[petsc-users] PETSc, C++ and Eclipse

[Mohammad Mirzadeh]

There two problems(I think) in this code.

1) there is no main function in your source code. If this is the only file
you are compiling, you need to change the function name to main.
2) linking should be done after object files are created. A simple g++ call
would first compile the main file and then link the object to the petsc lib
i.e

g++ -c -I($PETSC_INCLUDE) main.cpp
g++ -o main main.o $PETSC_LIBS

alternatively, you could do it in a single line if you like

g++ -o main -I($PETSC_INCLUDE) main.cpp $PETSC_LIBS

my point is you should link to petsc after compiling your own code. So
wherever in Eclipse that you are seting the parameters, make sure the
$PETSC_LIBS is in the linker option and not compiler.

Mohammad

On Wed, Jul 27, 2011 at 12:39 PM, Matt Bockman <mdbockma at ucsd.edu> wrote:

> I added the include directories from "make getincludedirs" and I added the
> line from "make getlinklib". Eclipse creates a gcc call as follows:
>
> /home/mdbockman/Documents/Research/codes/petsc/petsc-3.1-p8/linux-gnu-c-debug/bin/mpicc
> -I/home/mdbockman/Documents/Research/codes/petsc/petsc-3.1-p8/linux-gnu-c-debug/include
> -I/home/mdbockman/Documents/Research/codes/petsc/petsc-3.1-p8/include
> -I/home/mdbockman/Documents/Research/codes/petsc/petsc-3.1-p8/linux-gnu-c-debug/include
> -O0 -g3 -pg -p -Wall
> -Wl,-rpath,/home/mdbockman/Documents/Research/codes/petsc/petsc-3.1-p8/linux-gnu-c-debug/lib
> -Wl,-rpath,/home/mdbockman/Documents/Research/codes/petsc/petsc-3.1-p8/linux-gnu-c-debug/lib
> -L/home/mdbockman/Documents/Research/codes/petsc/petsc-3.1-p8/linux-gnu-c-debug/lib
> -lpetsc -lX11
> -Wl,-rpath,/home/mdbockman/Documents/Research/codes/petsc/petsc-3.1-p8/linux-gnu-c-debug/lib
> -L/home/mdbockman/Documents/Research/codes/petsc/petsc-3.1-p8/linux-gnu-c-debug/lib
> -lflapack -lfblas -lnsl -lrt -lm
> -L/home/mdbockman/Documents/Research/codes/petsc/petsc-3.1-p8/linux-gnu-c-debug/lib
> -L/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2
> -L/usr/lib/x86_64-linux-gnu -ldl -lmpich -lpthread -lrt -lgcc_s -lmpichf90
> -lgfortran -lm -lm -ldl -lmpich -lpthread -lrt -lgcc_s -ldl -MMD -MP
> -MF"SparseMatrixPetsc.d" -MT"SparseMatrixPetsc.d" -o"SparseMatrixPetsc.o"
> "../SparseMatrixPetsc.c
>
> And when it is compiled I get the following:
>
> http://pastebin.com/CbRzYcZj
>
> The source file which is being compiled is:
>
> http://pastebin.com/Q85hXvnS
>
> Please have a look. I'm not quite sure what I'm doing wrong but I feel like
> I'm getting closer and closer to the solution.
>
> Matt
>
>
> On Wed, Jul 27, 2011 at 11:52 AM, Satish Balay <balay at mcs.anl.gov> wrote:
>
>> use:
>> make getincludedirs
>>
>> Satish
>>
>> On Wed, 27 Jul 2011, Mohammad Mirzadeh wrote:
>>
>> > I applogize for the mistake; Include files are actually located
>> > in $PETSC_DIR/include
>> >
>> > On Wed, Jul 27, 2011 at 11:18 AM, Mohammad Mirzadeh <mirzadeh at gmail.com
>> >wrote:
>> >
>> > > Ok then. Now I don't have enough experience with Eclipse so
>> > > I apologize beforehand if you already know these/have tried them out.
>> If
>> > > not, hopefully they can be of help. I assume there should be a way in
>> > > Eclipse to give it the link lib directory. In plain makefile that's
>> just a
>> > > simple step when linking. To get all the needed linklibs for petsc,
>> you can
>> > > do
>> > >
>> > > make getlinklibs
>> > >
>> > > in the $PETSC_DIR. As for the needed include files, they are all
>> located
>> > > in
>> > >
>> > > $PETSC_DIR/$PETSC_ARCH/include
>> > >
>> > > Again, its easy to use these directories along with your makefile. I'm
>> not
>> > > sure about how you give them to Eclipse though. Hopefully this has
>> been
>> > > helpful.
>> > >
>> > > Best,
>> > > Mohammad
>> > >
>> > >
>> > >
>> > >
>> > > On Wed, Jul 27, 2011 at 10:52 AM, Matt Bockman <mdbockma at ucsd.edu>
>> wrote:
>> > >
>> > >> Just pointing it to the library would be sufficient.
>> > >>
>> > >> Matt
>> > >>
>> > >>
>> > >> On Wed, Jul 27, 2011 at 10:21 AM, Mohammad Mirzadeh <
>> mirzadeh at gmail.com>wrote:
>> > >>
>> > >>> So do you want to be able to compile PETSc with Eclipse or just
>> point it
>> > >>> to the library to use in your own applications?
>> > >>>
>> > >>>
>> > >>> On Wed, Jul 27, 2011 at 9:14 AM, Matt Bockman <mdbockma at ucsd.edu>
>> wrote:
>> > >>>
>> > >>>> Thanks Mohammad,
>> > >>>>
>> > >>>> I'll give that a shot. I use Qt Creator for some GUI applications
>> so I
>> > >>>> am familiar with it, but I've never tried doing a non-Qt project in
>> it. I'd
>> > >>>> really like to get Eclipse to work.
>> > >>>>
>> > >>>> Regarding the makefiles for eclipse. There are makefiles that it
>> > >>>> generates (which are for GNU make) but I think I can also manually
>> create my
>> > >>>> makefiles. After sleeping on it, it seems like this might be the
>> best
>> > >>>> option, unless I can figure out a way to configure eclipse to
>> include the
>> > >>>> conf/variables and conf/rules files in the makefile.
>> > >>>>
>> > >>>> Matt
>> > >>>>
>> > >>>>
>> > >>>> On Wed, Jul 27, 2011 at 12:01 AM, Mohammad Mirzadeh <
>> mirzadeh at gmail.com
>> > >>>> > wrote:
>> > >>>>
>> > >>>>> Although this is sort of orthogonal to what you do right now,
>> > >>>>> I recommend Qt Creator as an alternative IDE to Eclipse. It links
>> nicely
>> > >>>>> with PETSc(or any other library for that matter) and has excellent
>> c/c++
>> > >>>>> support.
>> > >>>>>
>> > >>>>> Mohammad
>> > >>>>>
>> > >>>>>
>> > >>>>> On Tue, Jul 26, 2011 at 7:22 PM, Barry Smith <bsmith at mcs.anl.gov
>> >wrote:
>> > >>>>>
>> > >>>>>>
>> > >>>>>>  There is a tiny bit of information in the PETSc users manual
>> about
>> > >>>>>> Eclipse:
>> > >>>>>>
>> > >>>>>> \section{Eclipse Users} \sindex{eclipse}
>> > >>>>>>
>> > >>>>>> If you are interested in developing code that uses PETSc from
>> Eclipse
>> > >>>>>> or developing PETSc in Eclipse and have knowledge of how to do
>> indexing and
>> > >>>>>> build libraries in Eclipse please contact us at \
>> > >>>>>> trl{petsc-dev at mcs.anl.gov}.
>> > >>>>>>
>> > >>>>>> To make PETSc an Eclipse package
>> > >>>>>> \begin{itemize}
>> > >>>>>> \item Install the Mecurial plugin for Eclipse and then import the
>> > >>>>>> PETSc repository to Eclipse.
>> > >>>>>> \item elected New->Convert to C/C++ project and selected shared
>> > >>>>>> library. After this point you can perform searchs in the code.
>> > >>>>>> \end{itemize}
>> > >>>>>>
>> > >>>>>>  A PETSc user has provided the following steps to build an
>> Eclipse
>> > >>>>>> index for PETSc that can be used with their own code without
>> compiling PETSc
>> > >>>>>> source into their project.
>> > >>>>>> \begin{itemize}
>> > >>>>>> \item In the user project source directory, create a symlink to
>> the
>> > >>>>>> petsc/src directory.
>> > >>>>>> \item Refresh the project explorer in Eclipse, so the new symlink
>> is
>> > >>>>>> followed.
>> > >>>>>> \item Right-click on the project in the project explorer, and
>> choose
>> > >>>>>> "Index -> Rebuild". The index should now be build.
>> > >>>>>> \item Right-click on the PETSc symlink in the project explorer,
>> and
>> > >>>>>> choose "Exclude from build..." to make sure Eclipse does not try
>> to compile
>> > >>>>>> PETSc with the project.
>> > >>>>>> \end{itemize}
>> > >>>>>>
>> > >>>>>> We'd love to have someone figure out how to do it right and
>> include
>> > >>>>>> that information.
>> > >>>>>>
>> > >>>>>>   Barry
>> > >>>>>>
>> > >>>>>> On Jul 26, 2011, at 4:32 PM, Matt Bockman wrote:
>> > >>>>>>
>> > >>>>>> > Has anyone gotten PETSc to work w/Eclipse? Eclipse nicely
>> generates
>> > >>>>>> all my makefiles for me for my current project (which is written
>> in C++).
>> > >>>>>> I'd like to link PETSc w/my application but I'm not sure how to
>> do this.
>> > >>>>>> >
>> > >>>>>> > Suggestions?
>> > >>>>>> >
>> > >>>>>> > Thanks,
>> > >>>>>> > Matt
>> > >>>>>>
>> > >>>>>>
>> > >>>>>
>> > >>>>
>> > >>>
>> > >>
>> > >
>> >
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110727/22dbf711/attachment-0001.htm>