Re: [petsc-dev] Is master broken?

[Smith, Barry F. via petsc-dev]

  Unrelated question: Surely on a 30 million dollar machine it can do better 
than --download-fblaslapack ?

> On Aug 1, 2019, at 11:18 AM, Mark Adams  wrote:
> 
> 12:10 master= ~/petsc-master$ ls arch-summit-dbg64-pgi-cuda
> bin  externalpackages  include  lib  obj  share  tests
> 
> 12:11 master= ~/petsc-master$ tar cvfz ../tt.tarz 
> arch-summit-dbg64-pgi-cuda/include/petscpkg_version.h arch-summure.log
> arch-summit-dbg64-pgi-cuda/include/petscpkg_version.h
> arch-summit-dbg64-pgi-cuda/lib/petsc/conf/configure.log
> 
> 
> 
> 
> On Thu, Aug 1, 2019 at 12:08 PM Mark Adams  wrote:
> 
> 
> On Thu, Aug 1, 2019 at 10:30 AM Smith, Barry F.  wrote:
> 
>   Send
> 
> ls arch-linux2-c-debug/include/
> 
> That is not my arch name. It is something like arch-summit-dbg64-pgi-cuda 
> 
>  arch-linux2-c-debug/include/petscpkg_version.h
> 
> and configure.log
> 
> 
> 
> > On Aug 1, 2019, at 5:23 AM, Mark Adams  wrote:
> > 
> > I get the same error with a fresh clone of master.
> > 
> > On Thu, Aug 1, 2019 at 6:03 AM Mark Adams  wrote:
> > Tried again after deleting the arch dirs and still have it.
> > This is my branch that just merged master. I will try with just master.
> > Thanks,
> > 
> > On Thu, Aug 1, 2019 at 1:36 AM Smith, Barry F.  wrote:
> > 
> >   It is generated automatically and put in 
> > arch-linux2-c-debug/include/petscpkg_version.h  this include file is 
> > included at top of the "bad" source  file crashes so in theory everything 
> > is in order check that arch-linux2-c-debug/include/petscpkg_version.h 
> > contains PETSC_PKG_CUDA_VERSION_GE and similar macros. If not send 
> > configure.lo
> > 
> > check what is in arch-linux2-c-debug/include/petscpkg_version.h it nothing 
> > or broken send configure.lo
> > 
> > 
> >   Barry
> > 
> > 
> > 
> > > On Jul 31, 2019, at 9:28 PM, Mark Adams via petsc-dev 
> > >  wrote:
> > > 
> > > I am seeing this when I pull master into my branch:
> > > 
> > > "/autofs/nccs-svm1_home1/adams/petsc/src/mat/impls/dense/seq/cuda/densecuda.cu"
> > >   , line 243: error: function call is not allowed in a constant
> > >   expression
> > >   #if PETSC_PKG_CUDA_VERSION_GE(10,1,0)
> > > 
> > > and I see that this macro does not seem to be defined:
> > > 
> > > 22:24 master= ~/Codes/petsc$ git grep PETSC_PKG_CUDA_VERSION_GE
> > > src/mat/impls/dense/seq/cuda/densecuda.cu:#if 
> > > PETSC_PKG_CUDA_VERSION_GE(10,1,0)
> > 
> 
> 

Re: [petsc-dev] Is master broken?

[Smith, Barry F. via petsc-dev]

  Please run with the branch barry/2019-09-01/robustify-version-check and send 
configure.log


> On Aug 1, 2019, at 11:18 AM, Mark Adams  wrote:
> 
> 12:10 master= ~/petsc-master$ ls arch-summit-dbg64-pgi-cuda
> bin  externalpackages  include  lib  obj  share  tests
> 
> 12:11 master= ~/petsc-master$ tar cvfz ../tt.tarz 
> arch-summit-dbg64-pgi-cuda/include/petscpkg_version.h arch-summure.log
> arch-summit-dbg64-pgi-cuda/include/petscpkg_version.h
> arch-summit-dbg64-pgi-cuda/lib/petsc/conf/configure.log
> 
> 
> 
> 
> On Thu, Aug 1, 2019 at 12:08 PM Mark Adams  wrote:
> 
> 
> On Thu, Aug 1, 2019 at 10:30 AM Smith, Barry F.  wrote:
> 
>   Send
> 
> ls arch-linux2-c-debug/include/
> 
> That is not my arch name. It is something like arch-summit-dbg64-pgi-cuda 
> 
>  arch-linux2-c-debug/include/petscpkg_version.h
> 
> and configure.log
> 
> 
> 
> > On Aug 1, 2019, at 5:23 AM, Mark Adams  wrote:
> > 
> > I get the same error with a fresh clone of master.
> > 
> > On Thu, Aug 1, 2019 at 6:03 AM Mark Adams  wrote:
> > Tried again after deleting the arch dirs and still have it.
> > This is my branch that just merged master. I will try with just master.
> > Thanks,
> > 
> > On Thu, Aug 1, 2019 at 1:36 AM Smith, Barry F.  wrote:
> > 
> >   It is generated automatically and put in 
> > arch-linux2-c-debug/include/petscpkg_version.h  this include file is 
> > included at top of the "bad" source  file crashes so in theory everything 
> > is in order check that arch-linux2-c-debug/include/petscpkg_version.h 
> > contains PETSC_PKG_CUDA_VERSION_GE and similar macros. If not send 
> > configure.lo
> > 
> > check what is in arch-linux2-c-debug/include/petscpkg_version.h it nothing 
> > or broken send configure.lo
> > 
> > 
> >   Barry
> > 
> > 
> > 
> > > On Jul 31, 2019, at 9:28 PM, Mark Adams via petsc-dev 
> > >  wrote:
> > > 
> > > I am seeing this when I pull master into my branch:
> > > 
> > > "/autofs/nccs-svm1_home1/adams/petsc/src/mat/impls/dense/seq/cuda/densecuda.cu"
> > >   , line 243: error: function call is not allowed in a constant
> > >   expression
> > >   #if PETSC_PKG_CUDA_VERSION_GE(10,1,0)
> > > 
> > > and I see that this macro does not seem to be defined:
> > > 
> > > 22:24 master= ~/Codes/petsc$ git grep PETSC_PKG_CUDA_VERSION_GE
> > > src/mat/impls/dense/seq/cuda/densecuda.cu:#if 
> > > PETSC_PKG_CUDA_VERSION_GE(10,1,0)
> > 
> 
> 

Re: [petsc-dev] Is master broken?

[Smith, Barry F. via petsc-dev]

  Mark,

Thanks, that was not expected to work, I was just verifying the exact cause 
of the problem and it was what I was guessing.

I believe I have fixed it. Please pull that branch again and let me know if 
it works. If it does we'll do rush testing and get it into master.

 Thanks

 Barry


> On Aug 1, 2019, at 11:08 AM, Mark Adams  wrote:
> 
> 
> 
> On Thu, Aug 1, 2019 at 10:30 AM Smith, Barry F.  wrote:
> 
>   Send
> 
> ls arch-linux2-c-debug/include/
> 
> That is not my arch name. It is something like arch-summit-dbg64-pgi-cuda 
> 
>  arch-linux2-c-debug/include/petscpkg_version.h
> 
> and configure.log
> 
> 
> 
> > On Aug 1, 2019, at 5:23 AM, Mark Adams  wrote:
> > 
> > I get the same error with a fresh clone of master.
> > 
> > On Thu, Aug 1, 2019 at 6:03 AM Mark Adams  wrote:
> > Tried again after deleting the arch dirs and still have it.
> > This is my branch that just merged master. I will try with just master.
> > Thanks,
> > 
> > On Thu, Aug 1, 2019 at 1:36 AM Smith, Barry F.  wrote:
> > 
> >   It is generated automatically and put in 
> > arch-linux2-c-debug/include/petscpkg_version.h  this include file is 
> > included at top of the "bad" source  file crashes so in theory everything 
> > is in order check that arch-linux2-c-debug/include/petscpkg_version.h 
> > contains PETSC_PKG_CUDA_VERSION_GE and similar macros. If not send 
> > configure.lo
> > 
> > check what is in arch-linux2-c-debug/include/petscpkg_version.h it nothing 
> > or broken send configure.lo
> > 
> > 
> >   Barry
> > 
> > 
> > 
> > > On Jul 31, 2019, at 9:28 PM, Mark Adams via petsc-dev 
> > >  wrote:
> > > 
> > > I am seeing this when I pull master into my branch:
> > > 
> > > "/autofs/nccs-svm1_home1/adams/petsc/src/mat/impls/dense/seq/cuda/densecuda.cu"
> > >   , line 243: error: function call is not allowed in a constant
> > >   expression
> > >   #if PETSC_PKG_CUDA_VERSION_GE(10,1,0)
> > > 
> > > and I see that this macro does not seem to be defined:
> > > 
> > > 22:24 master= ~/Codes/petsc$ git grep PETSC_PKG_CUDA_VERSION_GE
> > > src/mat/impls/dense/seq/cuda/densecuda.cu:#if 
> > > PETSC_PKG_CUDA_VERSION_GE(10,1,0)
> > 
> 

Re: [petsc-dev] Is master broken?

[Smith, Barry F. via petsc-dev]

  Yes, these are bugs in Stefano's work that got into master because we didn't 
have comprehensive testing. There are two branches in the PR list you can 
cherry pick that will fix this problem. Sorry about this. We're trying to get 
them into master as quickly as possible but 

   Barry


> On Aug 2, 2019, at 8:39 AM, Mark Adams  wrote:
> 
> closer,
> 
> On Fri, Aug 2, 2019 at 9:13 AM Smith, Barry F.  wrote:
> 
>   Mark,
> 
> Thanks, that was not expected to work, I was just verifying the exact 
> cause of the problem and it was what I was guessing.
> 
> I believe I have fixed it. Please pull that branch again and let me know 
> if it works. If it does we'll do rush testing and get it into master.
> 
>  Thanks
> 
>  Barry
> 
> 
> > On Aug 1, 2019, at 11:08 AM, Mark Adams  wrote:
> > 
> > 
> > 
> > On Thu, Aug 1, 2019 at 10:30 AM Smith, Barry F.  wrote:
> > 
> >   Send
> > 
> > ls arch-linux2-c-debug/include/
> > 
> > That is not my arch name. It is something like arch-summit-dbg64-pgi-cuda 
> > 
> >  arch-linux2-c-debug/include/petscpkg_version.h
> > 
> > and configure.log
> > 
> > 
> > 
> > > On Aug 1, 2019, at 5:23 AM, Mark Adams  wrote:
> > > 
> > > I get the same error with a fresh clone of master.
> > > 
> > > On Thu, Aug 1, 2019 at 6:03 AM Mark Adams  wrote:
> > > Tried again after deleting the arch dirs and still have it.
> > > This is my branch that just merged master. I will try with just master.
> > > Thanks,
> > > 
> > > On Thu, Aug 1, 2019 at 1:36 AM Smith, Barry F.  wrote:
> > > 
> > >   It is generated automatically and put in 
> > > arch-linux2-c-debug/include/petscpkg_version.h  this include file is 
> > > included at top of the "bad" source  file crashes so in theory everything 
> > > is in order check that arch-linux2-c-debug/include/petscpkg_version.h 
> > > contains PETSC_PKG_CUDA_VERSION_GE and similar macros. If not send 
> > > configure.lo
> > > 
> > > check what is in arch-linux2-c-debug/include/petscpkg_version.h it 
> > > nothing or broken send configure.lo
> > > 
> > > 
> > >   Barry
> > > 
> > > 
> > > 
> > > > On Jul 31, 2019, at 9:28 PM, Mark Adams via petsc-dev 
> > > >  wrote:
> > > > 
> > > > I am seeing this when I pull master into my branch:
> > > > 
> > > > "/autofs/nccs-svm1_home1/adams/petsc/src/mat/impls/dense/seq/cuda/densecuda.cu"
> > > >   , line 243: error: function call is not allowed in a constant
> > > >   expression
> > > >   #if PETSC_PKG_CUDA_VERSION_GE(10,1,0)
> > > > 
> > > > and I see that this macro does not seem to be defined:
> > > > 
> > > > 22:24 master= ~/Codes/petsc$ git grep PETSC_PKG_CUDA_VERSION_GE
> > > > src/mat/impls/dense/seq/cuda/densecuda.cu:#if 
> > > > PETSC_PKG_CUDA_VERSION_GE(10,1,0)
> > > 
> > 
> 
> 

Re: [petsc-dev] Is master broken?

[Karl Rupp via petsc-dev]

FYI: The two branches are currently testing in `next-tmp` and are likely 
to be merged to master in ~5 hours.


Best regards,
Karli


On 8/2/19 4:53 PM, Smith, Barry F. via petsc-dev wrote:


   Yes, these are bugs in Stefano's work that got into master because we didn't 
have comprehensive testing. There are two branches in the PR list you can 
cherry pick that will fix this problem. Sorry about this. We're trying to get 
them into master as quickly as possible but 

Barry



On Aug 2, 2019, at 8:39 AM, Mark Adams  wrote:

closer,

On Fri, Aug 2, 2019 at 9:13 AM Smith, Barry F.  wrote:

   Mark,

 Thanks, that was not expected to work, I was just verifying the exact 
cause of the problem and it was what I was guessing.

 I believe I have fixed it. Please pull that branch again and let me know 
if it works. If it does we'll do rush testing and get it into master.

  Thanks

  Barry



On Aug 1, 2019, at 11:08 AM, Mark Adams  wrote:



On Thu, Aug 1, 2019 at 10:30 AM Smith, Barry F.  wrote:

   Send

ls arch-linux2-c-debug/include/

That is not my arch name. It is something like arch-summit-dbg64-pgi-cuda

  arch-linux2-c-debug/include/petscpkg_version.h

and configure.log




On Aug 1, 2019, at 5:23 AM, Mark Adams  wrote:

I get the same error with a fresh clone of master.

On Thu, Aug 1, 2019 at 6:03 AM Mark Adams  wrote:
Tried again after deleting the arch dirs and still have it.
This is my branch that just merged master. I will try with just master.
Thanks,

On Thu, Aug 1, 2019 at 1:36 AM Smith, Barry F.  wrote:

   It is generated automatically and put in 
arch-linux2-c-debug/include/petscpkg_version.h  this include file is included at top of 
the "bad" source  file crashes so in theory everything is in order check that 
arch-linux2-c-debug/include/petscpkg_version.h contains PETSC_PKG_CUDA_VERSION_GE and 
similar macros. If not send configure.lo

check what is in arch-linux2-c-debug/include/petscpkg_version.h it nothing or 
broken send configure.lo


   Barry




On Jul 31, 2019, at 9:28 PM, Mark Adams via petsc-dev  
wrote:

I am seeing this when I pull master into my branch:

"/autofs/nccs-svm1_home1/adams/petsc/src/mat/impls/dense/seq/cuda/densecuda.cu"
   , line 243: error: function call is not allowed in a constant
   expression
   #if PETSC_PKG_CUDA_VERSION_GE(10,1,0)

and I see that this macro does not seem to be defined:

22:24 master= ~/Codes/petsc$ git grep PETSC_PKG_CUDA_VERSION_GE
src/mat/impls/dense/seq/cuda/densecuda.cu:#if PETSC_PKG_CUDA_VERSION_GE(10,1,0)

Re: [petsc-dev] Is master broken?

[Mark Adams via petsc-dev]

I picked these two into Barry's branch and it built.

I would like to get them into my cuda branch. Should I just pick them? And
not worry about Barry's branch. Or will that not work.

On Fri, Aug 2, 2019 at 12:03 PM Karl Rupp  wrote:

> FYI: The two branches are currently testing in `next-tmp` and are likely
> to be merged to master in ~5 hours.
>
> Best regards,
> Karli
>
>
> On 8/2/19 4:53 PM, Smith, Barry F. via petsc-dev wrote:
> >
> >Yes, these are bugs in Stefano's work that got into master because we
> didn't have comprehensive testing. There are two branches in the PR list
> you can cherry pick that will fix this problem. Sorry about this. We're
> trying to get them into master as quickly as possible but 
> >
> > Barry
> >
> >
> >> On Aug 2, 2019, at 8:39 AM, Mark Adams  wrote:
> >>
> >> closer,
> >>
> >> On Fri, Aug 2, 2019 at 9:13 AM Smith, Barry F. 
> wrote:
> >>
> >>Mark,
> >>
> >>  Thanks, that was not expected to work, I was just verifying the
> exact cause of the problem and it was what I was guessing.
> >>
> >>  I believe I have fixed it. Please pull that branch again and let
> me know if it works. If it does we'll do rush testing and get it into
> master.
> >>
> >>   Thanks
> >>
> >>   Barry
> >>
> >>
> >>> On Aug 1, 2019, at 11:08 AM, Mark Adams  wrote:
> >>>
> >>>
> >>>
> >>> On Thu, Aug 1, 2019 at 10:30 AM Smith, Barry F. 
> wrote:
> >>>
> >>>Send
> >>>
> >>> ls arch-linux2-c-debug/include/
> >>>
> >>> That is not my arch name. It is something like
> arch-summit-dbg64-pgi-cuda
> >>>
> >>>   arch-linux2-c-debug/include/petscpkg_version.h
> >>>
> >>> and configure.log
> >>>
> >>>
> >>>
>  On Aug 1, 2019, at 5:23 AM, Mark Adams  wrote:
> 
>  I get the same error with a fresh clone of master.
> 
>  On Thu, Aug 1, 2019 at 6:03 AM Mark Adams  wrote:
>  Tried again after deleting the arch dirs and still have it.
>  This is my branch that just merged master. I will try with just
> master.
>  Thanks,
> 
>  On Thu, Aug 1, 2019 at 1:36 AM Smith, Barry F. 
> wrote:
> 
> It is generated automatically and put in
> arch-linux2-c-debug/include/petscpkg_version.h  this include file is
> included at top of the "bad" source  file crashes so in theory everything
> is in order check that arch-linux2-c-debug/include/petscpkg_version.h
> contains PETSC_PKG_CUDA_VERSION_GE and similar macros. If not send
> configure.lo
> 
>  check what is in arch-linux2-c-debug/include/petscpkg_version.h it
> nothing or broken send configure.lo
> 
> 
> Barry
> 
> 
> 
> > On Jul 31, 2019, at 9:28 PM, Mark Adams via petsc-dev <
> petsc-dev@mcs.anl.gov> wrote:
> >
> > I am seeing this when I pull master into my branch:
> >
> > "/autofs/nccs-svm1_home1/adams/petsc/src/mat/impls/dense/seq/cuda/
> densecuda.cu"
> >, line 243: error: function call is not allowed in a
> constant
> >expression
> >#if PETSC_PKG_CUDA_VERSION_GE(10,1,0)
> >
> > and I see that this macro does not seem to be defined:
> >
> > 22:24 master= ~/Codes/petsc$ git grep PETSC_PKG_CUDA_VERSION_GE
> > src/mat/impls/dense/seq/cuda/densecuda.cu:#if
> PETSC_PKG_CUDA_VERSION_GE(10,1,0)
> 
> >>>
> >>
> >> 
> >
>

Re: [petsc-dev] Is master broken?

[Karl Rupp via petsc-dev]

You should be able to just cherry-pick the commits from Barry's branch 
as well as the two other branches.




On 8/2/19 8:13 PM, Mark Adams wrote:

I picked these two into Barry's branch and it built.

I would like to get them into my cuda branch. Should I just pick them? 
And not worry about Barry's branch. Or will that not work.


On Fri, Aug 2, 2019 at 12:03 PM Karl Rupp > wrote:


FYI: The two branches are currently testing in `next-tmp` and are
likely
to be merged to master in ~5 hours.

Best regards,
Karli


On 8/2/19 4:53 PM, Smith, Barry F. via petsc-dev wrote:
 >
 >    Yes, these are bugs in Stefano's work that got into master
because we didn't have comprehensive testing. There are two branches
in the PR list you can cherry pick that will fix this problem. Sorry
about this. We're trying to get them into master as quickly as
possible but 
 >
 >     Barry
 >
 >
 >> On Aug 2, 2019, at 8:39 AM, Mark Adams mailto:mfad...@lbl.gov>> wrote:
 >>
 >> closer,
 >>
 >> On Fri, Aug 2, 2019 at 9:13 AM Smith, Barry F.
mailto:bsm...@mcs.anl.gov>> wrote:
 >>
 >>    Mark,
 >>
 >>      Thanks, that was not expected to work, I was just verifying
the exact cause of the problem and it was what I was guessing.
 >>
 >>      I believe I have fixed it. Please pull that branch again
and let me know if it works. If it does we'll do rush testing and
get it into master.
 >>
 >>       Thanks
 >>
 >>       Barry
 >>
 >>
 >>> On Aug 1, 2019, at 11:08 AM, Mark Adams mailto:mfad...@lbl.gov>> wrote:
 >>>
 >>>
 >>>
 >>> On Thu, Aug 1, 2019 at 10:30 AM Smith, Barry F.
mailto:bsm...@mcs.anl.gov>> wrote:
 >>>
 >>>    Send
 >>>
 >>> ls arch-linux2-c-debug/include/
 >>>
 >>> That is not my arch name. It is something like
arch-summit-dbg64-pgi-cuda
 >>>
 >>>   arch-linux2-c-debug/include/petscpkg_version.h
 >>>
 >>> and configure.log
 >>>
 >>>
 >>>
  On Aug 1, 2019, at 5:23 AM, Mark Adams mailto:mfad...@lbl.gov>> wrote:
 
  I get the same error with a fresh clone of master.
 
  On Thu, Aug 1, 2019 at 6:03 AM Mark Adams mailto:mfad...@lbl.gov>> wrote:
  Tried again after deleting the arch dirs and still have it.
  This is my branch that just merged master. I will try with
just master.
  Thanks,
 
  On Thu, Aug 1, 2019 at 1:36 AM Smith, Barry F.
mailto:bsm...@mcs.anl.gov>> wrote:
 
     It is generated automatically and put in
arch-linux2-c-debug/include/petscpkg_version.h  this include file is
included at top of the "bad" source  file crashes so in theory
everything is in order check that
arch-linux2-c-debug/include/petscpkg_version.h contains
PETSC_PKG_CUDA_VERSION_GE and similar macros. If not send configure.lo
 
  check what is in
arch-linux2-c-debug/include/petscpkg_version.h it nothing or broken
send configure.lo
 
 
     Barry
 
 
 
 > On Jul 31, 2019, at 9:28 PM, Mark Adams via petsc-dev
mailto:petsc-dev@mcs.anl.gov>> wrote:
 >
 > I am seeing this when I pull master into my branch:
 >
 >

"/autofs/nccs-svm1_home1/adams/petsc/src/mat/impls/dense/seq/cuda/densecuda.cu
"
 >            , line 243: error: function call is not allowed in
a constant
 >            expression
 >    #if PETSC_PKG_CUDA_VERSION_GE(10,1,0)
 >
 > and I see that this macro does not seem to be defined:
 >
 > 22:24 master= ~/Codes/petsc$ git grep PETSC_PKG_CUDA_VERSION_GE
 > src/mat/impls/dense/seq/cuda/densecuda.cu:#if
PETSC_PKG_CUDA_VERSION_GE(10,1,0)
 
 >>>
 >>
 >> 
 >

Re: [petsc-dev] DMDAGlobalToNatural errors with Ubuntu:latest; gcc 7 & Open MPI 2.1.1

[Zhang, Junchao via petsc-dev]

Some updates for this OpenMPI bug:
 1) It appears to OpenMPI 2.1.x when configured with --enable-heterogeneous, 
which is not a default option and is not commonly used. But Ubuntu somehow used 
that.
 2) OpenMPI fixed it in 3.x
 3) It was reported to Ubuntu two years ago but is still unassigned. 
https://bugs.launchpad.net/ubuntu/+source/openmpi/+bug/1731938. A user's 
comment from last year, "We have just spent today hunting down a user bug 
report for Xyce (which uses Trilinos, and its Zoltan library) that turn out to 
be exactly this issue "

--Junchao Zhang


On Wed, Jul 31, 2019 at 2:17 PM Junchao Zhang 
mailto:jczh...@mcs.anl.gov>> wrote:
Hi, Fabian,
I found it is an OpenMPI bug w.r.t self-to-self MPI_Send/Recv using 
MPI_ANY_SOURCE for message matching. OpenMPI does not put correct value in recv 
buffer.
I have a workaround 
jczhang/fix-ubuntu-openmpi-anysource.
 I tested with your petsc_ex.F90 and $PETSC_DIR/src/dm/examples/tests/ex14.  
The majority of valgrind errors disappeared. A few left are in ompi_mpi_init 
and we can ignore them.
I filed a bug report to OpenMPI 
https://www.mail-archive.com/users@lists.open-mpi.org//msg33383.html and hope 
they can fix it in Ubuntu.
Thanks.

--Junchao Zhang


On Tue, Jul 30, 2019 at 9:47 AM Fabian.Jakub via petsc-dev 
mailto:petsc-dev@mcs.anl.gov>> wrote:
Dear Petsc Team,
Our cluster recently switched to Ubuntu 18.04 which has gcc 7.4 and
(Open MPI) 2.1.1 - with this I ended up with segfault and valgrind
errors in DMDAGlobalToNatural.

This is evident in a minimal fortran example such as the attached
example petsc_ex.F90

with the following error:

==22616== Conditional jump or move depends on uninitialised value(s)
==22616==at 0x4FA5CDB: PetscTrMallocDefault (mtr.c:185)
==22616==by 0x4FA4DAC: PetscMallocA (mal.c:413)
==22616==by 0x5090E94: VecScatterSetUp_SF (vscatsf.c:652)
==22616==by 0x50A1104: VecScatterSetUp (vscatfce.c:209)
==22616==by 0x509EE3B: VecScatterCreate (vscreate.c:280)
==22616==by 0x577B48B: DMDAGlobalToNatural_Create (dagtol.c:108)
==22616==by 0x577BB6D: DMDAGlobalToNaturalBegin (dagtol.c:155)
==22616==by 0x5798446: VecView_MPI_DA (gr2.c:720)
==22616==by 0x51BC7D8: VecView (vector.c:574)
==22616==by 0x4F4ECA1: PetscObjectView (destroy.c:90)
==22616==by 0x4F4F05E: PetscObjectViewFromOptions (destroy.c:126)

and consequently wrong results in the natural vec


I was looking at the fortran example if I did forget something but I can
also see the same error, i.e. not being valgrind clean, in pure C - PETSc:

cd $PETSC_DIR/src/dm/examples/tests && make ex14 && mpirun
--allow-run-as-root -np 2 valgrind ./ex14

I then tried various docker/podman linux distributions to make sure that
my setup is clean and to me it seems that this error is confined to the
particular gcc version 7.4 and (Open MPI) 2.1.1 from the ubuntu:latest repo.

I tried other images from dockerhub including

gcc:7.4.0 :: where I could neither install openmpi nor mpich through
apt, however works with --download-openmpi and --download-mpich

ubuntu:rolling(19.04) <-- work

debian:latest & :stable <-- works

ubuntu:latest(18.04) <-- fails in case of openmpi, but works with mpich
or with petsc-configure --download-openmpi or --download-mpich


Is this error with (Open MPI) 2.1.1 a known issue? In the meantime, I
guess I'll go with a custom mpi install but given that ubuntu:latest is
widely spread, do you think there is an easy solution to the error?

I guess you are not eager to delve into this issue with old mpi versions
but in case you find some spare time, maybe you find the root cause
and/or a workaround.

Many thanks,
Fabian

Re: [petsc-dev] Is master broken?

[Mark Adams via petsc-dev]

I have been cherry-picking, etc, branch mark/gamg-fix-viennacl-rebased and
it is very messed up. Can someone please update this branch when all the
fixes are settled down? eg, I am seeing dozens of modified files that I
don't know anything about and I certainly don't want to put in a PR for
them.

I also seem to lose my pinToCPU method for cuda matrices. I don't
understand how that conflicted with anyone else but it did.

Thanks,
Mark

Re: [petsc-dev] Is master broken?

[Balay, Satish via petsc-dev]

I've attempted to rebase this branch over latest master - and pushed
my changes to branch mark/gamg-fix-viennacl-rebased-v2

You might want to check each of your commits in this branch to see if
they are ok. I had to add one extra commit - to make it match 'merge
of mark/gamg-fix-viennacl-rebased and master'.

This branch has 21 commits. I think its best if you can collapse them
into reasonable chunks of changes. [presumably a single commit for all
the changes is not the correct thing here. But the current set of 21
commits are all over the place]

If you are able to migrate to this branch - its best to delete the old
one [i.e origin/mark/gamg-fix-viennacl-rebased]

Satish

On Fri, 2 Aug 2019, Mark Adams via petsc-dev wrote:

> I have been cherry-picking, etc, branch mark/gamg-fix-viennacl-rebased and
> it is very messed up. Can someone please update this branch when all the
> fixes are settled down? eg, I am seeing dozens of modified files that I
> don't know anything about and I certainly don't want to put in a PR for
> them.
> 
> I also seem to lose my pinToCPU method for cuda matrices. I don't
> understand how that conflicted with anyone else but it did.
> 
> Thanks,
> Mark
> 

Re: [petsc-dev] SeqSBAIJ v. MPISBAIJ

[Pierre Jolivet via petsc-dev]

I don’t know if this is related, but the following example triggers a [0]PETSC ERROR: Argument out of range[0]PETSC ERROR: New nonzero at (0,1) caused a mallocWhile everything works OK if I switch from MPISBAIJ to MPIBAIJ.Thanks,PierreOn 2 Aug 2019, at 1:49 AM, Smith, Barry F.  wrote: Yes it is a bug, working on it now. On Aug 1, 2019, at 9:13 AM, Pierre Jolivet via petsc-dev  wrote:Hello,The attached example is a little confusing for me.How come I don’t get the same matrix out-of-the-box?For me, the “correct” matrix is the SeqSBAIJ, how can I get MatMPISBAIJSetPreallocationCSR to assemble the same matrix?Do I have to resort to first assembling SeqSBAIJ matrices and then calling MatCreateMPIMatConcatenateSeqMat if I don’t want to play around with my input arrays?Thanks,Pierre

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