[petsc-users] petsc-users Digest, Vol 33, Issue 13
Kostas Kontzialis
ckontzialis at lycos.com
Wed Sep 7 11:41:16 CDT 2011
On 09/07/2011 04:53 PM, petsc-users-request at mcs.anl.gov wrote:
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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<aeronova.mailing at gmail.com>
> Subject: Re: [petsc-users] compilation with mumps on Mac OS 10.6.8
> To: PETSc users list<petsc-users at mcs.anl.gov>
> Message-ID:
> <CA+ZVpt9npcK+xJg1-Sbs__BvweVV_9tEp48ooc_BYza+m5G5gg at mail.gmail.com>
> 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<bsmith at mcs.anl.gov> wrote:
>
>> On Sep 6, 2011, at 10:41 PM, Kyunghoon Lee wrote:
>>
>>> Hi Barry,
>>>
>>> Thanks for the reply. I did install g95 through macports. (I could not
>> find gfortran.) I wonder g95 can do the job for me.
>> 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.
>>
>>
>>
>>> Re SuperLU_Dist, all I know is I need mumps to deal with complex numbers.
>> SuperLU_Dist can also be used with complex numbers (at least with
>> PETSc-dev/petsc-3.2)
>>
>>> K. Lee.
>>>
>>> On Wed, Sep 7, 2011 at 11:21 AM, Barry Smith<bsmith at mcs.anl.gov> wrote:
>>>
>>>> p.s.
>>>> I do not need to compile petsc for FORTRAN.
>>> Sadly you do because the packages MUMPS uses are all Fortran.
>>>
>>> So you will need a real Fortran compiler (perhaps gfortran) and you
>> will also need --download-blacs and you cannot use --download-c-blas-lapack
>> with scalapack.
>>> Note you can use SuperLU_Dist instead of MUMPS without a Fortran
>> compiler.
>>> Barry
>>>
>>> On Sep 6, 2011, at 10:17 PM, Kyunghoon Lee wrote:
>>>
>>>> Hello all,
>>>>
>>>> I need to compile petsc with mumps. First I tried
>>>>
>>>> ./configure
>> --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
>>>> 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
>> you have a fortran compiler?
>>>> After that, I tried several options with/without
>> --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.
>>>> Regards,
>>>> K. Lee.
>>>>
>>>> p.s.
>>>> I do not need to compile petsc for FORTRAN.
>>>>
>>>
>>
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> ------------------------------
>
> Message: 2
> Date: Tue, 6 Sep 2011 23:05:26 -0400
> From: Sravya Tirukkovalur<stirukkovalur at rnet-tech.com>
> Subject: [petsc-users] Build Petsc with single precision
> To: petsc-users at mcs.anl.gov
> Message-ID:
> <CABjTB1gOBgs4AuF7MFiEuM+_WohTdqOCh=zBS9rWFS_iOzB=Bg at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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
>
Barry,
I have the following code for implementing the setting up snes and the
numerical evaluation of the jacobian:
ierr = jacobian_matrix_nz_pattern(sys);
CHKERRQ(ierr);
ierr = MatCreateMPIBAIJ(sys.comm, sys.num->nbq[sys.con->n],
sys.ldof, sys.ldof, sys.gdof, sys.gdof, PETSC_NULL,
sys.idxm, PETSC_NULL, sys.idxn, &sys.P);
CHKERRQ(ierr);
ierr = SNESCreate(sys.comm, &sys.snes);
CHKERRQ(ierr);
ierr = SNESSetFunction(sys.snes, sys.gres[0],
base_residual_implicit, &sys);
CHKERRQ(ierr);
ierr = MatCreateSNESMF(sys.snes, &sys.J);
CHKERRQ(ierr);
ierr = MatMFFDSetFromOptions(sys.J);
CHKERRQ(ierr);
ierr = jacobian_diff_numerical(sys, &sys.P);
CHKERRQ(ierr);
ISColoring iscoloring;
MatFDColoring fdcoloring;
MatGetColoring(sys.P, MATCOLORING_SL, &iscoloring);
MatFDColoringCreate(sys.P, iscoloring, &fdcoloring);
ISColoringDestroy(iscoloring);
MatFDColoringSetFromOptions(fdcoloring);
ierr = SNESSetJacobian(sys.snes, sys.J, sys.P,
SNESDefaultComputeJacobianColor, fdcoloring);
CHKERRQ(ierr);
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:
Timestep 0: dt = 0.008, T = 0, Res[rho] = 0, Res[rhou] = 0, Res[rhov]
= 0, Res[E] = 0, CFL = 0.177549
/*********************Stage 1 of SSPIRK (3,4)******************/
0 SNES Function norm 2.755099585674e+01
[4]PETSC ERROR: --------------------- Error Message
------------------------------------
[4]PETSC ERROR: Object is in wrong state!
[4]PETSC ERROR: Must call MatFDColoringSetFunction()!
I haven't use the MatFDColoringSetFunction. But when I try to put it I
read on the help page:
Notes: This function is usually used automatically by SNES
<http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.1/docs/manualpages/SNES/SNES.html#SNES>
or TS
<http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.1/docs/manualpages/TS/TS.html#TS>
(when one uses SNESSetJacobian
<http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.1/docs/manualpages/SNES/SNESSetJacobian.html#SNESSetJacobian>()
with the argument SNESDefaultComputeJacobianColor
<http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.1/docs/manualpages/SNES/SNESDefaultComputeJacobianColor.html#SNESDefaultComputeJacobianColor>()
or TSSetRHSJacobian
<http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.1/docs/manualpages/TS/TSSetRHSJacobian.html#TSSetRHSJacobian>()
with the argument TSDefaultComputeJacobianColor
<http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.1/docs/manualpages/TS/TSDefaultComputeJacobianColor.html#TSDefaultComputeJacobianColor>())
and only needs to be used by someone computing a matrix via coloring
directly by calling MatFDColoringApply
<http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.1/docs/manualpages/MatFD/MatFDColoringApply.html#MatFDColoringApply>()
and furthermore I cannot figure out what the arguments are for the (*f)
function.
Any help?
Kostas
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