[petsc-users] Petscmatlabengine, libicudata not found, undefined symbol mexPrintf
Birendra jha
bjha7333 at yahoo.com
Wed Feb 16 01:35:00 CST 2011
Hi,
I removed -licudata at three places in petscvariables. The error just shifted to -licui18n:
bjha at ubuntu:~/src/petsc-dev$ make PETSC_DIR=/home/bjha/src/petsc-dev PETSC_ARCH=linux_gcc-4.4.1_64 test
Running test examples to verify correct installation
--------------Error detected during compile or link!-----------------------
See http://www.mcs.anl.gov/petsc/petsc-2/documentation/faq.html
mpicxx -o ex19.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/home/bjha/src/petsc-dev/include -I/home/bjha/src/petsc-dev/linux_gcc-4.4.1_64/include -I/home/bjha/src/petsc-dev/include/sieve -I/home/bjha/MATLAB/R2010b/extern/include -I/home/bjha/tools/gcc-4.4.1_64/include -D__INSDIR__=src/snes/examples/tutorials/ ex19.c
mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -o ex19 ex19.o -L/home/bjha/src/petsc-dev/linux_gcc-4.4.1_64/lib -lpetsc -Wl,-rpath,/home/bjha/src/petsc-dev/linux_gcc-4.4.1_64/lib -lparmetis -lmetis -Wl,-rpath,/home/bjha/MATLAB/R2010b/sys/os/glnx86:/home/bjha/MATLAB/R2010b/bin/glnx86:/home/bjha/MATLAB/R2010b/extern/lib/glnx86 -L/home/bjha/MATLAB/R2010b/bin/glnx86 -L/home/bjha/MATLAB/R2010b/extern/lib/glnx86 -leng -lmex -lmx -lmat -lut -licui18n -licuuc -lml -lchaco -L/usr/lib/atlas -llapack_atlas -llapack -latlas -lblas -L/home/bjha/tools/gcc-4.4.1_64/lib -L/usr/lib/gcc/i486-linux-gnu/4.4.3 -L/usr/lib/i486-linux-gnu -ldl -lmpi -lopen-rte -lopen-pal -lnsl -lutil -lgcc_s -lpthread -lmpi_f90 -lmpi_f77 -lgfortran -lm -lm -lm -lm -lmpi_cxx -lstdc++ -lmpi_cxx -lstdc++ -ldl -lmpi -lopen-rte -lopen-pal -lnsl -lutil -lgcc_s -lpthread -ldl
/usr/bin/ld: cannot find -licui18n
collect2: ld returned 1 exit status
make[3]: [ex19] Error 1 (ignored)
/bin/rm -f ex19.o
--------------Error detected during compile or link!-----------------------
See http://www.mcs.anl.gov/petsc/petsc-2/documentation/faq.html
mpif90 -c -Wall -Wno-unused-variable -g -I/home/bjha/src/petsc-dev/include -I/home/bjha/src/petsc-dev/linux_gcc-4.4.1_64/include -I/home/bjha/src/petsc-dev/include/sieve -I/home/bjha/MATLAB/R2010b/extern/include -I/home/bjha/tools/gcc-4.4.1_64/include -o ex5f.o ex5f.F
mpif90 -Wall -Wno-unused-variable -g -o ex5f ex5f.o -L/home/bjha/src/petsc-dev/linux_gcc-4.4.1_64/lib -lpetsc -Wl,-rpath,/home/bjha/src/petsc-dev/linux_gcc-4.4.1_64/lib -lparmetis -lmetis -Wl,-rpath,/home/bjha/MATLAB/R2010b/sys/os/glnx86:/home/bjha/MATLAB/R2010b/bin/glnx86:/home/bjha/MATLAB/R2010b/extern/lib/glnx86 -L/home/bjha/MATLAB/R2010b/bin/glnx86 -L/home/bjha/MATLAB/R2010b/extern/lib/glnx86 -leng -lmex -lmx -lmat -lut -licui18n -licuuc -lml -lchaco -L/usr/lib/atlas -llapack_atlas -llapack -latlas -lblas -L/home/bjha/tools/gcc-4.4.1_64/lib -L/usr/lib/gcc/i486-linux-gnu/4.4.3 -L/usr/lib/i486-linux-gnu -ldl -lmpi -lopen-rte -lopen-pal -lnsl -lutil -lgcc_s -lpthread -lmpi_f90 -lmpi_f77 -lgfortran -lm -lm -lm -lm -lmpi_cxx -lstdc++ -lmpi_cxx -lstdc++ -ldl -lmpi -lopen-rte -lopen-pal -lnsl -lutil -lgcc_s -lpthread -ldl
/usr/bin/ld: cannot find -licui18n
collect2: ld returned 1 exit status
make[3]: [ex5f] Error 1 (ignored)
/bin/rm -f ex5f.o
Completed test examples
I removed its references, error shifted to -licuuc, removed its references, error became:
...
/home/bjha/src/petsc-dev/linux_gcc-4.4.1_64/lib/libpetsc.a(aij.o): In function `MatCreate_SeqAIJ':
/home/bjha/src/petsc-dev/src/mat/impls/aij/seq/aij.c:3492: undefined reference to `MatGetFactor_seqaij_matlab'
...
It seems a linking issue.
I checked "file" for few other libraries--they are all ELF 32-bit:
bjha at ubuntu:~/MATLAB/R2010b/bin/glnx86$ file libmwblas.so
libmwblas.so: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), dynamically linked, stripped
bjha at ubuntu:~/MATLAB/R2010b/bin/glnx86$ file libjogl.so
libjogl.so: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), dynamically linked, not stripped
bjha at ubuntu:~/MATLAB/R2010b/bin/glnx86$ file libmwfftw.so
libmwfftw.so: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), dynamically linked, stripped
bjha at ubuntu:~/MATLAB/R2010b/bin/glnx86$ file libeng.so
libeng.so: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), dynamically linked, stripped
PyLith configure also gives Petsc linking error:
checking for PETSc dir... /home/bjha/src/petsc-dev
checking for PETSc arch... linux_gcc-4.4.1_64
checking for PETSc config... /home/bjha/src/petsc-dev/linux_gcc-4.4.1_64/conf/petscvariables
checking for PETSc version == 3.1.0... yes
checking for PetscInitialize... no
checking for the libraries used by mpicc... -pthread -L/home/bjha/tools/gcc-4.4.1_64/lib -lmpi -lopen-rte -lopen-pal -ldl -lnsl -lutil -lm -ldl
checking for PetscInitialize... no
configure: error: cannot link against PETSc libraries
Please help.
Thanks & regards
Bir
--- On Wed, 2/16/11, Barry Smith <bsmith at mcs.anl.gov> wrote:
> From: Barry Smith <bsmith at mcs.anl.gov>
> Subject: Re: [petsc-users] Petscmatlabengine, libicudata not found, undefined symbol mexPrintf
> To: "PETSc users list" <petsc-users at mcs.anl.gov>
> Date: Wednesday, February 16, 2011, 7:55 AM
>
> On Feb 15, 2011, at 8:14 PM, Birendra jha wrote:
>
> > Hi,
> >
> > I attached the output of ls -l. Below are the outputs
> of "file" command:
> >
> > bjha at ubuntu:~/src/pylith-dev/examples/3d/hex8$ file
> /home/bjha/MATLAB/R2010b/bin/glnx86/libicudata.so.42
> > /home/bjha/MATLAB/R2010b/bin/glnx86/libicudata.so.42:
> symbolic link to `libicudata.so.42.1'
> >
> > bjha at ubuntu:~/src/pylith-dev/examples/3d/hex8$ file
> /home/bjha/MATLAB/R2010b/bin/glnx86/libicudata.so.42.1
> >
> /home/bjha/MATLAB/R2010b/bin/glnx86/libicudata.so.42.1: ELF
> 32-bit LSB shared object, Intel 80386, version 1 (SYSV),
> dynamically linked, not stripped
>
> Humm. Run file on some of the other
> libraries in that directory. Are they also ELF 32 bit?
> You can try editing ${PETSC_ARCH/conf/petscvariables and
> removing the reference to libicudata then run make test. It
> may not be needed.
>
> Barry
>
> >
> >
> > Thanks
> > Bir
> >
> > --- On Wed, 2/16/11, Barry Smith <bsmith at mcs.anl.gov>
> wrote:
> >
> >> From: Barry Smith <bsmith at mcs.anl.gov>
> >> Subject: Re: [petsc-users] Petscmatlabengine,
> libicudata not found, undefined symbol mexPrintf
> >> To: "PETSc users list" <petsc-users at mcs.anl.gov>
> >> Date: Wednesday, February 16, 2011, 7:26 AM
> >>
> >> On Feb 15, 2011, at 6:56 PM, Birendra jha wrote:
> >>
> >>> Dear Petsc users,
> >>>
> >>> I am getting "cannot find -licudata" error
> during
> >> "make test" on petsc-dev, even when
> libicudata.so.42.1, and
> >> its link, libicudata.so.42 are in
> >> /home/bjha/MATLAB/R2010b/bin/glnx86. Petsc "make"
> was fine.
> >>
> >> Run ls -l
> /home/bjha/MATLAB/R2010b/bin/glnx86 and
> >> send the output
> >> also run file
> >>
> /home/bjha/MATLAB/R2010b/bin/glnx86/libicudata.so.42
> >>
> >>>
> >>> bjha at ubuntu:~/src/petsc-dev$ make
> >> PETSC_DIR=/home/bjha/src/petsc-dev
> >> PETSC_ARCH=linux_gcc-4.4.1_64 test
> >>> Running test examples to verify correct
> installation
> >>> --------------Error detected during compile
> or
> >> link!-----------------------
> >>> See http://www.mcs.anl.gov/petsc/petsc-2/documentation/faq.html
> >>> mpicxx -o ex19.o -c -Wall -Wwrite-strings
> >> -Wno-strict-aliasing -Wno-unknown-pragmas -g
> >> -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64
> >> -I/home/bjha/src/petsc-dev/include
> >>
> -I/home/bjha/src/petsc-dev/linux_gcc-4.4.1_64/include
> >> -I/home/bjha/src/petsc-dev/include/sieve
> >> -I/home/bjha/MATLAB/R2010b/extern/include
> >> -I/home/bjha/tools/gcc-4.4.1_64/include
> >> -D__INSDIR__=src/snes/examples/tutorials/ ex19.c
> >>> mpicxx -Wall -Wwrite-strings
> -Wno-strict-aliasing
> >> -Wno-unknown-pragmas -g -o ex19
> >> ex19.o
> >> -L/home/bjha/src/petsc-dev/linux_gcc-4.4.1_64/lib
>
> >> -lpetsc
> >>
> -Wl,-rpath,/home/bjha/src/petsc-dev/linux_gcc-4.4.1_64/lib
> >> -lparmetis -lmetis
> >>
> -Wl,-rpath,/home/bjha/MATLAB/R2010b/sys/os/glnx86:/home/bjha/MATLAB/R2010b/bin/glnx86:/home/bjha/MATLAB/R2010b/extern/lib/glnx86
> >> -L/home/bjha/MATLAB/R2010b/bin/glnx86
> >> -L/home/bjha/MATLAB/R2010b/extern/lib/glnx86 -leng
> -lmex
> >> -lmx -lmat -lut -licudata -licui18n -licuuc -lml
> -lchaco
> >> -L/usr/lib/atlas -llapack_atlas -llapack -latlas
> -lblas
> >> -L/home/bjha/tools/gcc-4.4.1_64/lib
> >> -L/usr/lib/gcc/i486-linux-gnu/4.4.3
> >> -L/usr/lib/i486-linux-gnu -ldl -lmpi -lopen-rte
> -lopen-pal
> >> -lnsl -lutil -lgcc_s -lpthread -lmpi_f90
> -lmpi_f77
> >> -lgfortran -lm -lm -lm -lm -lmpi_cxx -lstdc++
> -lmpi_cxx
> >> -lstdc++ -ldl -lmpi -lopen-rte -lopen-pal -lnsl
> -lutil
> >> -lgcc_s -lpthread -ldl
> >>> /usr/bin/ld: cannot find -licudata
> >>> collect2: ld returned 1 exit status
> >>> make[3]: [ex19] Error 1 (ignored)
> >>> /bin/rm -f ex19.o
> >>> --------------Error detected during compile
> or
> >> link!-----------------------
> >>> See http://www.mcs.anl.gov/petsc/petsc-2/documentation/faq.html
> >>> mpif90 -c -Wall -Wno-unused-variable
> >>
> -g -I/home/bjha/src/petsc-dev/include
> >>
> -I/home/bjha/src/petsc-dev/linux_gcc-4.4.1_64/include
> >> -I/home/bjha/src/petsc-dev/include/sieve
> >> -I/home/bjha/MATLAB/R2010b/extern/include
> >> -I/home/bjha/tools/gcc-4.4.1_64/include
> -o
> >> ex5f.o ex5f.F
> >>> mpif90 -Wall -Wno-unused-variable
> >> -g -o ex5f ex5f.o
> >> -L/home/bjha/src/petsc-dev/linux_gcc-4.4.1_64/lib
>
> >> -lpetsc
> >>
> -Wl,-rpath,/home/bjha/src/petsc-dev/linux_gcc-4.4.1_64/lib
> >> -lparmetis -lmetis
> >>
> -Wl,-rpath,/home/bjha/MATLAB/R2010b/sys/os/glnx86:/home/bjha/MATLAB/R2010b/bin/glnx86:/home/bjha/MATLAB/R2010b/extern/lib/glnx86
> >> -L/home/bjha/MATLAB/R2010b/bin/glnx86
> >> -L/home/bjha/MATLAB/R2010b/extern/lib/glnx86 -leng
> -lmex
> >> -lmx -lmat -lut -licudata -licui18n -licuuc -lml
> -lchaco
> >> -L/usr/lib/atlas -llapack_atlas -llapack -latlas
> -lblas
> >> -L/home/bjha/tools/gcc-4.4.1_64/lib
> >> -L/usr/lib/gcc/i486-linux-gnu/4.4.3
> >> -L/usr/lib/i486-linux-gnu -ldl -lmpi -lopen-rte
> -lopen-pal
> >> -lnsl -lutil -lgcc_s -lpthread -lmpi_f90
> -lmpi_f77
> >> -lgfortran -lm -lm -lm -lm -lmpi_cxx -lstdc++
> -lmpi_cxx
> >> -lstdc++ -ldl -lmpi -lopen-rte -lopen-pal -lnsl
> -lutil
> >> -lgcc_s -lpthread -ldl
> >>> /usr/bin/ld: cannot find -licudata
> >>> collect2: ld returned 1 exit status
> >>> make[3]: [ex5f] Error 1 (ignored)
> >>> /bin/rm -f ex5f.o
> >>> Completed test examples
> >>>
> >>>
> >>> It is correct that I didn't install matlab in
> the
> >> default directory (/usr/local) because I had some
> permission
> >> issues on Ubuntu. But I have been running matlab
> (by running
> >> /MATLAB/R2010b/bin/matlab.sh) without any issues
> >>> for some time now. So it should be that, I
> suppose.
> >>>
> >>> I still went ahead with compiling my
> application with
> >> few lines of PetscMatlabEngine functions, just to
> test:
> >>>
> >>> PetscMatlabEngine e;
> >>> PetscScalar *array;
> array[0]=0;
> >>> const char name[]="a";
> >>>
> >>
> PetscMatlabEngineCreate(PETSC_COMM_WORLD,PETSC_NULL,&e);
> >>> PetscMatlabEnginePutArray(e,1,1,array,name);
> >>> PetscMatlabEngineGetArray(e,1,1,array,name);
> >>> PetscMatlabEngineDestroy(e);
> >>>
> >>> Do I need to include any header file (e.g.
> >> petscmatlab.h) in the header of my class file?
> >>
> >> No
> >>
> >>> Right now, the application compiled (make,
> make
> >> install) fine without any such include file. The
> application
> >> have been using Petsc for its solver without any
> issues, so
> >> it includes all the necessary files. I just want
> to exten
> >> the application to call some matlab scripts by
> using
> >> PetscMatlabEngine.
> >>>
> >>> But, I get runtime error for mexPrintf:
> >>>
> >>> bjha at ubuntu:~/src/pylith-dev/examples/3d/hex8$
> pylith
> >> step06_pres.cfg
> >>> Traceback (most recent call last):
> >>> File
> "/home/bjha/tools/gcc-4.4.1_64/bin/pylith",
> >> line 37, in <module>
> >>> from
> pylith.apps.PyLithApp import
> >> PyLithApp
> >>> File
> >>
> "/home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages/pylith/apps/PyLithApp.py",
> >> line 23, in <module>
> >>> from PetscApplication
> import
> >> PetscApplication
> >>> File
> >>
> "/home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages/pylith/apps/PetscApplication.py",
> >> line 27, in <module>
> >>> class
> PetscApplication(Application):
> >>> File
> >>
> "/home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages/pylith/apps/PetscApplication.py",
> >> line 41, in PetscApplication
> >>> from
> pylith.utils.PetscManager import
> >> PetscManager
> >>> File
> >>
> "/home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages/pylith/utils/PetscManager.py",
> >> line 29, in <module>
> >>> import
> pylith.utils.petsc as petsc
> >>> File
> >>
> "/home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages/pylith/utils/petsc.py",
> >> line 25, in <module>
> >>> _petsc =
> swig_import_helper()
> >>> File
> >>
> "/home/bjha/tools/gcc-4.4.1_64/lib/python2.6/site-packages/pylith/utils/petsc.py",
> >> line 21, in swig_import_helper
> >>> _mod =
> imp.load_module('_petsc', fp,
> >> pathname, description)
> >>> ImportError:
> >> /home/bjha/tools/gcc-4.4.1_64/lib/libpylith.so.0:
> undefined
> >> symbol: mexPrintf
> >>
> >> Somehow all the Matlab shared
> libraries need to be
> >> found when python loads libpylith.so is
> loaded. I
> >> don't know how this is done in Linux. It is really
> a python
> >> question if you want to use a dynamic library in
> python that
> >> uses another shared library how do you make sure
> python gets
> >> all the shared libraries loaded to resolve the
> symbols?
> >>
> >> Barry
> >>
> >>>
> >>>
> >>> Can anyone help/suggest something?
> >>>
> >>> Thanks a lot
> >>> Bir
> >>>
> >>>
> >>>
> >>
> >>
> >
> >
> > <MATLAB_R2010b_bin_glnx86_files.txt>
>
>
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