[petsc-users] Including user made shared library in makefile.
Klaus Zimmermann
klaus.zimmermann at physik.uni-freiburg.de
Mon Oct 21 15:41:18 CDT 2013
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Hi Anthony,
the your binary does not use the library. Here is why:
g++ -shared -fPIC -o libpro.so 2D_CBS_Solver.cpp
creates the library with the contents of 2D_CBS_Solver.cpp.
But when you link your executable with
${CLINKER} -o pro pro.o 2D_CBS_Solver.o ${PETSC_LIB}
in your makefile you link 2D_CBS_Solver again. Therefore its contents
is linked statically to your executable "pro" and the library is not
needed to resolve any symbols. Hence the linker places no reference in
"pro".
Best
Klaus
Am 21.10.2013 22:33, schrieb Anthony Vergottis:
> 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
> <mailto: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
> <mailto: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 <mailto: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
> <mailto: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 <mailto: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
> <mailto: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 <mailto:a.vergottis at ucl.ac.uk>
>>>> Tel (UK Mobile): (+44) 079 1263 0064
> <tel:%28%2B44%29%20079%201263%200064>
>>>
>>>
>>>
>>>
>>>
>>>
>>> -- Anthony Vergottis
>>>
>>> PhD Student Department of Mechanical Engineering University
>>> College London Gower Street London WC1E 6BT
>>>
>>> E-mail: a.vergottis at ucl.ac.uk <mailto:a.vergottis at ucl.ac.uk>
>>> Tel (UK Mobile): (+44) 079 1263 0064
> <tel:%28%2B44%29%20079%201263%200064>
>>
>
>
>
>
>
>
> -- Anthony Vergottis
>
> PhD Student Department of Mechanical Engineering University College
> London Gower Street London WC1E 6BT
>
> E-mail: a.vergottis at ucl.ac.uk <mailto:i.stojanovic at ucl.ac.uk> Tel
> (UK Mobile): (+44) 079 1263 0064
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