[petsc-users] saving views as images
Theler German Guillermo
gtheler at cites-gss.com
Tue Mar 10 10:30:20 CDT 2015
On Sat, 2015-03-07 at 15:51 -0600, Barry Smith wrote:
> Did you follow the directions in the manual page for PetscDrawSetSave()?
> "Requires that PETSc be configured with the option --with-afterimage to save the images and ffmpeg must be in your path to make the movie"
Yes. For some reason configure does not find libAfterImage in Debian's
default location, but it works if I provide both with-afterimage-lib and
with-afterimage-include. Debian Jessie provides packages
libafterimage-dev and libafterimage0, both marked as version 2.2.12-3.
gtheler at blinky:~/libs/petsc-3.5.3$ ./configure
--with-afterimage-lib=/usr/lib/x86_64-linux-gnu/libAfterImage.so
--with-afterimage-include=/usr/include/libAfterImage
===============================================================================
Configuring PETSc to compile on your
system
===============================================================================
TESTING: alternateConfigureLibrary from
PETSc.packages.petsc4py(config/PETSc/packages/petsc4py.py:74)
Compilers:
C Compiler: mpicc -fPIC -Wall -Wwrite-strings
-Wno-strict-aliasing -Wno-unknown-pragmas -g3 -O0
C++ Compiler: mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing
-Wno-unknown-pragmas -g -O0 -fPIC
Fortran Compiler: mpif90 -fPIC -Wall -Wno-unused-variable
-ffree-line-length-0 -Wno-unused-dummy-argument -g -O0
Linkers:
Shared linker: mpicc -shared -fPIC -Wall -Wwrite-strings
-Wno-strict-aliasing -Wno-unknown-pragmas -g3 -O0
Dynamic linker: mpicc -shared -fPIC -Wall -Wwrite-strings
-Wno-strict-aliasing -Wno-unknown-pragmas -g3 -O0
make:
MPI:
Includes: -I/usr/include/mpich
BLAS/LAPACK: -llapack -lblas
cmake:
X:
Library: -lX11
pthread:
Library: -lpthread
ssl:
Library: -lssl -lcrypto
afterimage:
Includes: -I/usr/include/libAfterImage
Library: -Wl,-rpath,/usr/lib/x86_64-linux-gnu
-L/usr/lib/x86_64-linux-gnu -lAfterImage
valgrind:
Arch:
PETSc:
PETSC_ARCH: arch-linux2-c-debug
PETSC_DIR: /home/gtheler/libs/petsc-3.5.3
Clanguage: C
shared libraries: enabled
Scalar type: real
Precision: double
Memory alignment: 16
xxx=========================================================================xxx
Configure stage complete. Now build PETSc libraries with (gnumake
build):
make PETSC_DIR=/home/gtheler/libs/petsc-3.5.3
PETSC_ARCH=arch-linux2-c-debug all
xxx=========================================================================xxx
gtheler at blinky:~/libs/petsc-3.5.3$
Now, consider the attached source file (based on
mat/examples/tutorials/ex16.c). It does compile and gets linked to
libAfterImage:
gtheler at blinky:~/codigos/mat2img$ make
mpicc -c -o mat2img.o mat2img.c -Wall
-I/home/gtheler/libs/petsc-3.5.3/include
-I/home/gtheler/libs/petsc-3.5.3/arch-linux2-c-debug/include
-I/usr/include/libAfterImage -I/usr/include/mpich
mpicc -o mat2img mat2img.o
-Wl,-rpath,/home/gtheler/libs/petsc-3.5.3/arch-linux2-c-debug/lib
-L/home/gtheler/libs/petsc-3.5.3/arch-linux2-c-debug/lib -lpetsc
-llapack -lblas -Wl,-rpath,/usr/lib/x86_64-linux-gnu
-L/usr/lib/x86_64-linux-gnu -lAfterImage -lX11 -lpthread -lssl -lcrypto
-lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9
-L/usr/lib/gcc/x86_64-linux-gnu/4.9 -Wl,-rpath,/lib/x86_64-linux-gnu
-L/lib/x86_64-linux-gnu -lmpichf90 -lgfortran -lm -lgfortran -lm
-lquadmath -lm -lmpichcxx -lstdc++ -Wl,-rpath,/usr/lib/x86_64-linux-gnu
-L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9
-L/usr/lib/gcc/x86_64-linux-gnu/4.9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu
-L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu
-L/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu
-L/usr/lib/x86_64-linux-gnu -ldl -lmpich -lopa -lmpl -lrt -lcr -lpthread
-lgcc_s -ldl
gtheler at blinky:~/codigos/mat2img$ ldd mat2img | grep After
libAfterImage.so.0
=> /usr/lib/x86_64-linux-gnu/libAfterImage.so.0 (0x00007f95bc4b7000)
libAfterBase.so.0 => /usr/lib/x86_64-linux-gnu/libAfterBase.so.0
(0x00007f95b7ad4000)
gtheler at blinky:~/codigos/mat2img$
However, an empty directory called "test" is created when running the
code:
gtheler at blinky:~/codigos/mat2img$ ./mat2img -info
[0] PetscInitialize(): PETSc successfully started: number of processors
= 1
[0] PetscGetHostName(): Rejecting domainname, likely is NIS
blinky.(none)
[0] PetscInitialize(): Running on machine: blinky
[0] PetscCommDuplicate(): Duplicating a communicator 1140850688
-2080374784 max tags = 536870911
[0] PetscGetFileStat(): System call stat() succeeded on file matrix.bin
[0] PetscTestOwnership(): System call access() succeeded on file
matrix.bin
[0] PetscFileRetrieve(): Found file matrix.bin
[0] PetscGetFileStat(): System call stat() failed on file
matrix.bin.info
[0] PetscFileRetrieve(): Did not find file matrix.bin.info
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[0] MatAssemblyEnd_SeqAIJ(): Matrix size: 20 X 20; storage space: 0
unneeded,58 used
[0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is
0
[0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 3
[0] MatCheckCompressedRow(): Found the ratio (num_zerorows
0)/(num_localrows 20) < 0.6. Do not use CompressedRow routines.
[0] Mat_CheckInode(): Found 20 nodes out of 20 rows. Not using Inode
routines
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[0] PetscDrawSetUpColormap_Shared(): Successfully allocated colors
[0] PetscGetHostName(): Rejecting domainname, likely is NIS
blinky.(none)
[0] PetscPOpen(): Running command :rm -fr matrix matrix.m4v
[0] PetscGetHostName(): Rejecting domainname, likely is NIS
blinky.(none)
[0] PetscPOpen(): Running command :mkdir matrix
[0] PetscFinalize(): PetscFinalize() called
gtheler at blinky:~/codigos/mat2img$
I cannot find out what I am missing.
> So you have to install afterimage on your machine and then ./configure PETSc so it knows about it. If you have done all that and PETSc is being linked with the afterimage libraries then run your code with -info and send all the output; it may indicate why the images are not being saved.
>
> Barry
>
>
> > On Mar 7, 2015, at 3:38 PM, Theler German Guillermo <gtheler at cites-gss.com> wrote:
> >
> > Hi
> >
> > Last week I asked how to dump a matrix structure into an image and Barry kindly pointed me out the PetscDrawSetSave function. But I cannot figure out how to use it. So far, I can show my matrix structure into an X window with something like
> >
> > PetscViewerDrawOpen(PETSC_COMM_WORLD, PETSC_NULL, "R", 100, 100, size, size, &viewer);
> > MatView(milonga.R, viewer);
> >
> > I tried with this snippet of code but had no luck:
> >
> > PetscViewerDrawOpen(PETSC_COMM_WORLD, PETSC_NULL, "R", 100, 100, size, size, &viewer);
> > MatView(milonga.R, viewer);
> > PetscViewerDrawGetDraw(viewer, 0, &draw);
> > PetscDrawFlush(draw);
> > PetscDrawSetSave(draw, "test.gif", PETSC_FALSE);
> > PetscDrawSetSaveFinalImage(draw, "test2.gif");
> >
> > The result is that test.gif and test2.gif are created but they are empty directories.
> > What am I missing?
> >
> > --
> > jeremy
> >
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