[petsc-users] PETSc, C++ and Eclipse
Matt Bockman
mdbockma at ucsd.edu
Wed Jul 27 19:49:30 CDT 2011
Hi Berend,
Here is the complete output of the build:
http://pastebin.com/Es4ms4EF
and by the 2nd to last line "collect2: ld returned 1 exit status" I believe
it is failing during the linking step. I'm not 100% sure though.
Thanks for your quick response and help. Please advise,
Matt
On Wed, Jul 27, 2011 at 5:39 PM, Berend van Wachem <
b.van-wachem at imperial.ac.uk> wrote:
> Dear Matt,
>
> Does it say this during the compiling? Or linking?
>
> If it says this during the compiling, it means that eclipse cannot find the
> PETSc header files. So, it must be the setting of the "Includes". You might
> want to "hard-code" the directory, just to make sure.
>
> It is indeed not completely straightforward - eclipse has so many options.
> But trust me - many of them you will really learn to appreciate over time.
>
> Kind regards,
>
> Berend.
>
>
>
> On 07/28/2011 01:34 AM, Matt Bockman wrote:
>
>> Thanks Berend for your thorough response,
>>
>> I have done what you have said but I still get the same error regarding
>> "undefined references to PetscInitialize" etc. It's like I didn't
>> include the petscksp.h file, but it's there. I even tried petsc.h to no
>> avail.
>>
>> I'm not sure what the compiler is referring to when it says "Undefined
>> references to ...". What I think this is is in the assembly code
>> generated by the compiler, there is a PetscInitialize symbol that isn't
>> found in the library. But I'm soooooooooo confused at this point :(. How
>> did you guys all learn how to compile this?
>>
>> Matt
>>
>> On Wed, Jul 27, 2011 at 4:46 PM, Berend van Wachem
>> <b.van-wachem at imperial.ac.uk <mailto:b.van-wachem at imperial.**ac.uk<b.van-wachem at imperial.ac.uk>>>
>> wrote:
>>
>> Dear Matt,
>>
>> I use Eclipse and have eclipse make the makefiles.
>> It is just a matter of indicating to eclipse where the PETSc
>> headers/libraries are to be found, so if you have a C project which
>> needs PETSc headers and libraries:
>>
>> To do this, click on your managed C project with the right sided
>> mouse button, select
>>
>> Properties -> C/C++ Build -> Settings
>>
>> Then you get a new window with on the right hand side the various
>> setting options.
>>
>> Select Includes, and add the required PETSc paths. In my case I have
>> added
>> ${PETSC_DIR}/include
>> ${PETSC_DIR}/${PETSC_ARCH}/__**include
>>
>> Then select "Libraries" under the header Linker
>> and you should set the Library search path:
>> ${PETSC_DIR}/${PETSC_ARCH}/lib
>>
>> and then the libraries, in my case:
>> m, petsc, stdc++, mpichxx, mpich, lapack, blas, gfortran, dl,
>> rt,gcc_s, pthread, X11
>> (you can find these easily in
>> $PETSC_DIR/$PETSC_ARCH/__**petscmachineinfo.h)
>>
>> The nice thing is that in eclipse you can easily switch between
>> Debug/Release code, traverse into the PETSc source code etc. It's
>> really a very productive tool with PETSc I've found.
>>
>> Let me know if you have any questions.
>>
>> Kind regards,
>>
>> Berend.
>>
>>
>>
>> On 07/27/2011 11:25 PM, Matt Bockman wrote:
>>
>> Thanks everyone for the help,
>>
>> I was able to compile a single example in Eclipse using the
>> provided
>> makefile. I'm pretty new to makefiles so it's a LOT to digest.
>> I'm now
>> manually creating a makefile for my project in Eclipse (and I've
>> set
>> Eclipse up to use a makefile that I create instead of automatically
>> generating one). Unfortunately this is a big pain but since I can't
>> figure out how to make Eclipse automatically include a few files
>> in the
>> makefile I don't really have any other choices :(.
>>
>> Thanks again,
>> Matt
>>
>> On Wed, Jul 27, 2011 at 1:43 PM, Mohammad Mirzadeh
>> <mirzadeh at gmail.com <mailto:mirzadeh at gmail.com>
>> <mailto:mirzadeh at gmail.com <mailto:mirzadeh at gmail.com>>> wrote:
>>
>> 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 <mailto:mdbockma at ucsd.edu>
>> <mailto:mdbockma at ucsd.edu <mailto: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 <mailto:balay at mcs.anl.gov>
>> <mailto:balay at mcs.anl.gov <mailto: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 <mailto:mirzadeh at gmail.com>
>> <mailto:mirzadeh at gmail.com <mailto: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 <mailto:mdbockma at ucsd.edu>
>> <mailto:mdbockma at ucsd.edu <mailto: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 <mailto:mirzadeh at gmail.com>
>> <mailto:mirzadeh at gmail.com <mailto: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 <mailto:mdbockma at ucsd.edu>
>> <mailto:mdbockma at ucsd.edu <mailto: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 <mailto:mirzadeh at gmail.com>
>> <mailto:mirzadeh at gmail.com <mailto: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 <mailto:bsmith at mcs.anl.gov>
>> <mailto:bsmith at mcs.anl.gov <mailto: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
>> <mailto:trl%7Bpetsc-dev at mcs.**anl.gov<trl%257Bpetsc-dev at mcs.anl.gov>
>> >
>> <mailto:trl%7Bpetsc-dev at mcs.__**anl.gov <http://anl.gov>
>> <mailto:trl%257Bpetsc-dev at mcs.**anl.gov<trl%25257Bpetsc-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
>> > >>>>>>
>> > >>>>>>
>> > >>>>>
>> > >>>>
>> > >>>
>> > >>
>> > >
>> >
>>
>>
>>
>>
>>
>>
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