wrote:
> Satish, please revert the merge to next of my branch
> dalcinl/add-tsrestart. This branch has fixes that should go to new
> maint, but now I need to rework the commits, as they introduce new
> APIs.
>
> On 27 September 2017 at 11:02, Lisandro Dalcin  wrote:
>> I had a branch (PR 755) merged into next BEFORE (by looking at the
>> commit list in Bitbucket) the commits related to the release were
>> pushed. So this PR did not make in for the new release.
>>
>> On 27 September 2017 at 05:01, Balay, Satish  wrote:
>>> ref: https://lists.mcs.anl.gov/pipermail/petsc-dev/2016-April/019013.html
>>>
>>> I've recreated 'next' branch - and have a backup for current 'next' at
>>> 'next-sep-2017'.
>>>
>>> So *all git repo users* (if you have/use 'next' branch in your clone)
>>> - please do the following (in all your git clones):
>>>
>>> git checkout master
>>> git fetch
>>> git branch -D next
>>> git checkout next
>>>
>>> Please *do not push* to 'next' from a stale next branch in your clone.
>>>
>>> $ git log --oneline v3.8..next|wc -l
>>> 2
>>> $ git log --oneline v3.8..next-sep-2017|wc -l
>>> 300
>>>
>>> [i.e a 'small' number vs a 'huge' number in the diff].
>>>
>>> Satish
>>>
>>> --
>>> Ref:currently merged branches in old next
>>>
>>> $ comm -12 <(git branch -r --merged origin/next-sep-2017 | sort) <(git 
>>> branch -r --no-merged origin/master | sort)
>>>   origin/dalcinl/add-tsrestart
>>>   origin/dalcinl/fix-dmplex-draw
>>>   origin/hongzh/add-ell-format
>>
>>
>>
>> --
>> Lisandro Dalcin
>> 
>> Research Scientist
>> Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
>> Extreme Computing Research Center (ECRC)
>> King Abdullah University of Science and Technology (KAUST)
>> http://ecrc.kaust.edu.sa/
>>
>> 4700 King Abdullah University of Science and Technology
>> al-Khawarizmi Bldg (Bldg 1), Office # 0109
>> Thuwal 23955-6900, Kingdom of Saudi Arabia
>> http://www.kaust.edu.sa
>>
>> Office Phone: +966 12 808-0459
>
>
>
> --
> Lisandro Dalcin
> 
> Research Scientist
> Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
> Extreme Computing Research Center (ECRC)
> King Abdullah University of Science and Technology (KAUST)
> http://ecrc.kaust.edu.sa/
>
> 4700 King Abdullah University of Science and Technology
> al-Khawarizmi Bldg (Bldg 1), Office # 0109
> Thuwal 23955-6900, Kingdom of Saudi Arabia
> http://www.kaust.edu.sa
>
> Office Phone: +966 12 808-0459



-- 
Lisandro Dalcin

Research Scientist
Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/

4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 0109
Thuwal 23955-6900, Kingdom of Saudi Arabia
http://www.kaust.edu.sa

Office Phone: +966 12 808-0459

Re: [petsc-dev] *unwind* next branch

[Satish Balay]

>>
commit 8e80f76617739c84d1b952f9d3f7b8e359e84079
Merge: b5178cece8 5fbebc36b8
Author: Lisandro Dalcin 
Date:   Tue Sep 26 12:36:39 2017

Merge branch 'dalcinl/add-tsrestart' into next
<

Well I was looking for branches that were already tested in next. [i.e
branches that get merged sometime before midnight CST get tested by
9:00AM CST]

And there is always a next release.. [likely in a couple of months -
for some of the currently in progress features]

Jed suggests - updates can go into 3.8.1 - if there are 'no
incompatible interface changes' [but thats harder for me to verify for
non-bugfix changes]

Satish

On Wed, 27 Sep 2017, Lisandro Dalcin wrote:

> I had a branch (PR 755) merged into next BEFORE (by looking at the
> commit list in Bitbucket) the commits related to the release were
> pushed. So this PR did not make in for the new release.
> 
> On 27 September 2017 at 05:01, Balay, Satish  wrote:
> > ref: https://lists.mcs.anl.gov/pipermail/petsc-dev/2016-April/019013.html
> >
> > I've recreated 'next' branch - and have a backup for current 'next' at
> > 'next-sep-2017'.
> >
> > So *all git repo users* (if you have/use 'next' branch in your clone)
> > - please do the following (in all your git clones):
> >
> > git checkout master
> > git fetch
> > git branch -D next
> > git checkout next
> >
> > Please *do not push* to 'next' from a stale next branch in your clone.
> >
> > $ git log --oneline v3.8..next|wc -l
> > 2
> > $ git log --oneline v3.8..next-sep-2017|wc -l
> > 300
> >
> > [i.e a 'small' number vs a 'huge' number in the diff].
> >
> > Satish
> >
> > --
> > Ref:currently merged branches in old next
> >
> > $ comm -12 <(git branch -r --merged origin/next-sep-2017 | sort) <(git 
> > branch -r --no-merged origin/master | sort)
> >   origin/dalcinl/add-tsrestart
> >   origin/dalcinl/fix-dmplex-draw
> >   origin/hongzh/add-ell-format
> 
> 
> 
> 

Re: [petsc-dev] *unwind* next branch

[Lisandro Dalcin]

On 27 September 2017 at 16:18, Satish Balay  wrote:
>>>
> commit 8e80f76617739c84d1b952f9d3f7b8e359e84079
> Merge: b5178cece8 5fbebc36b8
> Author: Lisandro Dalcin 
> Date:   Tue Sep 26 12:36:39 2017
>
> Merge branch 'dalcinl/add-tsrestart' into next
> <
>
> Well I was looking for branches that were already tested in next. [i.e
> branches that get merged sometime before midnight CST get tested by
> 9:00AM CST]
>
> And there is always a next release.. [likely in a couple of months -
> for some of the currently in progress features]
>
> Jed suggests - updates can go into 3.8.1 - if there are 'no
> incompatible interface changes' [but thats harder for me to verify for
> non-bugfix changes]
>

This suggestion truly means that we can ADD public functions and
#defines to maint ?

-- 
Lisandro Dalcin

Research Scientist
Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/

4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 0109
Thuwal 23955-6900, Kingdom of Saudi Arabia
http://www.kaust.edu.sa

Office Phone: +966 12 808-0459

Re: [petsc-dev] why am I getting this message?

[Satish Balay]

petscnagupgrade.py will check and nag you only once a day.

You should verify if you have 3.8 - with 'git log' or 'git describe'

Satish

On Wed, 27 Sep 2017, Mark Adams wrote:

> This message seems to have gone away ...
> 
> On Wed, Sep 27, 2017 at 8:14 AM, Mark Adams  wrote:
> 
> > I just pulled maint but still get a message that I am out of date:
> >
> > 1072  git pull origin
> >  1073  h
> > 05:12 cori01 maint= ~/petsc_install/petsc$ ../arch-cori-knl-opt-intel.py
> > PETSC_DIR=$PWD
> > 
> > +++
> > The version of PETSc you are using is out-of-date, we recommend updating
> > to the new release
> >  Available Version: 3.8   Installed Version: 3.7.6
> > http://www.mcs.anl.gov/petsc/download/index.html
> > 
> > +++
> > 
> > ===
> >  Configuring PETSc to compile on your system
> >
> > 
> > ===
> >
> >
> 

Re: [petsc-dev] *unwind* next branch

[Jed Brown]

Lisandro Dalcin  writes:

>> Jed suggests - updates can go into 3.8.1 - if there are 'no
>> incompatible interface changes' [but thats harder for me to verify for
>> non-bugfix changes]
>>
>
> This suggestion truly means that we can ADD public functions and
> #defines to maint ?

Yeah, we've done that occasionally in the past.  I would also say there
should not be any semantic behavioral changes.  We want people to apply
subminor releases without stressing that it could give them different
answers or otherwise invalidate their V&V work.  If we can ship a
performance boost or an important feature without any changes to the
interface or behavior for existing users, I think it's fair game.  Just
need to be very confident that it doesn't change existing semantics,
which can be hard.

Re: [petsc-dev] why am I getting this message?

[Mark Adams]

Well I am on v3.8 now and I did pull ... oh well, not a biggy.

On Wed, Sep 27, 2017 at 9:27 AM, Satish Balay  wrote:

> petscnagupgrade.py will check and nag you only once a day.
>
> You should verify if you have 3.8 - with 'git log' or 'git describe'
>
> Satish
>
> On Wed, 27 Sep 2017, Mark Adams wrote:
>
> > This message seems to have gone away ...
> >
> > On Wed, Sep 27, 2017 at 8:14 AM, Mark Adams  wrote:
> >
> > > I just pulled maint but still get a message that I am out of date:
> > >
> > > 1072  git pull origin
> > >  1073  h
> > > 05:12 cori01 maint= ~/petsc_install/petsc$
> ../arch-cori-knl-opt-intel.py
> > > PETSC_DIR=$PWD
> > > 
> > > +++
> > > The version of PETSc you are using is out-of-date, we recommend
> updating
> > > to the new release
> > >  Available Version: 3.8   Installed Version: 3.7.6
> > > http://www.mcs.anl.gov/petsc/download/index.html
> > > 
> > > +++
> > > 
> > > ===
> > >  Configuring PETSc to compile on your system
> > >
> > > 
> > > ===
> > >
> > >
> >
>
>

Re: [petsc-dev] why am I getting this message?

[Mark Adams]

On Wed, Sep 27, 2017 at 9:00 AM, Satish Balay  wrote:

> What url do you have for origin? Send output from:
>
> git config --local -l
>

07:53 cori01 maint= ~/petsc_install/petsc$ git config --local -l
core.repositoryformatversion=0
core.filemode=true
core.bare=false
core.logallrefupdates=true
remote.origin.url=https://mad...@bitbucket.org/petsc/petsc.git
remote.origin.fetch=+refs/heads/*:refs/remotes/origin/*
branch.master.remote=origin
branch.master.merge=refs/heads/master
branch.mark/snes-ex56c.remote=origin
branch.mark/snes-ex56c.merge=refs/heads/mark/snes-ex56c
branch.maint.remote=origin
branch.maint.merge=refs/heads/maint
branch.hzhang/fix-nonscalable-ctable-use.remote=origin
branch.hzhang/fix-nonscalable-ctable-use.merge=refs/heads/hzhang/fix-nonscalable-ctable-use
07:53 cori01 maint= ~/petsc_install/petsc$


>
> And do you have to list 'origin' in pull? [I guess you need to do that
> if you have multiple remotes?]
>

I don't have multiple remotes


>
> And what do you have for:
>
> git fetch origin
> git describe origin/maint
> git describe maint
>

07:54 cori01 maint= ~/petsc_install/petsc$ git fetch origin
07:55 cori01 maint= ~/petsc_install/petsc$ git describe origin/maint
v3.8
07:55 cori01 maint= ~/petsc_install/petsc$ git describe origin/maint
v3.8
07:55 cori01 maint= ~/petsc_install/petsc$


> Satish
>
> On Wed, 27 Sep 2017, Mark Adams wrote:
>
> > I just pulled maint but still get a message that I am out of date:
> >
> > 1072  git pull origin
> >  1073  h
> > 05:12 cori01 maint= ~/petsc_install/petsc$ ../arch-cori-knl-opt-intel.py
> > PETSC_DIR=$PWD
> > 
> +++
> > The version of PETSc you are using is out-of-date, we recommend updating
> to
> > the new release
> >  Available Version: 3.8   Installed Version: 3.7.6
> > http://www.mcs.anl.gov/petsc/download/index.html
> > 
> +++
> > 
> ===
> >  Configuring PETSc to compile on your system
> >
> > 
> ===
> >
>
>

Re: [petsc-dev] why am I getting this message?

[Satish Balay]

On Wed, 27 Sep 2017, Mark Adams wrote:

> On Wed, Sep 27, 2017 at 9:00 AM, Satish Balay  wrote:
> 
> > What url do you have for origin? Send output from:
> >
> > git config --local -l
> >
> 
> 07:53 cori01 maint= ~/petsc_install/petsc$ git config --local -l
> core.repositoryformatversion=0
> core.filemode=true
> core.bare=false
> core.logallrefupdates=true
> remote.origin.url=https://mad...@bitbucket.org/petsc/petsc.git
> remote.origin.fetch=+refs/heads/*:refs/remotes/origin/*
> branch.master.remote=origin
> branch.master.merge=refs/heads/master
> branch.mark/snes-ex56c.remote=origin
> branch.mark/snes-ex56c.merge=refs/heads/mark/snes-ex56c
> branch.maint.remote=origin
> branch.maint.merge=refs/heads/maint
> branch.hzhang/fix-nonscalable-ctable-use.remote=origin
> branch.hzhang/fix-nonscalable-ctable-use.merge=refs/heads/hzhang/fix-nonscalable-ctable-use
> 07:53 cori01 maint= ~/petsc_install/petsc$
> 
> 
> >
> > And do you have to list 'origin' in pull? [I guess you need to do that
> > if you have multiple remotes?]
> >
> 
> I don't have multiple remotes
> 
> 
> >
> > And what do you have for:
> >
> > git fetch origin
> > git describe origin/maint
> > git describe maint
> >
> 
> 07:54 cori01 maint= ~/petsc_install/petsc$ git fetch origin
> 07:55 cori01 maint= ~/petsc_install/petsc$ git describe origin/maint
> v3.8
> 07:55 cori01 maint= ~/petsc_install/petsc$ git describe origin/maint

This should be 'git describe maint'

Satish

> v3.8
> 07:55 cori01 maint= ~/petsc_install/petsc$
> 
> 
> > Satish
> >
> > On Wed, 27 Sep 2017, Mark Adams wrote:
> >
> > > I just pulled maint but still get a message that I am out of date:
> > >
> > > 1072  git pull origin
> > >  1073  h
> > > 05:12 cori01 maint= ~/petsc_install/petsc$ ../arch-cori-knl-opt-intel.py
> > > PETSC_DIR=$PWD
> > > 
> > +++
> > > The version of PETSc you are using is out-of-date, we recommend updating
> > to
> > > the new release
> > >  Available Version: 3.8   Installed Version: 3.7.6
> > > http://www.mcs.anl.gov/petsc/download/index.html
> > > 
> > +++
> > > 
> > ===
> > >  Configuring PETSc to compile on your system
> > >
> > > 
> > ===
> > >
> >
> >
> 

Re: [petsc-dev] why am I getting this message?

[Satish Balay]

If you are indeed on 3.8 - and petscnagupgrade.py gave a warning -
then something was not right..

Well as long as you've verified that you are on 3.8 - it should be
fine.

Satish

On Wed, 27 Sep 2017, Mark Adams wrote:

> Well I am on v3.8 now and I did pull ... oh well, not a biggy.
> 
> On Wed, Sep 27, 2017 at 9:27 AM, Satish Balay  wrote:
> 
> > petscnagupgrade.py will check and nag you only once a day.
> >
> > You should verify if you have 3.8 - with 'git log' or 'git describe'
> >
> > Satish
> >
> > On Wed, 27 Sep 2017, Mark Adams wrote:
> >
> > > This message seems to have gone away ...
> > >
> > > On Wed, Sep 27, 2017 at 8:14 AM, Mark Adams  wrote:
> > >
> > > > I just pulled maint but still get a message that I am out of date:
> > > >
> > > > 1072  git pull origin
> > > >  1073  h
> > > > 05:12 cori01 maint= ~/petsc_install/petsc$
> > ../arch-cori-knl-opt-intel.py
> > > > PETSC_DIR=$PWD
> > > > 
> > > > +++
> > > > The version of PETSc you are using is out-of-date, we recommend
> > updating
> > > > to the new release
> > > >  Available Version: 3.8   Installed Version: 3.7.6
> > > > http://www.mcs.anl.gov/petsc/download/index.html
> > > > 
> > > > +++
> > > > 
> > > > ===
> > > >  Configuring PETSc to compile on your system
> > > >
> > > > 
> > > > ===
> > > >
> > > >
> > >
> >
> >
> 

Re: [petsc-dev] PetscSF in Fortran

[Matthew Knepley]

On Tue, Sep 26, 2017 at 11:49 PM, Adrian Croucher  wrote:

> hi Matt,
>
> On 25/09/17 23:12, Matthew Knepley wrote:
>
>
> If you truly need the exact same SF for your grid, you should be able to
> use DMGet/SetPointSF() since it will just reference count it for you. Then
> the default SF is created automatically from the point SF. Does this work?
>
>
> It doesn't seem to work, unfortunately. If I run in parallel I get an
> error on each processor like this:
>
> [0]PETSC ERROR: Nonconforming object sizes
> [0]PETSC ERROR: SF roots 447 < pEnd 543
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.7.6-5886-gc423942  GIT
> Date: 2017-06-28 18:43:52 -0500
> [0]PETSC ERROR: test_all on a linux-gnu-c-opt named en-354401 by acro018
> Wed Sep 27 16:31:28 2017
> [0]PETSC ERROR: Configure options --with-x --download-hdf5
> --download-netcdf --download-exodusii --downloa
> d-triangle --download-ptscotch --download-chaco
> --download-hypre
> [0]PETSC ERROR: #1 PetscSectionCreateGlobalSection() line 929 in
> /home/acro018/software/PETSc/code/src/vec
> /is/utils/vsectionis.c
>
> [0]PETSC ERROR: #2 DMGetDefaultGlobalSection() line 3458 in
> /home/acro018/software/PETSc/code/src/dm/inter
> face/dm.c
>
> [0]PETSC ERROR: #3 User provided function() line 0 in User file
>
> The reason I thought just copying the SF across might work is that the
> partition ghost cells in my modified DMPlex should be in the same locations
> (DMPlex points) as they were in the original DMPlex. My understanding was
> that the SF just stores the root corresponding to a leaf (ghost point?) on
> the current processor, so those ought to be unchanged. But maybe there are
> subtleties about the SF stuff that I don't yet understand.
>
> What I am doing is adding new points for the dual-porosity mesh into my
> modified DMPlex. I have added the new cells after the partition ghost
> cells, and before the boundary ghost cells (and similarly for other depth
> strata). So I have shifted the locations of the boundary ghost cells, but
> not the partition ghost cells. I give the new points the appropriate depth
> label values so that the depth stratum bounds are updated correctly. I also
> shift the end_interior value for each depth stratum, so that code relying
> on DMPlexGetHybridBounds() should still work.
>
> Would you expect copying the SF to work in this case?
>

Okay, I think this should be easy to solve.

First a little bit about SF. There are two parts to the specification. You
have the communication part, which maps
a certain location p on this process to another location q on another
process. This might not change for you. The
second part just tells it how big the data array is (numRoots), which is
the thing that the locations in the communication
part index into.

So my question is, where did you put the numbers for the points you added?
Are they after all points, or only after the old cells?
I think you can easily create the new SF using the info from SFGetGraph().

   Matt


>
> - Adrian
>
> --
> Dr Adrian Croucher
> Senior Research Fellow
> Department of Engineering Science
> University of Auckland, New Zealand
> email: a.crouc...@auckland.ac.nz
> tel: +64 (0)9 923 4611 <+64%209-923%204611>
>
>


-- 
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

https://www.cse.buffalo.edu/~knepley/ 

Re: [petsc-dev] MatAssembly removes all preallocation info

[Kong, Fande]

Hi Barry,

Just added a PR for this.
https://bitbucket.org/petsc/petsc/pull-requests/760/matresetpreallocation/diff


Fande,

On Mon, Sep 25, 2017 at 12:35 PM, Kong, Fande  wrote:

>
>
> On Mon, Sep 25, 2017 at 12:26 PM, Barry Smith  wrote:
>
>>
>> > On Sep 25, 2017, at 1:17 PM, Kong, Fande  wrote:
>> >
>> >
>> >
>> > On Mon, Sep 25, 2017 at 11:41 AM, Barry Smith 
>> wrote:
>> >
>> > > On Sep 25, 2017, at 11:22 AM, Kong, Fande  wrote:
>> > >
>> > >
>> > >
>> > > On Mon, Sep 25, 2017 at 10:05 AM, Stefano Zampini <
>> stefano.zamp...@gmail.com> wrote:
>> > > If you know the union of the different sparsity patterns, after you
>> preallocate you can set all zeros to use all the entries. This way PETSc
>> will not complain about new nonzeros in successive assemblies.
>> > >
>> > >
>> > > Thanks, Stefano,
>> > >
>> > > Yes, we are actually using this way right now. We are explicitly
>> setting zeros to the matrix to stop petsc shrinking the memory.
>> >
>> >This
>> > >  But we want to know why we free the extra memory? Yes, we shrink
>> the memory by moving all data together to have an efficiency computation.
>> But it is still possible to not throw away our  preallocated memory space
>> if we  want to use latter.
>>
>>We don't actually "throw out" the extra memory we just don't use it
>> and it becomes unaccessible.
>>
>>Yes, one could actually keep the preallocation information. This would
>> essentially require
>>
>> 1) an additional array of length number of rows that is allocated and
>> filled with the user provide nonzero counts when the user sets the
>> preallocation (currently this information is lost when the matrix is
>> "shrunk")  and
>>
>> 2) A API say MatResetPreallocation() that used this saved information to
>> fill in the ilen and other integer arrays in the matrix as if the user had
>> called MatPreallocateXXX() again.
>>
>>   Actually now that I say this I realize it is pretty easy. You could
>> make a pull request and introduce this functionality.
>>
>
> Yes, this is what I want. I will be working on this and making a PR.
>
> Fande,
>
>
>>
>>   Barry
>>
>>
>> >
>> >contradicts this.
>> >
>> >If at the beginning you put in all the zeros you will ever need then
>> PETSc will not "throw away" preallocated space. Most likely you are not
>> actually setting the initial nonzero structure using the union of all
>> future nonzero structures.
>> >
>> > We are explicitly setting zeros, and the code is working. But setting
>> zeros is not a free function. In this email, I am trying to understand why
>> we have to do in this way.  If we could not throw away the extra memory
>> when we do not explicitly set zeros, it would be nice.
>> >
>> >
>> >If the nonzero structure changes dramatically over time, for
>> instance if the mesh is moving around removing lots of old connections and
>> introducing lots of new ones then you do not want to just preallocate.
>> Instead you need to preallocate for each totally new nonzero structure.
>> >
>> >There is no way to "preserve" the initial preallocation information
>> through later time except by explicitly putting zero entries into the
>> matrix.
>> >
>> > OK. Got it.
>> >
>> > Thanks,
>> >
>> > Fande,
>> >
>> >
>> >   Barry
>> >
>> > >
>> > >
>> > > Fande,
>> > >
>> > >
>> > > Il 25 Set 2017 7:01 PM, "Kong, Fande"  ha
>> scritto:
>> > > Hi Matt,
>> > >
>> > > Thanks for your reply.
>> > >
>> > > The sparsity pattern is slightly different from one Newton iteration
>> to another. We preallocate  enough memory at the beginning, and want to use
>> that memory for the following iterations.
>> > >
>> > > Does PETSc accutally free the preallocated (extra) memory? I so
>> cannot use it during the second iteration.
>> > >
>> > >
>> > >
>> > > Fande,
>> > >
>> > > On Mon, Sep 25, 2017 at 9:43 AM, Matthew Knepley 
>> wrote:
>> > > On Mon, Sep 25, 2017 at 11:39 AM, Kong, Fande 
>> wrote:
>> > > Hi All,
>> > >
>> > > A matrix is created with the right preallocation, and then
>> MatAssembly is called. The preallocation info will be removed. We insert
>> any values then, and will encounter an malloc error.
>> > >
>> > > My question is that we was intending to design like this way?
>> Attached simple example demonstrates what I am talking about.
>> > >
>> > > Yes, this is the intent. Why are you assembling? Could you use
>> MAT_ASSEMBLY_FLUSH?
>> > >
>> > >   Matt
>> > >
>> > >
>> > > Fande,
>> > >
>> > >
>> > >
>> > > --
>> > > 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
>> > >
>> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cse
>> .buffalo.edu_-7Eknepley_&d=DwIFAg&c=54IZrppPQZKX9mLzcGdPfFD1
>> hxrcB__aEkJFOKJFd00&r=DUUt3SRGI0_JgtNaS3udV68GRkgV4t
>> s7XKfj2opmiCY&m=U9L00IdHyC-4OTIJws8B4BeQTX1DBhNdzqB-NGUI3Es&
>> s=ZakQrYVOAFg6ShY9i0MSYHkgGWvqwRfACulWOiIX07o&e=
>> > >
>> > >
>>
>>
>

Re: [petsc-dev] *unwind* next branch

[Balay, Satish]

All (next users),

We had to unwind next again - so you would also have to do the delete
and recreate next again!

Sorry about that.

If you try to merge across the old and new next versions - you should
get a merge conflict on include/petscversion.h. [i.e this merge
conflict indicates you have to recreate next - and *not* resolve/push]


$ git fetch
$ git merge origin/next
Auto-merging include/petscversion.h
CONFLICT (content): Merge conflict in include/petscversion.h
Automatic merge failed; fix conflicts and then commit the result.

Satish

On Wed, 2017-09-27 at 02:01 +, Balay, Satish wrote:

> So *all git repo users* (if you have/use 'next' branch in your clone)
> - please do the following (in all your git clones):
> 
> git checkout master
> git fetch
> git branch -D next
> git checkout next
> 

Re: [petsc-dev] *unwind* next branch

[Balay, Satish]

Next is recreated (again) so these branches are no longer there.


Satish

On Wed, 2017-09-27 at 16:17 +0300, Lisandro Dalcin wrote:
> Also revert the merge of dalcinl/fix-dmplex-draw, I have to decline
> the PR and make a new one targeting maint.
> 
> On 27 September 2017 at 16:16, Lisandro Dalcin 
> wrote:
> > Satish, please revert the merge to next of my branch
> > dalcinl/add-tsrestart. This branch has fixes that should go to new
> > maint, but now I need to rework the commits, as they introduce new
> > APIs.
> > 

[petsc-dev] Getting credit for Contributors graph on github?

[Barry Smith]

  Just a reminder for developers who want to get credit for their PETSc commits.


> Begin forwarded message:
> 
> From: Jed Brown 
> Subject: Re: [petsc-maint] Contributors graph on github?
> Date: September 27, 2017 at 11:01:48 AM CDT
> To: Richard Tran Mills , PETSc-maint 
> 
> 
> Add the addresses to your account or add yourself to .mailmap.
> 
> Richard Tran Mills  writes:
> 
>> I hadn't seen this "contributors" graph before and found it interesting:
>> 
>> https://github.com/petsc/petsc/graphs/contributors
>> 
>> What would I need to do to get the various commits I've made over there
>> years to be associated with my 'rtmills' github account?
>> 
>> --Richard

Re: [petsc-dev] PetscSF in Fortran

[Adrian Croucher]

hi

On 28/09/17 04:18, Matthew Knepley wrote:


Okay, I think this should be easy to solve.

First a little bit about SF. There are two parts to the specification. 
You have the communication part, which maps
a certain location p on this process to another location q on another 
process. This might not change for you. The
second part just tells it how big the data array is (numRoots), which 
is the thing that the locations in the communication

part index into.

So my question is, where did you put the numbers for the points you 
added? Are they after all points, or only after the old cells?

I think you can easily create the new SF using the info from SFGetGraph().


I've had a closer look at how the SF stuff works (partly by viewing the 
point SF from the original DM) and I think I understand it now. There 
were two things I hadn't realised:


1) It looks like all DM points are always considered potential roots for 
leaves on another process, which is why it complained with an error 
message when the number of roots was less than pEnd . I don't think this 
really makes so much sense in the dual-porosity mesh case I'm working 
on, because the new points I'm adding are all 'inside' the original 
cells and have no possible connection with any other points. So they 
can't be roots for any off-process leaf points. But I guess it won't 
hurt to tell it that they can (by increasing the number of roots passed 
to PetscSFSetGraph so it's equal to the new pEnd).


2) Because I'm doing finite volume I had only thought about ghost cells, 
but the SF needs to include leaf points in other height strata as well 
(vertices, edges and faces). My new points in each stratum have been 
added after the partition ghost points, so the leaf cells won't have 
changed their point indices. However the leaf points in other strata 
will have been shifted (because of points added into preceding strata).



So I think I will need to use PetscSFSetGraph() after all, so I can 
increase the number of roots, update the leaf point indices, and also 
update the remote root index for each leaf (presumably I can use the 
original SF and PetscSFBcastBegin/ PetscSFBcastEnd to do that).


If you agree, then I will need working Fortran interfaces to the 
PetscSFGetGraph/ PetscSFSetGraph functions, which are missing at 
present. Are you able to add those easily?


Thanks,
Adrian

--
Dr Adrian Croucher
Senior Research Fellow
Department of Engineering Science
University of Auckland, New Zealand
email: a.crouc...@auckland.ac.nz
tel: +64 (0)9 923 4611

Re: [petsc-dev] PetscSF in Fortran

[Adrian Croucher]

hi


On 28/09/17 15:34, Adrian Croucher wrote:


So I think I will need to use PetscSFSetGraph() after all, so I can 
increase the number of roots, update the leaf point indices, and also 
update the remote root index for each leaf (presumably I can use the 
original SF and PetscSFBcastBegin/ PetscSFBcastEnd to do that).


If you agree, then I will need working Fortran interfaces to the 
PetscSFGetGraph/ PetscSFSetGraph functions, which are missing at 
present. Are you able to add those easily?


It looks like the Fortran interfaces for PetscSFBcastBegin/ 
PetscSFBcastEnd are missing as well. I would need those to make this work.


- Adrian

--
Dr Adrian Croucher
Senior Research Fellow
Department of Engineering Science
University of Auckland, New Zealand
email: a.crouc...@auckland.ac.nz
tel: +64 (0)9 923 4611