<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Sat, Apr 2, 2016 at 8:18 AM, Rongliang Chen <span dir="ltr"><<a href="mailto:rl.chen@siat.ac.cn" target="_blank">rl.chen@siat.ac.cn</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>On 04/02/2016 09:08 PM, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Sat, Apr 2, 2016 at 8:03 AM,
Rongliang Chen <span dir="ltr"><<a href="mailto:rl.chen@siat.ac.cn" target="_blank">rl.chen@siat.ac.cn</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Matt,<br>
<br>
Many thanks for your helps. I will change the way that
I used for the boundary condition setup.<br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>I will note that we (Barry, Jed, Mark, and I at least)
have adopted the view that by and large</div>
<div><br>
</div>
<div> a) global vectors are for solvers</div>
<div><br>
</div>
<div> b) local vectors are for assembly</div>
<div><br>
</div>
<div>For me, that means local vectors have ghost values and
boundary conditions, but global vectors</div>
<div>have them removed. This is how SNES ex12 and ex62 are
organized.</div>
<div><br>
</div>
</div>
</div>
</div>
</blockquote>
Does this means that if I want to use the local vector (obtained by
DMGlobalToLocalBegin and DMGlobalToLocalEnd), I need to reset the
boundary conditions for the local vector before I use it?<br></div></blockquote><div><br></div><div>Yes, that is how PETSc is setup internally.</div><div><br></div><div> 1) The solver generates a new initial guess</div><div><br></div><div> 2) PETSc calls DMGlobalToLocal(). In Plex, this adds in ghosts and BC</div><div><br></div><div> 3) The local guess is passed to FormFunctionLocal()</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">
Best regards,<br>
Rongliang<br>
<br>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div> Best regards,<br>
Rongliang
<div>
<div><br>
<br>
<br>
On 04/02/2016 08:49 PM, Matthew Knepley wrote:<br>
</div>
</div>
</div>
<div>
<div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Sat, Apr 2, 2016
at 7:46 AM, Rongliang Chen <span dir="ltr"><<a href="mailto:rl.chen@siat.ac.cn" target="_blank">rl.chen@siat.ac.cn</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>But I need to setup the boundary
conditions for the solution vector X,
which is in FormMassTimeStep(). <br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>Make a copy. The solution vector is
used in the solver, and you have no idea
exactly what it is doing with it.</div>
<div>Or put your boundary conditions in the
initial guess to SNESSolve().</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div> Best regards,<br>
Rongliang<br>
<br>
<br>
On 04/02/2016 08:37 PM, Matthew
Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Sat,
Apr 2, 2016 at 7:37 AM,
Rongliang Chen <span dir="ltr"><<a href="mailto:rl.chen@siat.ac.cn" target="_blank">rl.chen@siat.ac.cn</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Matt,<br>
<br>
How to check in the
explicit method? This kind
of errors does come out in
the explicit method. <br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>You said "that is I use the
explicit method with the same
function FormMassTimeStep(),
this error disappeared"</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div> What do you mean "You
should never be changing
the input guess"? Do you
mean that the value of the
solution vector X in
FormFunction are not
allowed to be changed by
the user defined function?<br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>Yes.</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div> Best regards,<br>
Rongliang<br>
<br>
On 04/02/2016 08:19 PM,
Matthew Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On
Sat, Apr 2, 2016 at
7:15 AM, Rongliang
Chen <span dir="ltr"><<a href="mailto:rl.chen@siat.ac.cn" target="_blank">rl.chen@siat.ac.cn</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Matt,<br>
<br>
That's right.
The
FormMassTimeStep()
is inside the
FormFunction()
and I call the
FormFunction()
in this way:
SNESSetFunction(user->snes,
algebra->f,
FormFunction,
(void*)user).
How can I know
the X is
read-only or
not? <br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>Exactly that
you get this error
message, and it
should be in the
documentation.</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div> If I do
not use the
SNESSolve,
that is I use
the explicit
method with
the same
function
FormMassTimeStep(),
this error
disappeared.
So it seems
that the
SNESSolve
locked the
vector X. <br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>Then we need to
put that check in
the explicit
method as well.
You should never
be changing the
input guess.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div> Best
regards,<br>
Rongliang<br>
<br>
On 04/02/2016
07:59 PM,
Matthew
Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On
Sat, Apr 2,
2016 at 6:49
AM, Rongliang
Chen <span dir="ltr"><<a href="mailto:rl.chen@siat.ac.cn" target="_blank">rl.chen@siat.ac.cn</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Dave,<br>
<br>
I did not call
any
VecGetArrary
and
VecGetArraryRead
in function
FormMassTimeStepFunction().<br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>It looks
like you have
a function
FormMassTimeStep()
inside your
FormFunction()
method. This</div>
<div>has an
argument X,
the solution
guess, which
is read-only.
However, you
are calling
DMLocalToGlobal()</div>
<div>using
that X, which
is illegal,
since its
read-only. Is
this right?</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div> Best
regards,<br>
Rongliang<br>
<br>
On 04/02/2016
06:20 PM, Dave
May wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr"><br>
<div class="gmail_extra"><br>
<div class="gmail_quote">On
2 April 2016
at 11:18,
Rongliang Chen
<span dir="ltr"><<a href="mailto:rl.chen@siat.ac.cn" target="_blank">rl.chen@siat.ac.cn</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">Hi
Shri,<br>
<br>
Thanks for
your reply.<br>
<br>
Do you mean
that I need to
change the
VecGetArrary()
in
/home/rlchen/soft/petsc-3.6.3/src/dm/interface/dm.c
to
VecGetArrayRead()?<br>
</blockquote>
<div><br>
</div>
<div>No - you
should change
it in your
function
FormMassTimeStepFunction().<br>
</div>
<div>The input
vector x
passed into
SNESComputeFunction()
is read only.<br>
</div>
<div> <br>
<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<br>
I tried it and
I got a
warning when I
make the
petsc:<br>
<br>
/home/rlchen/soft/petsc-3.6.3/src/dm/interface/dm.c:
In function
‘DMLocalToGlobalBegin’:<br>
/home/rlchen/soft/petsc-3.6.3/src/dm/interface/dm.c:1913:5:
warning:
passing
argument 2 of
‘VecGetArrayRead’
from
incompatible
pointer type
[enabled by
default]<br>
In file
included from
/home/rlchen/soft/petsc-3.6.3/include/petscmat.h:6:0,<br>
from
/home/rlchen/soft/petsc-3.6.3/include/petscdm.h:6,<br>
from
/home/rlchen/soft/petsc-3.6.3/include/petsc/private/dmimpl.h:6,<br>
from
/home/rlchen/soft/petsc-3.6.3/src/dm/interface/dm.c:1:<br>
/home/rlchen/soft/petsc-3.6.3/include/petscvec.h:420:29:
note: expected
‘const
PetscScalar
**’ but
argument is of
type
‘PetscScalar
**’<br>
<br>
Best regards,<br>
Rongliang<br>
<br>
---------------------<br>
Rongliang
Chen, PhD<br>
Associate
Professor<br>
<br>
Laboratory for
Engineering
and Scientific
Computing<br>
Shenzhen
Institutes of
Advanced
Technology<br>
Chinese
Academy of
Sciences<br>
Address: 1068
Xueyuan
Avenue,
Shenzhen
University
Town,
Shenzhen,
Guangdong
(518055), P.
R. China<br>
E-mail: <a href="mailto:rl.chen@siat.ac.cn" target="_blank">rl.chen@siat.ac.cn</a><br>
Phone: <a href="tel:%2B86-755-86392312" value="+8675586392312" target="_blank">+86-755-86392312</a>
<div>
<div><br>
<br>
On 04/02/2016
05:03 PM,
Abhyankar,
Shrirang G.
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
Use
VecGetArrayRead
instead of
VecGetArray<br>
<br>
<a href="http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecGetArray" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecGetArray</a><br>
Read.html<br>
<br>
<br>
Shri<br>
<br>
-----Original
Message-----<br>
From:
Rongliang Chen
<<a href="mailto:rl.chen@siat.ac.cn" target="_blank">rl.chen@siat.ac.cn</a>><br>
Date:
Saturday,
April 2, 2016
at 3:51 AM<br>
To: PETSc
users list
<<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>>,
"<a href="mailto:rongliang.chan@gmail.com" target="_blank">rongliang.chan@gmail.com</a>"<br>
<<a href="mailto:rongliang.chan@gmail.com" target="_blank">rongliang.chan@gmail.com</a>><br>
Subject:
[petsc-users]
Vec is locked
read only<br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
Dear All,<br>
<br>
My code got
the following
error
messages, but
the code works
well for<br>
the petsc
optimized
version
(--with-debugging=0).
Anyone can
tell me how<br>
to fix this
problem?<br>
<br>
Best regards,<br>
Rongliang<br>
<br>
<br>
[0]PETSC
ERROR:
---------------------
Error Message<br>
--------------------------------------------------------------<br>
[0]PETSC
ERROR: Object
is in wrong
state<br>
[0]PETSC
ERROR: Vec is
locked read
only, argument
# 1<br>
[0]PETSC
ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a><br>
for trouble
shooting.<br>
[0]PETSC
ERROR: Petsc
Release
Version 3.6.3,
Dec, 03, 2015<br>
[0]PETSC
ERROR: ./Nwtun
on a
64bit-debug
named rlchen
by rlchen Sat
Apr<br>
2 15:40:32
2016<br>
[0]PETSC
ERROR:
Configure
options
--download-blacs
--download-scalapack<br>
--download-metis
--download-parmetis
--download-exodusii<br>
--download-netcdf
--download-hdf5<br>
--with-mpi-dir=/home/rlchen/soft/Program/mpich2-shared<br>
--with-debugging=1
--download-fblaslapack
--download-chaco<br>
[0]PETSC
ERROR: #1
VecGetArray()
line 1646 in<br>
/home/rlchen/soft/petsc-3.6.3/src/vec/vec/interface/rvector.c<br>
[0]PETSC
ERROR: #2
DMLocalToGlobalBegin()
line 1913 in<br>
/home/rlchen/soft/petsc-3.6.3/src/dm/interface/dm.c<br>
[0]PETSC
ERROR: #3
FormMassTimeStepFunction()
line 191 in<br>
/home/rlchen/soft/3D_fluid/FiniteVolumeMethod/PETScCodes/codefor3.6/SetupF<br>
unctions.c<br>
[0]PETSC
ERROR: #4
FormFunction()
line 46 in<br>
/home/rlchen/soft/3D_fluid/FiniteVolumeMethod/PETScCodes/codefor3.6/SetupF<br>
unctions.c<br>
[0]PETSC
ERROR: #5
SNESComputeFunction()
line 2067 in<br>
/home/rlchen/soft/petsc-3.6.3/src/snes/interface/snes.c<br>
[0]PETSC
ERROR: #6
SNESSolve_NEWTONLS()
line 184 in<br>
/home/rlchen/soft/petsc-3.6.3/src/snes/impls/ls/ls.c<br>
[0]PETSC
ERROR: #7
SNESSolve()
line 3906 in<br>
/home/rlchen/soft/petsc-3.6.3/src/snes/interface/snes.c<br>
[0]PETSC
ERROR: #8
SolveTimeDependent()
line 843 in<br>
/home/rlchen/soft/3D_fluid/FiniteVolumeMethod/PETScCodes/codefor3.6/Nwtun.<br>
c<br>
[0]PETSC
ERROR: #9
main() line
452 in<br>
/home/rlchen/soft/3D_fluid/FiniteVolumeMethod/PETScCodes/codefor3.6/Nwtun.<br>
c<br>
<br>
<br>
</blockquote>
<br>
</blockquote>
<br>
<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
<br>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<span><font color="#888888">
<span><font color="#888888">
<div><br>
</div>
-- <br>
<div>What most
experimenters
take for
granted before
they begin
their
experiments is
infinitely
more
interesting
than any
results to
which their
experiments
lead.<br>
-- Norbert
Wiener</div>
</font></span></font></span></div>
<span><font color="#888888">
</font></span></div>
<span><font color="#888888">
</font></span></blockquote>
<span><font color="#888888">
<br>
</font></span></div>
<span><font color="#888888">
</font></span></blockquote>
<span><font color="#888888">
</font></span></div>
<span><font color="#888888"> <br>
<br clear="all">
<span><font color="#888888">
<div><br>
</div>
-- <br>
<div>What most
experimenters
take for
granted before
they begin
their
experiments is
infinitely
more
interesting
than any
results to
which their
experiments
lead.<br>
-- Norbert
Wiener</div>
</font></span></font></span></div>
<span><font color="#888888"> </font></span></div>
<span><font color="#888888"> </font></span></blockquote>
<span><font color="#888888">
<br>
</font></span></div>
<span><font color="#888888"> </font></span></blockquote>
<span><font color="#888888"> </font></span></div>
<span><font color="#888888"> <br>
<br clear="all">
<div><br>
</div>
-- <br>
<div>What most experimenters
take for granted before they
begin their experiments is
infinitely more interesting
than any results to which
their experiments lead.<br>
-- Norbert Wiener</div>
</font></span></div>
</div>
</blockquote>
<br>
</div>
</blockquote>
</div>
<br>
<br clear="all"><span class="HOEnZb"><font color="#888888">
<div><br>
</div>
-- <br>
<div>What most experimenters take for granted
before they begin their experiments is
infinitely more interesting than any results
to which their experiments lead.<br>
-- Norbert Wiener</div>
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></blockquote><span class="HOEnZb"><font color="#888888">
<br>
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></blockquote><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div>What most experimenters take for
granted before they begin their experiments is infinitely
more interesting than any results to which their experiments
lead.<br>
-- Norbert Wiener</div>
</font></span></div>
</div>
</blockquote>
<br>
</div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div>
</div></div>