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

[Birendra jha]

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.

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? 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


Can anyone help/suggest something?

Thanks a lot
Bir