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

Tue Feb 15 21:00:30 CST 2011

   The MATLAB libraries are listed in the $PETSC_ARCH/conf/petscvariables file in the variable PETSC_EXTERNAL_LIB_BASIC  This was changed recently in PETSc-dev perhaps the pylith configure has not yet been updated to handle this.

   Barry

On Feb 15, 2011, at 8:44 PM, Brad Aagaard wrote:

> Birendra-
> 
> PyLith extracts the link flags from PETSc during the PyLith configure, so any libraries PETSc uses should automatically get linked into the PyLith Python modules and libraries. Only if these libraries end up in some unusual PETSc make related variable would they be missed in the PyLith linking. You can also run "ldd libpylith.so" in the directory containing libpylith.so to make sure it is finding the shared libraries.
> 
> Brad
> 
> 
> On 2/15/11 5:56 PM, Barry Smith wrote:
>> 
>> 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
>>> 
>>> 
>>> 
>> 
>> 
> 