[petsc-users] Including user made shared library in makefile.

Anthony Vergottis a.vergottis at ucl.ac.uk
Mon Oct 21 15:33:04 CDT 2013 

When running ./pro the program works as expected, but when the .so file is
recompiled ./pro does not show any change. Change occurs only when the
makefile is rerun. When moving ${LIBS} before ${PETSC_LIB} there is no
change as well.


On 21 October 2013 21:19, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>    Please always make sure to include the mailing list in your list of
> emails. Otherwise it just goes to me, and I don't know what I am talking
> about.
>
>
>    Barry
>
> On Oct 21, 2013, at 3:18 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
> >
> >   What happens when you run
> >
> > ./pro
> >
> > ?
> >
> >  Try putting ${LIBS}  before the ${PETSC_LIB}  in the makefile
> >
> >   Barry
> >
> >
> > On Oct 21, 2013, at 3:10 PM, Anthony Vergottis <a.vergottis at ucl.ac.uk>
> wrote:
> >
> >> OK this is the makefile,
> >>
> >> include ${PETSC_DIR}/conf/variables
> >> include ${PETSC_DIR}/conf/rules
> >> LIBS=-L/home/adonis/Dropbox/ParallelSolver
> -Wl,-rpath,/home/adonis/Dropbox/ParallelSolver -lpro
> >>
> >>
> >> pro: pro.o 2D_CBS_Solver.o
> >>            ${CLINKER} -o pro pro.o 2D_CBS_Solver.o ${PETSC_LIB} ${LIBS}
> >>            ${RM} pro.o 2D_CBS_Solver.o
> >>
> >>
> >> The terminal output (in bold are my commands),
> >>
> >> adonis at LinuxBox:~/Dropbox/ParallelSolver$ g++ -shared -fPIC -o
> libpro.so 2D_CBS_Solver.cpp
> >> adonis at LinuxBox:~/Dropbox/ParallelSolver$ ls -l
> >> total 84
> >> -rw-rw-r-- 1 adonis adonis   144 Oct 21 20:56 2D_CBS_Solver.cpp
> >> -rw-rw-r-- 1 adonis adonis   144 Oct 21 20:50 2D_CBS_Solver.cpp~
> >> -rw-rw-r-- 1 adonis adonis   429 Oct 21 19:13 2D_CBS_Solver.h
> >> drwxrwxr-x 2 adonis adonis  4096 Oct 18 14:31 include
> >> -rwxrwxr-x 1 adonis adonis  7968 Oct 21 21:02 libpro.so
> >> -rw------- 1 adonis adonis   291 Oct 21 21:01 Makefile
> >> -rw------- 1 adonis adonis   291 Oct 21 21:01 Makefile~
> >> -rwxrwxr-x 1 adonis adonis 42896 Oct 21 21:02 pro
> >> -rw-rw-r-- 1 adonis adonis   940 Oct 21 20:42 pro.cpp
> >> drwxrwxr-x 2 adonis adonis  4096 Oct 21 20:54 Solvers
> >> adonis at LinuxBox:~/Dropbox/ParallelSolver$ file libpro.so
> >> libpro.so: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV),
> dynamically linked,
> BuildID[sha1]=0x928d227f5816b3de3329f4364a688b6146df8c60, not stripped
> >> adonis at LinuxBox:~/Dropbox/ParallelSolver$ make pro
> >> /home/adonis/Documents/petsc-3.4.2/linux-gnu-c-debug/bin/mpicxx -o
> pro.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g
>  -fPIC    -I/home/adonis/Documents/petsc-3.4.2/include
> -I/home/adonis/Documents/petsc-3.4.2/linux-gnu-c-debug/include
>  -D__INSDIR__= pro.cpp
> >> /home/adonis/Documents/petsc-3.4.2/linux-gnu-c-debug/bin/mpicxx -o
> 2D_CBS_Solver.o -c -Wall -Wwrite-strings -Wno-strict-aliasing
> -Wno-unknown-pragmas -g  -fPIC
>  -I/home/adonis/Documents/petsc-3.4.2/include
> -I/home/adonis/Documents/petsc-3.4.2/linux-gnu-c-debug/include
>  -D__INSDIR__= 2D_CBS_Solver.cpp
> >> /home/adonis/Documents/petsc-3.4.2/linux-gnu-c-debug/bin/mpicxx -Wall
> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g  -o pro pro.o
> 2D_CBS_Solver.o
> -Wl,-rpath,/home/adonis/Documents/petsc-3.4.2/linux-gnu-c-debug/lib
> -L/home/adonis/Documents/petsc-3.4.2/linux-gnu-c-debug/lib  -lpetsc
> -Wl,-rpath,/home/adonis/Documents/petsc-3.4.2/linux-gnu-c-debug/lib
> -lflapack -lfblas -lX11 -lpthread -lparmetis -lmetis -lm
> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.6
> -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -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 -lmpichf90 -lgfortran -lm -lgfortran -lm -lquadmath
> -lm -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s
> -ldl  -L/home/adonis/Dropbox/ParallelSolver
> -Wl,-rpath,/home/adonis/Dropbox/ParallelSolver -lpro
> >> /bin/rm -f pro.o 2D_CBS_Solver.o
> >> adonis at LinuxBox:~/Dropbox/ParallelSolver$ ldd pro
> >>    linux-vdso.so.1 =>  (0x00007fff1dffe000)
> >>    libpetsc.so =>
> /home/adonis/Documents/petsc-3.4.2/linux-gnu-c-debug/lib/libpetsc.so
> (0x00007f24f4da6000)
> >>    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
> (0x00007f24f4b88000)
> >>    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
> (0x00007f24f4888000)
> >>    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
> (0x00007f24f4672000)
> >>    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f24f42b2000)
> >>    libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6
> (0x00007f24f3f7d000)
> >>    libparmetis.so =>
> /home/adonis/Documents/petsc-3.4.2/linux-gnu-c-debug/lib/libparmetis.so
> (0x00007f24f3d2f000)
> >>    libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3
> (0x00007f24f3a17000)
> >>    libmpich.so.10 =>
> /home/adonis/Documents/petsc-3.4.2/linux-gnu-c-debug/lib/libmpich.so.10
> (0x00007f24f364b000)
> >>    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f24f3447000)
> >>    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f24f314a000)
> >>    /lib64/ld-linux-x86-64.so.2 (0x00007f24f6176000)
> >>    libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1
> (0x00007f24f2f2c000)
> >>    libmetis.so =>
> /home/adonis/Documents/petsc-3.4.2/linux-gnu-c-debug/lib/libmetis.so
> (0x00007f24f2cb0000)
> >>    libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0
> (0x00007f24f2a7a000)
> >>    libmpl.so.1 =>
> /home/adonis/Documents/petsc-3.4.2/linux-gnu-c-debug/lib/libmpl.so.1
> (0x00007f24f2875000)
> >>    librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f24f266c000)
> >>    libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6
> (0x00007f24f2469000)
> >>    libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6
> (0x00007f24f2263000)
> >>
> >>
> >> I hope this helps and is more clear. The  libpro.so object for some
> reason is not being linked.
> >>
> >> Thanks
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> On 21 October 2013 20:56, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >>
> >>  Please cut and paste everything you've done in this process, the make,
> the running of ldd etc
> >>
> >>   Barry
> >>
> >> On Oct 21, 2013, at 2:53 PM, Anthony Vergottis <a.vergottis at ucl.ac.uk>
> wrote:
> >>
> >>> Thanks for the replies. Unfortunatly this has still not worked. When
> using the ldd command the shared library libpro.so is not listed there. Any
> other ideas why this may be not linking?
> >>>
> >>> Thanks again.
> >>>
> >>>
> >>> On 21 October 2013 20:35, Satish Balay <balay at mcs.anl.gov> wrote:
> >>> On Mon, 21 Oct 2013, Anthony Vergottis wrote:
> >>>
> >>>> Dear All,
> >>>>
> >>>> I was wondering how does one include a .so object when compiling with
> a
> >>>> PETSc makefile? I have made various .so object for many projects and
> they
> >>>> work properly by specifying the -L location and the -lLibrary name.
> But
> >>>> when I try to link the .so object via a PETSc make file (after
> compilation
> >>>> with no errors) the ldd command does not show the library as being
> linked.
> >>>>
> >>>> Is there any internal behaviour of PETSc I should be aware of?  Have
> tried
> >>>> everything possible.
> >>>>
> >>>> I have configure PETSc with the following flags (if this helps).
> >>>>
> >>>> --download-mpich --with-clanguage=c++ --download-f-blas-lapack
> >>>> --download-metis --download-parmetis --with-shared-libraries=1
> >>>> --with-dynamic-loading=1
> >>>>
> >>>> This is the sample makefile:
> >>>>
> >>>> include ${PETSC_DIR}/conf/variables
> >>>> include ${PETSC_DIR}/conf/rules
> >>>> LIBS=-L/home/adonis/Dropbox/ParallelSolver -lpro
> >>>
> >>> you need:
> >>>
> >>> LIBS=-L/home/adonis/Dropbox/ParallelSolver
> -Wl,-rpath,/home/adonis/Dropbox/ParallelSolver -lpro
> >>>
> >>> Satish
> >>>
> >>>>
> >>>> pro: pro.o 2D_CBS_Solver.o
> >>>>            ${CLINKER} -o pro pro.o 2D_CBS_Solver.o ${PETSC_LIB}
> ${LIBS}
> >>>>            ${RM} pro.o 2D_CBS_Solver.o
> >>>>
> >>>> After this makefile is run still ldd does not show linkage.
> >>>>
> >>>> Any help would be appreciated. Thanks in advance.
> >>>>
> >>>> Best regards,
> >>>> Anthony
> >>>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> --
> >>> Anthony Vergottis
> >>>
> >>> PhD Student
> >>> Department of Mechanical Engineering
> >>> University College London
> >>> Gower Street
> >>> London
> >>> WC1E 6BT
> >>>
> >>> E-mail: a.vergottis at ucl.ac.uk
> >>> Tel (UK Mobile): (+44) 079 1263 0064
> >>
> >>
> >>
> >>
> >>
> >>
> >> --
> >> Anthony Vergottis
> >>
> >> PhD Student
> >> Department of Mechanical Engineering
> >> University College London
> >> Gower Street
> >> London
> >> WC1E 6BT
> >>
> >> E-mail: a.vergottis at ucl.ac.uk
> >> Tel (UK Mobile): (+44) 079 1263 0064
> >
>
>
>
>


-- 
Anthony Vergottis

PhD Student
Department of Mechanical Engineering
University College London
Gower Street
London
WC1E 6BT

E-mail: a.vergottis at ucl.ac.uk <i.stojanovic at ucl.ac.uk>
Tel (UK Mobile): (+44) 079 1263 0064
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