[petsc-users] Petscmatlabengine, libicudata not found, undefined symbol mexPrintf

Barry Smith bsmith at mcs.anl.gov
Tue Feb 15 20:25:11 CST 2011 

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>

More information about the petsc-users mailing list