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On 09/07/2011 04:53 PM, <a class="moz-txt-link-abbreviated" href="mailto:petsc-users-request@mcs.anl.gov">petsc-users-request@mcs.anl.gov</a> wrote:
<blockquote
cite="mid:mailman.10240.1315403586.6420.petsc-users@mcs.anl.gov"
type="cite">
<pre wrap="">Send petsc-users mailing list submissions to
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or, via email, send a message with subject or body 'help' to
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Today's Topics:
1. Re: compilation with mumps on Mac OS 10.6.8 (Kyunghoon Lee)
2. Build Petsc with single precision (Sravya Tirukkovalur)
3. Re: Build Petsc with single precision (Satish Balay)
4. Re: Still no luck (Satish Balay)
5. Coloring of a parallel matrix (Kostas Kontzialis)
6. Re: Coloring of a parallel matrix (Jed Brown)
7. Re: Coloring of a parallel matrix (Barry Smith)
8. petsc with slepc (Micheal Lysaght)
----------------------------------------------------------------------
Message: 1
Date: Wed, 7 Sep 2011 12:04:38 +0800
From: Kyunghoon Lee <a class="moz-txt-link-rfc2396E" href="mailto:aeronova.mailing@gmail.com"><aeronova.mailing@gmail.com></a>
Subject: Re: [petsc-users] compilation with mumps on Mac OS 10.6.8
To: PETSc users list <a class="moz-txt-link-rfc2396E" href="mailto:petsc-users@mcs.anl.gov"><petsc-users@mcs.anl.gov></a>
Message-ID:
<a class="moz-txt-link-rfc2396E" href="mailto:CA+ZVpt9npcK+xJg1-Sbs__BvweVV_9tEp48ooc_BYza+m5G5gg@mail.gmail.com"><CA+ZVpt9npcK+xJg1-Sbs__BvweVV_9tEp48ooc_BYza+m5G5gg@mail.gmail.com></a>
Content-Type: text/plain; charset="windows-1252"
Thanks for the help. Now I finished the installation successfully. :)
K. Lee.
On Wed, Sep 7, 2011 at 11:49 AM, Barry Smith <a class="moz-txt-link-rfc2396E" href="mailto:bsmith@mcs.anl.gov"><bsmith@mcs.anl.gov></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">
On Sep 6, 2011, at 10:41 PM, Kyunghoon Lee wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Barry,
Thanks for the reply. I did install g95 through macports. (I could not
</pre>
</blockquote>
<pre wrap="">find gfortran.) I wonder g95 can do the job for me.
</pre>
<blockquote type="cite">
<pre wrap="">
</pre>
</blockquote>
<pre wrap=""> g95 might work, give it a try. BTW: on Macs you don't need to provide
blas/lapack with --download; Apple provides them on the system.
</pre>
<blockquote type="cite">
<pre wrap="">Re SuperLU_Dist, all I know is I need mumps to deal with complex numbers.
</pre>
</blockquote>
<pre wrap="">
SuperLU_Dist can also be used with complex numbers (at least with
PETSc-dev/petsc-3.2)
</pre>
<blockquote type="cite">
<pre wrap="">
K. Lee.
On Wed, Sep 7, 2011 at 11:21 AM, Barry Smith <a class="moz-txt-link-rfc2396E" href="mailto:bsmith@mcs.anl.gov"><bsmith@mcs.anl.gov></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">p.s.
I do not need to compile petsc for FORTRAN.
</pre>
</blockquote>
<pre wrap="">
Sadly you do because the packages MUMPS uses are all Fortran.
So you will need a real Fortran compiler (perhaps gfortran) and you
</pre>
</blockquote>
<pre wrap="">will also need --download-blacs and you cannot use --download-c-blas-lapack
with scalapack.
</pre>
<blockquote type="cite">
<pre wrap="">
Note you can use SuperLU_Dist instead of MUMPS without a Fortran
</pre>
</blockquote>
<pre wrap="">compiler.
</pre>
<blockquote type="cite">
<pre wrap="">
Barry
On Sep 6, 2011, at 10:17 PM, Kyunghoon Lee wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hello all,
I need to compile petsc with mumps. First I tried
./configure
</pre>
</blockquote>
</blockquote>
<pre wrap="">--prefix=/Users/aeronova/Development/local/lib64/petsc/petsc-3.1-p8
--download-c-blas-lapack=1 ?download-parmetis=1 --download-scalapack=1
--download-mumps=1
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">
but I got the following message:
Fortran error! mpif.h could not be located at: []
So I included "-download-mpich=1," then I got the following:
Should request f-blas-lapack, not --download-c-blas-lapack=yes since
</pre>
</blockquote>
</blockquote>
<pre wrap="">you have a fortran compiler?
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">
After that, I tried several options with/without
</pre>
</blockquote>
</blockquote>
<pre wrap="">--download-f-blas-lapack or --download-mpich=1, but none of them worked out.
I'd appreciate it if someone can help me with this compilation problem with
mumps.
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">
Regards,
K. Lee.
p.s.
I do not need to compile petsc for FORTRAN.
</pre>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
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Message: 2
Date: Tue, 6 Sep 2011 23:05:26 -0400
From: Sravya Tirukkovalur <a class="moz-txt-link-rfc2396E" href="mailto:stirukkovalur@rnet-tech.com"><stirukkovalur@rnet-tech.com></a>
Subject: [petsc-users] Build Petsc with single precision
To: <a class="moz-txt-link-abbreviated" href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>
Message-ID:
<a class="moz-txt-link-rfc2396E" href="mailto:CABjTB1gOBgs4AuF7MFiEuM+_WohTdqOCh=zBS9rWFS_iOzB=Bg@mail.gmail.com"><CABjTB1gOBgs4AuF7MFiEuM+_WohTdqOCh=zBS9rWFS_iOzB=Bg@mail.gmail.com></a>
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Hi,
I am trying to build petsc with single precision. The options I am using
are:
./configure options --download-f-blas-lapack=1 --with-x=0 --with-debugging=1
--CFLAGS="-O3 -g -ggdb" --FFLAGS="-O3 -g" --with-hdf5=1 --download-hdf5=1
--with-batch=0 --known-mpi-shared-libraries=no --with-cuda=1
--with-cudac="nvcc -m64" --with-cusp=1 --with-thrust=1 PETSC_ARCH=SOMETHING
Configuration step is being completed successfully. And while doing $make
all, it compiles a few source files and prints an error message which says
cannot build petsc with this options, contact the mailing list.
Did anyone face a similar problem while building petsc with single precision
or has anyone successfully built it?
Thanks
</pre>
</blockquote>
<br>
Barry,<br>
<br>
I have the following code for implementing the setting up snes and
the numerical evaluation of the jacobian:<br>
<br>
<br>
ierr = jacobian_matrix_nz_pattern(sys);<br>
CHKERRQ(ierr);<br>
<br>
ierr = MatCreateMPIBAIJ(sys.comm, sys.num->nbq[sys.con->n],<br>
sys.ldof, sys.ldof, sys.gdof, sys.gdof,
PETSC_NULL,<br>
sys.idxm, PETSC_NULL, sys.idxn, &sys.P);<br>
CHKERRQ(ierr);<br>
<br>
ierr = SNESCreate(sys.comm, &sys.snes);<br>
CHKERRQ(ierr);<br>
<br>
ierr = SNESSetFunction(sys.snes, sys.gres[0],
base_residual_implicit, &sys);<br>
CHKERRQ(ierr);<br>
<br>
ierr = MatCreateSNESMF(sys.snes, &sys.J);<br>
CHKERRQ(ierr);<br>
<br>
ierr = MatMFFDSetFromOptions(sys.J);<br>
CHKERRQ(ierr);<br>
<br>
<br>
ierr = jacobian_diff_numerical(sys, &sys.P);<br>
CHKERRQ(ierr);<br>
<br>
ISColoring iscoloring;<br>
<br>
MatFDColoring fdcoloring;<br>
<br>
MatGetColoring(sys.P, MATCOLORING_SL, &iscoloring);<br>
<br>
MatFDColoringCreate(sys.P, iscoloring, &fdcoloring);<br>
ISColoringDestroy(iscoloring);<br>
MatFDColoringSetFromOptions(fdcoloring);<br>
<br>
ierr = SNESSetJacobian(sys.snes, sys.J, sys.P,<br>
SNESDefaultComputeJacobianColor, fdcoloring);<br>
CHKERRQ(ierr);<br>
<br>
<br>
As you can see I'm using a matrix free algorithm, However, when I
run the code with with the -snes_mf_operator option I get on return
the following error:<br>
<br>
Timestep 0: dt = 0.008, T = 0, Res[rho] = 0, Res[rhou] = 0,
Res[rhov] = 0, Res[E] = 0, CFL = 0.177549<br>
<br>
/*********************Stage 1 of SSPIRK (3,4)******************/<br>
<br>
0 SNES Function norm 2.755099585674e+01 <br>
[4]PETSC ERROR: --------------------- Error Message
------------------------------------<br>
[4]PETSC ERROR: Object is in wrong state!<br>
[4]PETSC ERROR: Must call MatFDColoringSetFunction()!<br>
<br>
I haven't use the MatFDColoringSetFunction. But when I try to put it
I read on the help page:<br>
<br>
Notes: This function is usually used automatically by <a
href="http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.1/docs/manualpages/SNES/SNES.html#SNES">SNES</a>
or <a
href="http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.1/docs/manualpages/TS/TS.html#TS">TS</a>
(when one uses <a
href="http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.1/docs/manualpages/SNES/SNESSetJacobian.html#SNESSetJacobian">SNESSetJacobian</a>()
with the argument
<a
href="http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.1/docs/manualpages/SNES/SNESDefaultComputeJacobianColor.html#SNESDefaultComputeJacobianColor">SNESDefaultComputeJacobianColor</a>()
or <a
href="http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.1/docs/manualpages/TS/TSSetRHSJacobian.html#TSSetRHSJacobian">TSSetRHSJacobian</a>()
with the argument <a
href="http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.1/docs/manualpages/TS/TSDefaultComputeJacobianColor.html#TSDefaultComputeJacobianColor">TSDefaultComputeJacobianColor</a>())
and only needs to be used
by someone computing a matrix via coloring directly by calling <a
href="http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.1/docs/manualpages/MatFD/MatFDColoringApply.html#MatFDColoringApply">MatFDColoringApply</a>()
<br>
<br>
and furthermore I cannot figure out what the arguments are for the
(*f) function. <br>
<br>
Any help?<br>
<br>
Kostas<br>
<br>
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